Books by Subject
- Accurate methods for ancestry and relatedness inference — Epigenetics protocols. 2nd ed. (156)
- Epigenetics, the environment, and children's health across lifespans — Investigations in yeast functional genomics and molecular biology (156)
- Kallmann syndrome and hypogonadotropic hypogonadism — Proteins and proteomics of Leishmania and Trypanosoma (156)
- Proteogenomics — Zebrafish-- genetics, genomics, and transcriptomics. Fourth edition. [4th ed.] (155)
- 2016 SpringerÁkos Végvári, editor.Proteogenomic tools and approaches to explore protein coding landscapes of eukaryotic genomes / Dhirendra Kumar, Debasis Dash -- Next generation sequencing data and proteogenomics / Kelly V. Ruggles, David Feny̲ -- Proteogenomics: key driver for clinical discovery and personalized medicine / Ruggero Barbieri, Victor Guryev, Corry-Anke Brandsma, Frank Suits, Rainer Bischoff [and others] -- Identification of small novel coding sequences, a proteogenomics endeavor / Volodimir Olexiouk, Gerben Menschaert -- Using proteomics bioinformatics tools and resources in proteogenomic studies / Marc Vaudel, Harald Barsnes, Helge Ræder, Frode S. Berven -- Mutant proteogenomics / Ákos Végvári -- Proteogenomic analysis of single amino acid polymorphisms in cancer research / Alba Garin-Muga, Fernando J. Corrales, Victor Segura -- Developments for personalized medicine of lung cancer subtypes: mass spectrometry-based clinical proteogenomic analysis of oncogenic mutations / Toshihide Nishimura, Haruhiko Nakamura -- Proteogenomics for the study of gastrointestinal stromal tumors / Tadashi Kondo -- Proteogenomics for the comprehensive analysis of human cellular and serum antibody repertoires / Paula Díez, Manuel Fuentes -- Antibody-based proteomics / Christer Wingren.Also available: Print – 2016
- 2006 Springer Protocolsedited by Elena Hilario, John Mackay.Genomic DNA isolation from different biological materials / Duckchul Park -- Extraction of plant RNA / Elspeth MacRae -- Overview on hybridization and detection techniques / Elena Hilario -- Checkerboard DNA/DNA hybridization technology : using DIG detection / Lisa S. Gellen, Glenn Wall-Manning, and Chris H. Sissons -- Nonradioactive northern and southern analyses from plant samples / Christoph Peterhaensel, Dagmar Weier, and Thomas Lahaye -- Screening a BAC library with nonradioactive overlapping oligonucleotide (overgo) probes / Elena Hilario, Tiffany F. Bennell, and Erik Rikkerink -- Direct in-gel hybridization of DNA with digoxigenin-labeled probes / Saeed A. Khan and Mohamed S. Nawaz -- In situ hybridization of termite microbes / Shigeharu Moriya ... [et al.] -- RNA electrophoretic mobility shift assay using a fluorescent DNA sequencer / Yukinori Eguchi -- Comparative quantitation of mRNA expression in the central nervous system using fluorescence in situ hybridization / Darren J. Day, Eli M. Mrkusich, and John H. Miller -- Visualization of gene expression by fluorescent multiplex real-time PCR amplification / Maria Rosa Ponce ... [et al.] -- Fluorescence in situ hybridization for the identification of environmental microbes / Annelie Pernthaler and Jakob Pernthaler -- Introduction to kinetic (real-time) PCR / John Mackay -- Validation of siRNA knockdowns by quantitative real-time PCR / Sukru Tuzmen -- Real-time quantitative PCR as an alternative to southern blot or fluorescence in situ hybridization for detection -- Of gene-copy number changes / Jasmien Hoebeeck, Frank Speleman, and Jo Vandesompele -- Design and work-up of a new molecular diagnostic assay based on real-time PCR / Harald Kessler -- Real-time PCR fluorescent chemistries / John Mackay and Olfert Landt -- Microarrays : an overview / Norman H. Lee and Alexander I. Saeed -- Oligonucleotide microarrays for the study of coastal microbial communities / Gaspar Taroncher-Oldenburg and Bess B. Ward.
- 2014 Springer Protocolsedited by Laura Poliseno.Pseudogene redux with new biological significance / Leonardo Salmena -- Contribution of pseudogenes to sequence diversity / Mauno Vihinen -- Computational methods for pseudogene annotation based on sequence homology / Paul M. Harrison -- Computational methods of identification of pseudogenes based on functionality : entropy and GC content / Evgeniy S. Balakirev ... [et al.] -- Methods of identification of pseudogenes based on functionality : hybridization of 18S rRNA and mRNA during translation / Chuanhua Xing -- Whole-genome identification of neutrally evolving pseudogenes using the evolutionary measure dN/dS / Lise Olivia Andrieux and David Torrents Arenales -- Methods to study the occurrence and the evolution of pseudogenes through a phylogenetic approach / Jacques Dainat and Pierre Pontarotti -- Methods for detecting transcribed pseudogenes : PCR on regions of high sequence similarity followed by cloning and sequencing / Wenyong Ding and Jianwu Dai -- RNA amplification for pseudogene detection using RNA-Seq / Stephen C. M. Tsoi and Michael K. Dyck -- GENCODE pseudogenes / Adam Frankish and Jennifer Harrow -- Methods to detect transcribed pseudogenes : RNA-Seq discovery allows learning through features / Camilo Valdes and Enrico Capobianco -- Proteomics techniques for the detection of translated pseudogenes / Nadia Ucciferri and Silvia Rocchiccioli -- Pseudogenes as competitive endogenous RNAs : target prediction and validation / Florian A. Karreth ... [et al.] -- Pseudogenes : a novel source of trans-acting antisense RNAs / Per Johnsson, Kevin V. Morris, and Dan Grandér -- Pseudogene-derived endogenous siRNAs and their function / Wen-Ling Chan and Jan-Gowth Chang -- Methods to study translated pseudogenes : in vitro translation, fusion with a tag/reporter gene, and complementation assay / Anne Parle-McDermott
- 2006 Springer Protocolsedited by Sharon Marsh.The history of pyrosequencing / Pol Nyron -- Pyrosequencing applications / Sharon Marsh -- Web-based primer design software for genome-scale genotyping by pyrosequencing / Steven Ringquist ... [et al.] -- Pyrosequencing : a simple method for accurate genotyping / Cristi R. King and Tiffany Scott-Horton -- Universal primer applications for pyrosequencing / Dong-Chuan Guo and Dianna M. Milewicz -- Allele quantification and DNA pooling methods / Jonathon Wasson -- Multiplex pyrosequencing for DNA variation analysis / Pritesh Patel, Yih-Horng Shiao, and Paolo Fortina -- Analysis of gene-specific DNA methylation patterns by the pyrosequencing technology / Jørg Tost and Ivo Glynne Gut -- Detecting mutations that confer oxazolidinone resistance in gram-positive bacteria / Neil Woodford, Sarah E. North, and Matthew J. Ellington -- Pyrosequencing-based strategies for improved allele typing of HLA loci / Steven Ringquist ... [et al.] -- Pyrosequencing of phage display libraries for the identification of cell-specific targeting ligands / Ahad A. Rahim -- Gene copy number detection in animal studies / Gerli Pielberg and Leif Andersson -- Detection of allelic imbalance in gene expression using pyrosequencing / Hua Wang and Steven C. Elbein -- Pyrosequencing genotype storage techniques / Derek J. Van Booven.
- 2011Sun-Hae Hong.Replication and segregation of the chromosome in the bacterium Caulobacter crescentus takes place simultaneously. Although it is known that each arm of the circular chromosome is on average linearly positioned along the cell length, the detailed configuration of the DNA in the cell is not well understood. Furthermore, in replicating bacterial cells, the centromere is segregated by a ParA-dependent mechanism and anchored at the pole, but the segregation mechanism for the rest of the chromosome is not known. To address these questions, I tracked the position and motion of multiple chromosomal loci both in non-replicating and replicating cells. By characterizing compaction of the DNA in non-replicating cells, I show that the DNA in the Caulobacter cells has the mean end-to-end distance that scale as (contour length)0.22, which suggests that compaction of the bacterial DNA is primarily driven by supercoiling. Analysis of the replication/segregation dynamics revealed that Caulobacter chromosome segregation is bimodal: Centromere-proximal DNA is segregated with the centromere at a slow pace whereas the rest of the DNA is segregated much faster. The dynamics of the centromere-distal DNA are consistent with a model where continuous compaction pulls the DNA toward the pole. The results provide a new perspective on the physical configuration of the non-replicating DNA and on the movement and compaction of newly replicated DNA immediately after replication and during its transport from the replisome to the cell poles.
- 2014 Springer Protocolsedited by Roberto Biassoni, Laboratorio Medicina Molecolare, Dipartimento Medicina Traslazionale, Instituto Giannina Gaslini, Genova, Italy, Alessandro Raso, Laboratorio U.O.C. Neurochirugia, Instituto Giannina Gaslini, Genova, Italy.Twenty years of qPCR: A mature technology? -- Minimum information necessary for quantitative real-time PCR experiments -- Selection of reliable reference genes for RT-qPCR analysis -- Introduction to digital PCR -- mRNA and microRNA purity and integrity: The key to success in expression profiling -- Mediator probe PCR: Detection of real-time PCR by label-free probes and a universal fluorogenic reporter -- Absolute quantification of viral DNA: The quest for perfection -- A multiplex real-time PCR-platform integrated into automated extraction method for the rapid detection and measurement of oncogenic HPV type-specific viral DNA load from cervical samples -- Real-time PCR detection of mycoplasma pneumoniae in the diagnosis of community-acquired pneumonia -- A sensible technique to detect mollicutes impurities in human cells cultured in GMP condition -- Real-time quantification assay to monitor BCR-ABL1 transcripts in chronic myeloid leukemia -- A reliable assay for rapidly defining transplacental metastasis using quantitative PCR -- Circulating cell-free DNA in cancer -- Gene expression analysis by qPCR in clinical kidney transplantation -- Posttranscriptional regulatory networks: From expression profiling to integrative analysis of mRNA and microRNA data -- Clinical applications using digital PCR -- Developing noninvasive diagnosis for single-gene disorders: the role of digital PCR.
- 2012 Springer Protocolsedited by Scott A. Rifkin.Backcross populations and near isogenic lines / Rik Kooke, Erik Wijnker, and Joost J.B. Keurentjes -- F2 designs for QTL analysis / Yuan-Ming Zhang -- Design and construction of recombinant inbred lines / Daniel A. Pollard -- Two flavors of bulk segregant analysis in yeast / Maitreya J. Dunham -- Selecting markers and evaluating coverage / Matthew A. Cleveland and Nader Deeb -- Composite interval mapping and multiple interval mapping : procedures and guidelines for using windows QTL cartographer / Luciano Da Costa E. Silva, Shengchu Wang, and Zhao-Bang Zeng -- Design database for quantitative trait loci (QTL) data warehouse, data mining, and meta-analysis / Zhi-Liang Hu, James M. Reecy, and Xiao-Lin Wu -- Meta-analysis of QTL mapping experiments / Xiao-Lin Wu and Zhi-Liang Hu -- Using eQTLs to reconstruct gene regulatory networks / Lin S. Chen -- Estimation and interpretation of genetic effects with epistasis using the NOIA model / Jose M. Alvarez-Castro, Orjan Carlborg, and Lars Ronnegard -- Identifying QTL for multiple complex traits in experimental crosses / Samprit Banerjee and Nengjun Yi -- Functional mapping of developmental processes : theory, applications, and prospects / Kiranmoy Das [and others] -- Statistical models for genetic mapping in polyploids : challenges and opportunities / Jiahan Li [and others] -- eQTL / Lun Li, Xianghua Zhang, and Hongyu Zhao -- Genetic mapping of quantitative trait loci for disease -- related phenotypes / Marcella Devoto and Mario Falchi -- Quantitative trait locus analysis in haplodiploid hymenoptera / Jssurgen Gadau, Christof Pietsch, and Leo W. Beukeboom.
- 2016 SpringerEsteban Domingo, Peter Schuster, editors.What is a quasispecies?- Historical origins and current scope -- The nucleation of semantic information in prebiotic matter -- Evolution of RNA-based networks -- Quasispecies on fitness landscapes -- Mathematical models of quasispecies theory and exact results for the dynamics -- Theoretical Models of Generalized Quasispecies -- Theories of lethal mutagenesis: from error catastrophe to lethal defection -- Estimating fitness of viral quasispecies from next-generation sequencing data -- Getting to know viral evolutionary strategies: Towards the next generation of quasispecies models -- Cooperative Interaction within RNA Virus Mutant Spectra -- Arenavirus Quasispecies And Their Biological Implications -- Models of viral population dynamics -- Fidelity variants and RNA quasispecies -- Antiviral strategies based on lethal mutagenesis and error threshold.
- 2013 SpringerDariusz Leszczynski, editor.Methods of proteomics have been shown to be powerful tools in search of target proteins - proteins that respond in cells to an internal or an external stimulus. Proteomics is widely used in biomedical research. However, in radiation biology research, following exposures of living matter to low doses of either ionizing or non-ionizing radiation, proteomics approach is only very slowly gaining support. This book, by presenting the current status of the use of proteomics in radiation biology, will help to attract attention to the field of radiation proteomics.Also available: Print – 2013Also available: Print – 2013
- Reaping the benefits of genomic and proteomic research : intellectual property rights, innovation, and public health2006 NAP2006 ProQuest Ebook CentralStephen A. Merrill and Anne-Marie Mazza, editors.The patenting and licensing of human genetic material and proteins represents an extension of intellectual property (IP) rights to naturally occurring biological material and scientific information, much of it well upstream of drugs and other disease therapies. This report concludes that IP restrictions rarely impose significant burdens on biomedical research, but there are reasons to be apprehensive about their future impact on scientific advances in this area. The report recommends 13 actions that policy-makers, courts, universities, and health and patent officials should take to prevent the increasingly complex web of IP protections from getting in the way of potential breakthroughs in genomic and proteomic research. It endorses the National Institutes of Health guidelines for technology licensing, data sharing, and research material exchanges and says that oversight of compliance should be strengthened. It recommends enactment of a statutory exception from infringement liability for research on a patented invention and raising the bar somewhat to qualify for a patent on upstream research discoveries in biotechnology. With respect to genetic diagnostic tests to detect patient mutations associated with certain diseases, the report urges patent holders to allow others to perform the tests for purposes of verifying the results.
- 2010 SpringerJohn F. Atkins, Raymond F. Gesteland, editors.Part I. Redefinition -- 1. Selenocysteine Biosynthesis, Selenoproteins, and Selenoproteomes / Vadim N. Gladyshev and Dolph L. Hatfield -- 2. Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors / Marla J. Berry and Michael T. Howard -- 3. Translation of UAG as Pyrrolysine / Joseph A. Krzycki -- 4. Specification of Standard Amino Acids by Stop Codons / Olivier Namy and Jean-Pierre Rousset -- 5. Ribosome “Skipping”: “Stop-Carry On” or “StopGo” Translation / Jeremy D. Brown and Martin D. Ryan -- 6. Recoding Therapies for Genetic Diseases / Kim M. Keeling and David M. Bedwell -- Part II. Frameshifting - Redirection of Linear Readout -- 7. Pseudoknot-Dependent Programmed -1 Ribosomal Frameshifting: Structures, Mechanisms and Models / Ian Brierley, Robert J.C. Gilbert, and Simon Pennell -- 8. Programmed -1 Ribosomal Frameshift in the Human Immunodeficiency Virus of Type 1 / Léa Brakier-Gingras and Dominic Dulude -- 9. Ribosomal Frameshifting in Decoding Plant Viral RNAs / W. Allen Miller and David P. Giedroc -- 10. Programmed Frameshifting in Budding Yeast / Philip J. Farabaugh -- 11. Recoding in Bacteriophages / Roger W. Hendrix -- 12. Programmed Ribosomal -1 Frameshifting as a Tradition: The Bacterial Transposable Elements of the IS3 Family / Olivier Fayet and Marie-Françoise Prère -- 13. Autoregulatory Frameshifting in Antizyme Gene Expression Governs Polyamine Levels from Yeast to Mammals / Ivaylo P. Ivanov and Senya Matsufuji -- 14. Sequences Promoting Recoding Are Singular Genomic Elements / Pavel V. Baranov and Olga Gurvich -- 15. Mutants That Affect Recoding / Jonathan D. Dinman and Michael O'Connor -- 16. The E Site and Its Importance for Improving Accuracy and Preventing Frameshifts / Markus Pech, Oliver Vesper, Hiroshi Yamamoto, Daniel N. Wilson, and Knud H. Nierhaus -- Part III. Discontiguity -- 17. Translational Bypassing - Peptidyl-tRNA Re-pairing at Non-overlapping Sites / Norma M. Wills -- 18. trans-Translation / Kenneth C. Keiler and Dennis M. Lee -- Part IV. Transcription Slippage -- 19. Transcript Slippage and Recoding / Michael Anikin, Vadim Molodtsov, Dmitry Temiakov, and William T. McAllister -- Part V. Appendix -- 20. Computational Resources for Studying Recoding / Andrew E. Firth, Michaël Bekaert, and Pavel V. Baranov.
- 2012 Springer Protocolsedited by Graeme L. Conn.Purification of RNA expressed in vivo inserted in a tRNA scaffold / Luc Ponchon and Frederic Dardel -- Selective RNase H cleavage of target RNAs from a tRNA scaffold / Luc Ponchon [and others] -- Preparation of long templates for RNA in vitro transcription by recursive PCR / Jessica C. Bowman [and others] -- General protocols for preparation of plasmid DNA template, RNA in vitro transcription, and RNA purification by denaturing PAGE / Jo L. Linpinsel and Graeme L. Conn -- Preparation of short RNA by in vitro transcription / Cheng Lu and Pingwei Li -- Native RNA purification by gel filtration chromatography / Evan P. Booy, Hui Meng, and Sean A. McKenna -- Cis-acting ribozymes for the production of RNA in vitro transcripts with defined 5ʹ and 3ʹ ends / Johanna M. Avis, Graeme L. Conn, and Scott C. Walker -- Trans-acting antigenomic HDV ribozyme for production of in vitro transcripts with homogenous 3ʹ ends / Milena Szafraniec [and others] -- Rapid preparation of RNA samples using DNA-affinity chromatography and DNAzyme methods / Hae-Kap Cheong, Eunha Hwang, and Chaejoon Cheong -- Preparation of lN-GST fusion protein for affinity immobilization of RNA / Genevieve Di Tomasso [and others] -- Affinity purification of RNA using an ARiBo tag / Genevieve Di Tomasso [and others] -- Plasmid template design and in vitro transcription of short RNAs within a "structure cassette" for structure probing experiments / Virginia K. Vachon and Graeme L. Conn -- In vitro transcription of modified RNAs / Stephanie L. Moon and Jeffrey Wilusz -- End-labeling oligonucleotides with chemical tags after synthesis / N. Ruth Zearfoss and Sean P. Ryder -- High-purity enzymatic synthesis of site-specifically modified tRNA / Ya-Ming Hou -- Se-derivatized RNAs for x-ray crystallography / Lina Lin and Zhen Huang -- Biosynthetic preparation of 13C/15N-labeled rNTPs for high-resolution NMR studies of RNAs / Luigi Martino and Maria R. Conte -- Preparative separation of ribonucleoside monophosphates by ion-pair reverse-phase HPLC / Pierre Dagenais and Pascale Legault -- Splint ligation of RNA with T4 DNA ligase / Christopher J. Kershaw and Raymond T. O'Keefe.
- 2012 Springer Protocolsedited by Argelia Lorence.Using folding promoting agents in recombinant protein production : a review / Beatrix Fahnert -- Routine identity confirmation of recombinant proteins by MALDI-TOF mass spectrometry / Brett J. Savary and Prasanna Vasu -- A matter of packaging : influence of nucleosome positioning on heterologous gene expression / María de la Cruz Muñoz-Centeno, Gonzalo Millán-Zambrano, and Sebastián Chávez -- Tools of the trade : developing antibody-based detection capabilities for recombinant proteins / Maureen C. Dolan [and others] -- Heat-shock protein fusion vectors for improved expression of soluble recombinant proteins in Escherichia coli / Christos A. Kyratsous and Christos A. Panagiotidis -- The use of a flagellar export signal for the secretion of recombinant proteins in salmonella / Ferenc Vonderviszt [and others] -- Optimization of purification protocols based on the step-by-step monitoring of the protein aggregates in soluble fractions / Ario de Marco -- Heterologous protein expression by Lactococcus lactis / Julio Villator-Hernández [and others] -- An extended suite of genetic tools for use in bacteria of the halomonadaceae : an overview / Montserrat Argandoña [and others] -- Regulated recombinant protein production in the antarctic bacterium Pseudoalteromonas haloplanktis TAC125 / Valentina Rippa [and others] -- A novel strategy for the construction of genomic mutants of the antarctic bacterium Pseudoalteromonas haloplanktis TAC125 / Maria Giuliani [and others] -- A new bacterial co-expression system for over-expressing soluble protein and validating protein-protein interaction / Jumei Zeng and Zheng-Guo He -- Heterologous high-level gene expression in the photosynthetic bacterium Rhodobacter capsulatus / Nadine Katzke [and others] -- Plasmid DNA production for therapeutic applications / Alvaro R. Lara and Octavio T. Ramírez -- Recombinant protein production in the eukaryotic protozoan parasite Leishmania tarentolae : a review / Tomoaki Niimi -- Expression of multisubunit proteins in Leishmania tarentolae / Marisa Sugino and Tomoaki Niimi -- Recombinant protein production in yeasts / Diethard Mattanovich [and others] -- Yeasts as a tool for heterologous gene expression / Raja Mokdad-Gargouri [and others] -- The Cre/Lox system : a practical tool to efficiently eliminate selectable markers in fungal endophytes / Simona Florea [and others] -- Aptamer-regulated expression of essential genes in yeast / Beatrix Suess [and others] -- Cloning and expression of hemicellulases from Aspergillus nidulans in Pichia pastoris / Prasanna Vasu, Stefan Bauer, and Brett J. Savary -- A thiamine-regulatable epitope-tagged protein expression system in fission yeast / Tiina Tamm -- Heterologous gene expression by chromosomal integration in fission yeast / Akihisa Matsuyama and Minoru Yoshida -- Genetic engineering of industrial strains of Saccharomyces cerevisiae / Sylvie le Borgne -- Recombinant protein production in plants : challenges and solutions / Elizabeth E. Hood and Deborah V. Vicuna Requesens -- A novel plant cell bioproduction platform for high-yield secretion of recombinant proteins / Jianfeng Xu and Marcia J. Kieliszewski -- Super-promoter :TEV, a powerful gene expression system for tobacco hairy roots / Luis Ñopo [and others] -- Bioseparation of recombinant proteins from plant extract with hydrophobin fusion technology / Jussi J. Joensuu [and others] -- Quality assessment of recombinant proteins produced in plants / Giuliana Medrano [and others] -- Cell-free protein synthesis as a promising expression system for recombinant proteins / Xumeng Ge and Jianfeng Xu -- The use of bacterial artificial chromosomes for recombinant protein production in mammalian cell lines / Leander Blaas [and others] -- Engineering the chaperone network of CHO cells for optimal recombinant protein production and authenticity / Lyne Jossé, C. Mark Smales, and Mick F. Tuite -- High-throughput baculovirus expression in insect cells / Richard B. Hitchman, Robert D. Possee, and Linda A. King -- Recombinant protein expression in milk of livestock species / Zsuzsanna Bösze and László Hiripi.
- 2012 Springer Protocolsedited by Roslyn M. Bill.Optimising yeast as a host for recombinant protein production (review) / Nicklas Bonander and Roslyn M. Bill -- Which yeast species shall I choose? : Saccharomyces cerevisiae versus Pichia pastoris (review) / Richard A.J. Darby [and others] -- Preparation of Pichia pastoris expression plasmids / Christel Logez [and others] -- Preparation of Saccharomyces cerevisiae expression plasmids / David Drew and Hyun Kim -- Codon optimisation for heterologous gene expression in yeast / Kristina Hedfalk -- Yeast transformation to generate high-yielding clones / Mohammed Jamshad and Richard A.J. Darby -- Screening for high-yielding Pichia pastoris clones : the production of G protein-coupled receptors as a case study / Shweta Singh [and others] -- Screening for high-yielding Saccharomyces cerevisiae clones: using a green fluorescent protein fusion strategy in the production of membrane proteins / David Drew and Hyun Kim -- The effect of antifoam addition on protein production yields / Sarah J. Routledge and Roslyn M. Bill -- Setting up a bioreactor for recombinant protein production in yeast / Sarah J. Routlledge and Michelle Clare -- The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review) / Nagamani Bora [and others] -- Online analysis and process control in recombinant protein production (review) / Shane M. Palmer and Edmund R.S. Kunji -- Monitoring the biomass accumulation of recombinant yeast cultures : offline estimations of dry cell mass and cell counts / Shane M. Palmer and Edmund R.S. Kunji -- Online monitoring of biomass accumulation in recombinant yeast cultures / Shane M. Palmer and Edmund R.S. Kunji -- Optimising Pichia pastoris induction / Zharain Bawa and Richard A.J. Darby -- Optimizing Saccharomyces cerevisiae induction regimes / David Drew and Hyun Kim -- Large-scale production of membrane proteins in Pichia pastoris : the production of G protein-coupled receptors as a case study / Shweta Singh [and others] -- Large-scale production of secreted proteins in Pichia pastoris / Nagamani Bora -- Disruption of yeast cells to isolate recombinant proteins / Mohammed Jamshad and Richard A.J. Darby.
- 2008 Springervolume editors, Richard Egel, Dirk-Henner Lankenau."Once per life cycle, mitotic nuclear divisions are replaced by meiosis I and II - reducing chromosome number from the diploid level to a haploid genome, reshuffling the homologous chromosomes by their centromeres, and recombining chromosome arms by crossing-over. In animals, including humans, all this happens during the germ cell formation of eggs and sperm. Due to the reign of meiosis, no child is a true genetic copy of either parent. Questions still open primarily concern the placement of and mutual coordination between neighboring crossover events. The current book addresses these processes and mechanisms in multicellular eukaryotes, such as Drosophila, Anibidopsis, mice and humans. The pioneering model systems of yeasts, as well as evolutionary aspects, will be addressed in a forthcoming volume."--Jacket.
- 2008 Springervolume editors, Richard Egel, Dirk-Henner Lankenau.Once per life cycle, mitotic nuclear divisions are replaced by meiosis I and II - reducing chromosome number from the diploid level to a haploid genome and recombining chromosome arms by crossing-over. In animals, all this happens during formation of eggs and sperm - in yeasts before spore formation. The mechanisms of reciprocal exchange at crossover/chiasma sites are central to mainstream meiosis. To initiate the meiotic exchange of DNA, surgical cuts are made as a form of calculated damage that subsequently is repaired by homologous recombination. These key events are accompanied by ancillar.
- pt. A-B, 2002. ScienceDirectpt. B ScienceDirectedited by Chandan K. Sen, Lester Packer ; editorial advisory board, John F. Engelhardt ... [et al.].Also available: Print – pt. A-B, 2002.
- 2012George Church & Ed Regis.Status: Not Checked OutLane Catalog RecordFrom bioplastics to H. sapiens 2.0 -- -3,800 Myr, Late Hadean : at the inorganic/organic interface -- -3,500 Myr, Archean : reading the most ancient texts and the future of living software -- -500 Myr, Cambrian : the mirror world and the explosion of diversity ; How fast can evolution go and how diverse can it be? -- -360 Myr, Carboniferous : "the best substitute for petroleum is petroleum" -- -60 Myr, Paleocene : emergence of mammalian immune system ; Solving the health care crisis through genome engineering -- -30,000 Yr, Pleistocene Park : engineering extinct genomes -- -10,000 Yr, Neolithic : industrial revolutions ; The agricultural revolution and synthetic genomics ; The BioFab Manifesto -- -100 Yr, Anthropocene : the third industrial revolution ; iGEM -- -1 Yr, Holocene : from personal genomes to immortal human components -- Epigenetic epilogue. +1 Yr, the end of the beginning, transhumanism, and the Panspermia Era : societal risks and countermeasures.
- Regulation and coordination of homologous pairing and synapsis during Caenorhabditis elegans meiosis2012Weibin Zhang.For successful segregation of chromosomes during meiosis, chromosomes have to recognize and align with their correct homologous partners, and then stabilize the homologous alignment with assembly of a proteinaceous structure, called the synaptonemal complex (SC), between them. SC assembly is highly processive and cooperative, yet the SC structure does not distinguish between homologous and nonhomologous associations. Thus SC assembly has to be tightly regulated and coordinated with homologous pairing to ensure that the SC is stabilizing productive homologous associations. Moreover, homologous pairing is accompanied by dramatic chromosome movement and nuclear reorganization of chromosomes into a clustered configuration during C. elegans early meiotic prophase. Subsequently, the clustered chromosomes are redispersed into aligned homologs upon SC assembly. The exact mechanisms involved in regulation and coordination of homologous pairing and synapsis are poorly understood, and this thesis was aimed at gaining a better understanding of the coordination of these two inter-related meiotic events. We identified HAL-2 as a major player in this coordination. We demonstrated that HAL-2 promotes homologous pairing mainly by preventing detrimental effects of SC precursors (SYP proteins). Homologous pairing is not established in hal-2 mutants, and several markers indicative of pairing center-mediated chromosome movement are also absent in hal-2 mutants. Pairing centers (PCs) are cis-acting chromosomal sites that mediate chromosome movement by connecting chromosomes to cytoplasmic microtubules via the conserved SUN-1/ZYG-12 nuclear envelope-spanning complexes. hal-2 mutants also exhibit defective SC assembly, with SYP proteins being loaded inappropriately along single unpaired chromosomes in hal-2 mutants. Moreover markers of PC-mediated chromosome movement and function are coordinately restored in hal-2 mutants by the removal of SYP proteins. Combined with other data, these findings indicate that SYP proteins can inhibit homologous pairing and that HAL-2 promotes pairing largely by antagonizing this inhibition, thus allowing activation and regulation of PC function. Given that HAL-2 concentrates in the nucleoplasm of meiotic germ cells and colocalizes with SYP proteins in nuclear aggregates when SC assembly is prevented, we propose that HAL-2 functions to shepherd SYP proteins prior to licensing of SC assembly, preventing SC precursors from interacting inappropriately with chromosomes and allowing them to accumulate sufficiently for rapid cooperative assembly upon homology verification. In this thesis, we also identified and characterized me16, a hypomorphic allele of scc-3. SCC-3 is a conserved component of the cohesin complex, and the scc-3(me16) mutant was demonstrated to be a partial loss of function mutation by comparative analyses with a null mutant, scc-3(ku263). Besides reduced chromosomal localization of cohesin, scc-3(me16) mutants also display an extended region of clustered chromosomes, incomplete SC assembly and defective recombination. Further, analyses of nuclear aggregates that form in the scc-3(ku263) null mutants led to the findings that components of the lateral elements, including cohesin, colocalize into these nuclear aggregates and that this localization is not dependent on REC-8.
- 2012Alicia Roberta Shields.Adult stem cells generate short-lived but highly differentiated cells that maintain and repair tissues which exhibit high turnover rates or tissues prone to wear and tear including sperm, skin, blood, intestinal epithelium and muscle. Adult stem cells typically reside in specialized microenvironments or stem cell niches, and a major goal of stem cell biology is to understand how these specialized microenvironments regulate adult stem cell self-renewal, proliferation and differentiation to maintain tissue homeostasis. Drosophila spermatogenesis provides an in vivo model system to investigate how the niche governs adult stem cell behavior. At the apical tip of the Drosophila testis, a cluster of post-mitotic support cells called the hub maintains two adult stem cell populations, germline stem cells (GSCs) and somatic cyst stem cells (CySCs). Hub cells secrete the Unpaired ligand, which activates JAK-STAT signaling in the neighboring GSCs and CySCs. JAK-STAT signaling and coordinated crosstalk between the germ line and soma together maintain GSCs and CySCs within the stem cell niche and direct proper association between their differentiating daughter cells. In this dissertation, I address two questions: (1) how a putative gene target of JAK-STAT influences stem cell self-renewal and maintenance and (2) how a transcriptional co-activator controls stem cell differentiation. To investigate the mechanism by which JAK-STAT signaling regulates GSC maintenance, I probed the function of profilin, a regulator of filamentous actin (F-actin). Profilin had been identified as a STAT target gene in the testis stem cell niche by performing chromatin immunoprecipitation with antibodies against phosphorylated STAT (activated STAT), followed by high throughput sequencing (ChIP-Seq) (Davies et al., submitted). It was already known that profilin mutants lose early germ cells (Gönczy and DiNardo, 1996) but the germline stem cell phenotype had not been characterized. I showed that GSCs were lost throughout development with markedly reduced GSC numbers in testes from late third instar larval hypomorphs and strong loss-of-function profilin mutants. By performing clonal analysis with null profilin alleles, I found that wild-type function of profilin was required cell autonomously for GSC maintenance. GSCs homozygous mutant for profilin detached from the hub and differentiated. F-actin and Adenomatous Polyposis Coli 2 (APC2) localization at the hub-GSC interface was disrupted in testes from profilin mutants. Interestingly, germline specific over-expression of APC2 rescued GSC loss in profilin hypomorphs. My studies suggested that profilin may be indirectly required to stabilize APC2 and [beta]-catenin at E-cadherin-based adherens junctions between hub cells and GSCs. Intercellular conversations between the germ line and the soma regulate the behavior of the stem cells in both lineages. I showed that a mutation in the MED20 gene, which encodes one of the subunits of Mediator, a multiprotein complex that acts as an interface between gene-specific regulatory proteins and the general transcriptional machinery to stimulate transcription, resulted in over-proliferation of both germline stem cells (GSCs) and somatic cyst stem cells (CySCs). Mediator function was required cell autonomously for CySCs to differentiate into somatic cyst cells, and non-autonomously for germ cell differentiation. This study reinforced the importance of crosstalk between stem cell lineages that work together to maintain tissue homeostasis.
- 2016 SpringerXiaojing Ma, editor.Regulation of IFN-[gamma] expression / John Fenimore, Howard A. Young -- The interleukin-1 family / Amir S. Yazdi, Kamran Ghoreschi -- Regulation of IL-4 expression in immunity and diseases / I-Cheng Ho, Shi-Chuen Miaw -- Regulation of IL-6 in immunity and diseases / Toshio Tanaka, Masashi Narazaki, Kazuya Masuda, Tadamitsu Kishimoto -- Regulation of interleukin-10 expression / Sascha Rutz, Wenjun Ouyang -- Regulation of interleukin-12 production in antigen-presenting cells / Hua Zheng, Yi Ban, Fang Wei, Xiaojing Ma -- Regulation of interleukin-17 production / Wenjuan Dong, Xiaojing Ma -- Regulation of interleukin-23 expression in health and disease / Iain Welsby, Stanislas Goriely -- Regulation and immune function of IL-27 / Qinghong Wang, Jianguo Liu -- The immunobiology of interleukin-35 and its regulation and gene expression / Mei Song, Xiaojing Ma.Also available: Print – 2016
- 2009 CRCnetBASEedited by Rajesh K. Gaur and John J. Rossi.Micro mining : computational approaches to miRNA discovery / Adam Grundhoff -- Animal microRNA gene prediction / Ola Snv?e and Pa<U+030a>l St?rom -- A suite of resources for the study of miRNA ontology and function / Praveen Sethupathy, Molly Megraw, and Artemis G. Hatzigeorgiou -- Regulation of translation and mRNA stability by Hfq-binding small RNAs in Escherichia coli / Hiroji Aiba -- Mechanisms by which microRNAs regulate gene expression in animal cells / Yang Yu and Timothy W. Nilsen -- The microRNAs of C. elegans / Mona J. Nolde and Frank J. Slack -- Isolation and characterization of small RNAs in C. elegans / Chisato Ushida and Yusuke Hokii -- MicroRNA tales in fly development / Utpal Bhadra ... [et al.] -- RNA interference and miRNAs in zebrafish / Alex S. Flynt, Elizabeth J. Thatcher, and James G. Patton -- Biogenesis and function of plant microRNAs / Zoltan Havelda -- Endogenous small RNA pathways in Arabidopsis / Manu Agarwal, Julien Curaba, and Xuemei Chen. How to assay miRNA expression : a technology guide / Mirco Castoldi, Vladimir Benes, and Martina U. Muckenthaler -- Methods to quantify microRNA gene expression / Lori A. Neely -- Regulation of alternative splicing by microRNAs / Rajesh K. Gaur -- Recent progress in polymerase II-mediated intronic microRNA expression systems / Shi-Lung Lin and Shao-Yao Ying -- MicroRNA-based RNA polymerase II expression vectors for RNA interference in mammalian cells / Anne B. Vojtek ... [et al.] -- Transgenic RNAi : a fast and low-cost approach to reverse genetics in mammals / Linghua Qiu and Zuoshang Xu -- Symphony of AIDS : an miRNA-based therapy / Yoichi R. Fujii -- MicroRNAs and cancer : connecting the dots / Sumedha D. Jayasena -- Mammalian transcriptional gene silencing by small RNAs / Daniel H. Kim and John J. Rossi -- Regulation of gene expression by RNA mediated transcriptional gene silencing / Kevin V. Morris.
- 2007 Springeredited by Carole L. Bassett.
- 2012Simona Rosu.Sexually reproducing organisms undergo meiotic recombination to increase genetic diversity and to ensure correct segregation of chromosomes at the first meiotic division. During meiotic recombination, DNA double-strand breaks (DSBs) are deliberately induced, and a subset of the breaks are repaired as inter-homolog crossovers (COs). Inter-homolog COs provide physical connections between homologous chromosomes that enable them to segregate away from each other. Despite reliance on COs for chromosome segregation, few COs are made per chromosome pair, implying mechanisms for robust CO control. In addition, DNA breaks are potentially dangerous lesions, therefore DSB formation and repair must be tightly regulated, both to ensure the formation of COs, but also to protect against deleterious effects. This thesis provides new insights into mechanisms that regulate DSB formation and repair, using the nematode Caenorhabditis elegans as a model organism. CO regulation mechanisms were probed by monitoring the repair outcome of a DSB induced at a defined site at different stages of meiotic progression, in WT and mutant situations. This analysis uncovered a previously unappreciated level of control in restricting CO number, which is to limit the duration of access to the homolog as a repair template. In addition, this work showed that when no competing breaks are present, a single induced DSB is converted to a CO with high efficiency. This feature helps achieve CO assurance. Insights into regulation of DSB formation were uncovered from the identification and characterization of novel protein DSB-2. DSB-2 is required for break formation, but is dispensable for later steps of meiotic recombination. DSB-2 localizes to chromatin during the time of break formation, suggesting it acts to promote competence for DSB formation. Both approaches presented in this thesis uncovered evidence for negative feedback regulatory mechanisms, suggesting a model wherein formation of CO-eligible recombination intermediates signals shutdown of DSB formation as well as shutdown of inter-homolog access. The proposed regulatory networks provide a mechanism to both ensure sufficient breaks and COs are made, and to shut down these processes to prevent deleterious effects as meiosis progresses.
- 2011 Springeredited by Helge Grosshans.MicroRNA biogenesis and function : an overview / Rene F. Ketting -- Regulation of pri-miRNA processing through Smads / Akiko Hata and Brandi N. Davis -- Stimulation of pri-miR-18a processing by hnRNP A1 / Gracjan Michlewski, Sonia Guil, and Javier F. Cáceres -- KSRP promotes the maturation of a group of miRNA precursors / Michele Trabucchi ... [et al.] -- Hormonal repression of miRNA biosynthesis through a nuclear steroid hormone receptor / Sally Fujiyama-Nakamura, Kaoru Yamagata, and Shigeaki Kato -- Autoregulatory mechanisms controlling the microprocessor / Robinson Triboulet and Richard I. Gregory -- Regulation of pre-miRNA processing / Nicolas J. Lehrbach and Eric A. Miska -- The effect of RNA editing and ADARs on miRNA biogenesis and function / Bret S.E. Heale, Liam P. Keegan, and Mary A. O'Connell -- MiRNAs need a trim regulation of miRNA activity by trim-NHL proteins / F. Gregory Wulczyn ... [et al.] -- Properties of the regulatory RNA-binding protein HuR and its role in controlling miRNA repression / Nicole-Claudia Meisner and Witold Filipowicz -- Turnover of mature miRNAs and siRNAs in plants and algae / Heriberto Cerutti and Fadia Ibrahim -- MicroRNases and the regulated degradation of mature animal miRNAs / Helge Grosshans and Saibal Chatterjee.Also available: Print – 2010
- 2012Christopher Paul Arnold.Stem cell self-renewal is dynamically regulated in response to extrinsic stimuli, but the intrinsic mechanisms that mediate the effects of these stimuli remain elusive. Emerging evidence suggests that miRNAs, an abundant class of ~22-nt small regulatory RNAs, play key roles in controlling the post-transcriptional genetic programs in stem and progenitor cells. We systematically examined miRNA expression profiles in various normal and aberrant adult tissue-specific stem and progenitor cells. Delineation of miRNAs whose expression correlated with changes in the self-renewal properties during normal development and as the result of mutant perturbations permitted the identification of miRNAs that marked stem to progenitor transition, termed SPT-miRNAs. Expression of SPT-miRNAs correlated with the exit from a self-renewing state as well as reduced self-renewal capacity in various normal and leukemia stem cells, suggesting that they may play a role in post-transcriptional gene silencing of key mediators of stem cell self-renewal. Consistent with this hypothesis, premature expression of a subset of these miRNAs could diminish the reconstitution potential of hematopoietic stem cells (HSCs) and the self-renewal of embryonic stem cells (ESCs). Furthermore, SPT-miRNAs targeted genes necessary for the self-renewal of HSCs, suggesting that up-regulation of these miRNAs permitted the efficient silencing of self-renewal programs during the stem to progenitor transition. Given the functional overlap of SPT-miRNAs in both embryonic and adult stem cells, we hypothesized that the expression of some SPT-miRNAs may be actively repressed by extrinsic signaling cues in stem cells at multiple developmental stages to potentiate their self-renewal. By subjecting ESCs to various culture conditions that diminished their self-renewal efficiency, we observed an up-regulation of a subset of SPT-miRNAs; in particular, members of the miR-181 family. Ectopic expression of this miRNA reduced ESC self-renewal whereas its deletion augmented ESC self-renewal in serum-free medium. These changes in self-renewal were attributable to simultaneous modulation of ESC proliferation and lineage commitment via target interactions with Lin28A, Spry4, and Dusp6. Finally, we found that the BMP-signaling pathway, necessary for the efficient self-renewal of ESCs, played a key role in the suppression of miR-181a. Collectively, these results reveal how extrinsic signaling cues mediate the quantitative post-transcriptional regulation of stem cell self-renewal programs via the modulation of miRNAs. Our study demonstrated one approach to identify and investigate the role of intrinsic regulators and provided novel insight into how to uncover the intrinsic regulators of stem cell self-renewal with implications on manipulation of stem cell expansion ex vivo.
- 2010Gwen Liu.MicroRNA (miRNA) genes, which encode an abundant class of ~22-nucleotide (nt), evolutionarily conserved small RNAs, control a fundamental layer of genetic programs at the post-transcriptional level. However, little is known about how the activity of miRNA genes is regulated and how the regulatory information controlling their activity is encoded. Interestingly, mature miRNAs can often be classified into large families consisting of members with identical seeds (nucleotides 2 through 8 of the mature miRNAs) and highly homologous ~22-nt mature miRNA sequences, but with divergent sequences and structural elements beyond their mature miRNAs. Here we investigated whether members of a miRNA gene family that encode identical or nearly identical mature miRNAs are functionally interchangeable in vivo and if not, why? We compare the activities of the mir-181 gene family in promoting double positive T cell development and show that miRNA genes that encode identical to nearly identical mature miRNAs can have distinct activities. The differences in activity between mir-181a-1 and mir-181c are largely determined by their unique primary/precursor-miRNA (pri/pre-miRNA) loop nucleotides, and the differences in activity between mir-181a-1 and mir-181b-1 are determined by both the pri/pre-miRNA loop and stem. Furthermore, the organization of mir-181a-1/b-1 in a cluster is important for its full activity. We also show that mir-181 family members can differentially regulate target genes quantitatively, and that some target genes can be upregulated. Taken together, we have demonstrated that regulatory information encoded in a miRNA gene beyond the mature miRNA plays a critical role in controlling the activity of the miRNA gene, suggesting that miRNA family members could have evolved different functions through their divergent miRNA gene sequences and structural elements beyond their mature miRNAs. Although, proteins may have evolved to recognize the structural and sequence elements of the pri/pre-miRNAs, we suggest that the regulatory information encoded in the structured pri/pre-miRNA may be directly interpreted through target and pri/pre-miRNA interactions.
- 2006 ScienceDirectEric H. Davidson.
- 2015 Springer Protocols2014 Springer Protocolsedited by Gordon G. Carmichael.Diverse functions and mechanisms of mammalian long noncoding RNAs -- Sequence-defined oligoaminoamides for the delivery of siRNAs -- A biochemical approach to identify direct microRNA targets -- Native gel analysis for mammalian microRNPs assembled from pre-microRNAs -- Identification and validation of miRNA target sites within nontraditional miRNA targets -- Fractionation of non-polyadenylated and ribosomal-free RNAs from mammalian cells -- Affinity purification of long noncoding RNA-protein complexes from formaldehyde cross-linked mammalian cells -- RNA pulldown protocol for in vitro detection and identification of RNA-associated proteins -- nRIP-seq: A technique to identify RNA targets of an RNA binding protein on a genome-wide scale -- Analysis of the subcellular distribution of RNA by fluorescence in situ hybridization -- RNA fluorescence in situ hybridization in cultured mammalian cells -- Locating RNAs in situ with FISH-STIC probes -- Rapid and efficient elimination of specific nuclear noncoding RNAs in mammalian cells with antisense oligonucleotides -- On using magnesium and potassium ions in RNA experiments -- Studying the affinity, kinetic stability, and specificity of RNA/protein interactions: SINE ncRNA/Pol II complexes as a model system
- 2006 Cold Spring Harb Lab PressSU Catalog (SearchWorks) Click LINK above for Print location/circulation status.meeting organized by Bruce Stillman and David Stewart.Mechanism and biology of RNAi -- Genome-wide approaches -- Small RNAs in development -- Telomeres and cancer -- End regulation of transcripts -- RNPs and RNA editing -- Biology of short RNAs -- Control of gene expression by noncoding RNAs -- Heterochromatin -- Quality control, messenger RNA turnover, and translational control.
- 2012 SpringerBibekanand Mallick, Zhumur Ghosh, editors.pt. 1. Basics -- pt. 2. Methods -- pt. 3. Applications.
- 2012 SpringerWolfgang R. Hess, Anita Marchfelder.This book provides a comprehensive and up-to-date collection of review articles focusing on RNA-mediated regulation in prokaryotes. The various modes of action include the direct interaction with proteins, direct sensing of metabolites or of physical parameters, and the interaction with RNAs to stimulate or prevent binding of ribosomes or to stimulate degradation. Written by leading experts in the field, the book covers small RNA functions, RNA thermometers, riboswitches, the diversity of small RNA-guided CRISPR-Cas defense systems and selected RNA chaperons in both prokaryotic domains, bacteria and archaea. Recent advances towards the computational identification of regulatory RNAs and their targets are included and particular attention is paid to small RNA in pathogenic bacteria. This volume is the only one exclusively covering regulatory RNAs in the prokaryotic domains to date, making it essential literature for anyone interested in RNA function and gene regulation and a valuable resource for teaching these concepts.
- 2012 Kargervolume editor, Manuel A. Garrido-Ramos.The Repetitive DNA Content of Eukaryotic Genomes / López-Flores, I.; Garrido-Ramos, M.A. -- Telomere Dynamics in Mammals / Silvestre, D.C.; Londoño-Vallejo, A. -- Drosophila Telomeres: an Example of Co-Evolution with Transposable Elements / Silva-Sousa, R.; López-Panadès, E.; Casacuberta, E. -- The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes / Tollis, M.; Boissinot, S. -- SINEs as Driving Forces in Genome Evolution / Schmitz, J. -- Unstable Microsatellite Repeats Facilitate Rapid Evolution of Coding and Regulatory Sequences / Jansen, A.; Gemayel, R.; Verstrepen, K.J. -- Satellite DNA Evolution / Plohl, M.; Meštrović, N.; Mravinac, B. -- Satellite DNA-Mediated Effects on Genome Regulation / Pezer, Ž.; Brajković, J.; Feliciello, I.; Ugarković, Đ. -- The Birth-and-Death Evolution of Multigene Families Revisited / Eirín-López, J.M.; Rebordinos, L.; Rooney, A.P.; Rozas, J. -- Chromosomal Distribution and Evolution of Repetitive DNAs in Fish / Cioffi, M.B.; Bertollo, L.A.C..
- 2007 Springer Protocolsedited by Donald S. Anson.Methodologies for staining and visualization of [beta]-galactosidase in mouse embryos and tissues / Siobhan Loughna and Deborah Henderson -- Immunohistochemical detection of [beta]-galactosidase or green fluorescent protein on tissue sections / Philip A. Seymour and Maike Sander -- Detection of reporter gene expression in murine airways / Maria Limberis, Peter Bell, and James M. Wilson -- Three-dimensional analysis of molecular signals with episcopic imaging techniques / Wolfgang J. Weninger and Timothy J. Mohun -- Fluorescent proteins for cell biology / George H. Patterson -- Detection of GFP during nervous system development in Drosophila melanogaster / Karin Edoff, James S. Dods, and Andrea H. Brand -- Autofluorescent proteins for flow cytometry / Charles G. Bailey and John E. J. Rasko -- Fluorescent protein reporter systems for single-cell measurements / Steven K. Dower, Eva E. Qwarnstrom, and Endre Kiss-Toth -- Subcellular imaging of cancer cells in live mice / Robert M. Hoffman -- Noninvasive imaging of molecular events with bioluminescent reporter genes in living subjects / Pritha Ray and Sanjiv Sam Gambhir -- Green fluorescent protein as a tracer in chimeric tissues : the power of vapor fixation / Harald Jockusch and Daniel Eberhard.
- Research in computational molecular biology : 11th annual international conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007 : proceedingsSpringer, 2007Terry Speed, Haiyan Huang (eds.).
- 2008 SpringerFred Gage, Yves Christen, (eds.).
- 2013Edward Bo-yi Chuong.The placenta plays a fundamental role supporting pregnancy in all mammals, but exhibits unexpected and striking morphological and physiological variation across species. The rapid evolutionary diversification of the mammalian placenta is hypothesized to be a product of recurrent genetic conflict between parent and offspring. In this work, I investigate the genetic basis of rapid placenta evolution by using high-throughput genomic approaches, and address three major issues in placental biology. First, given that highly conserved genes govern placental development, the molecular mechanisms underlying the rapid diversification of placental morphology have remained unresolved. Our study reveals that the genome-wide regulatory landscape of placental development is highly divergent between closely related species, strongly implicating non-coding regulatory evolution as the major force driving placental morphological diversity. Second, endogenous retroviruses (ERVs) that are normally repressed throughout the embryo are rampantly expressed in the placenta, but the biological rationale--if any-- behind this apparent paradox has been unclear. We demonstrate that species-specific ERVs serve as a major source of functional enhancers during placental development, which provides a clear mechanism where placental ERV activity may facilitate the evolutionary diversification of placental morphology. Finally, our findings suggest a novel evolutionary model where placental ERVs provide an adaptive benefit under parent-offspring conflict. Given that genetic conflict predicts rapid diversifying evolution to maintain maximal fitness, we propose that placental ERVs act to dramatically increase the developmental evolvability of the placenta by serving as a rapidly evolving, epigenetically restricted source of polymorphic regulatory elements.
- 2006 Springeredited by Jean-Marie Buerstedde and Shunichi Takeda.Ch. 1. DT40 gene disruptions: a how-to for the design and the construction of targeting vectors / Hiroshi Arakawa and Jean-Marie Buerstedde -- Ch. 2. Immunoglobulin gene conversion or hypermutation: That's the question / Jean-Marie Buerstedde and Hiroshi Arakawa -- Ch. 3. Genome resources for the DT40 community / Randolph B Caldwell and Andrzej M. Kierzek -- Ch. 4. Chromosome engineering in DT40 cells and mammalian centromere function / William R.A. Brown ... [et al.] -- Ch. 5. Function of recQ family helicase in genome stability / Masayuki Seki, Shusuke Tada and Takemi Enomoto -- Ch. 6. Genetic analysis of apoptotic execution / Sandrine Ruchaud ... [et al.] -- Ch. 7. The DT40 system as a tool for analyzing kinetochore assembly / Masahiro Okada, Tesuya Hori and Tatsuo Fukagawa -- Ch. 8. Analysing the DNA damage and replication checkpoints in DT40 cells / Michael D Rainey, George Zachos, and David AF Gillespie -- Ch. 9. Using DT40 to study clathrin function / Frank R. Wettey and Antony P. Jackson -- Ch. 10. Genetic analysis OF B cell signaling / Hisaaki Shinohara and Tomohiro Kurosaki -- Ch. 11. DT40 mutants: a model to study transcriptional regulation of B cell development and function / Jukka Alinikula, Olli Lassila and Kalle-Pekka Nera -- Ch. 12. Transcription and RNA processing factors play complex roles IN DT40 cells / Stephanie Bush and James L. Manley -- Ch. 13. Participation of histones, histone modifying enzymes and histone chaperones in vertebrate cell functions / Hidehiko Kikuchi ... [et al.] -- Ch. 14. Analysis of gene expression, copy number and palindrome formation with a DT40 enriched cDNA Microarray / Paul E. Neima ... [et al.] -- Ch. 15. Analysis of DNA replication damage bypass and its role in immunoglobulin repertoire development / Julian E. Sale, Anna-Laura Ross and Laura J. Simpson -- Ch. 16. The fanconi anemia pathway promotes homologous recombination repair in DT40 cell line / Julian E. Sale, Anna-Laura Ross and Laura J. Simpson -- Ch. 17. Calcium signaling, ion channels and more / Anne-Laure Perraud, Carsten Schmitz, Andrew M. Scharenberg -- Ch. 18. Phenotypic analysis of cellular responses to DNA damage / Helfrid Hochegger and Shunichu Takeda -- Ch. 19. ATM, a paradigm for a stress-responsive signal transducer in higher vertebrate cells / Ken-ichi Yamamoto, Masahiko Kobayashi and Hiroko Shimizu -- METHOD 1. Stable transfection of DT40 / Julian E. Sale -- METHOD 2. Basic cell culture conditions / Huseyin Saribasak and Hiroshi Arakawa -- METHOD 3. Excision of floxed-DNA sequences by transient induction of Mer-Cre-Mer / Hiroshi Arakawa -- METHOD 4. Immunoglobulin gene conversion and hypermutation assay by FACS / Hiroshi Arakawa -- METHOD 5. Target screening by PCR / Hiroshi Arakawa -- METHOD 6. Mitotic index determination by flow cytometry / David AF Gillespie and Mark Walker -- METHOD 7. Centrifugal elutriation as a means of cell cycle phase separation and synchronization / David AF Gillespie and Catarina Henriques -- METHOD 8. Preparation of genomic DNA for microarray-based comparative genome hybridization / Robert Kimmel, Amalia Icreverzi, Paul Neiman -- METHOD 9. Analysis of cellular Mg2+ in DT40 cells / Anne-Laure Perraud, Carsten Schmitz, Andrew M. Scharenberg -- METHOD 10. Transient transfection of DT40 / Roger Franklin & Julian E. Sale -- METHOD 11. Retroviral transduction of DT40 / Felix Randow & Julian E. Sale -- METHOD 12. Colony survival assay / Laura. J. Simpson & Julian E. Sale -- METHOD 13. Subcloning DT40 by limiting dilution / Jean-Marie Buerstedde -- METHOD 14. Subnuclear immunofluorescence / Dávid Szüts & Julian E. Sale -- METHOD 15. Sister chromatid exchange assay / Laura J. Simpson & Julian E. Sale -- METHOD 16. 2D cell cycle analysis / Roger Franklin & Julian E. Sale -- METHOD 17. Purification of tap-tagged proteins by two-step pull down from DT40 cells / Hiroyuki Kitao and Minoru Takata -- METHOD 18. Synchronization of cells / Eiichiro Sonoda -- METHOD 19. Tranfection of DT40 cells / Huseyin Saribasak and Hiroshi Arakawa -- METHOD 20. Luciferase reporter assay / Frank R. Wettey and Antony P. Jackson -- METHOD 21. Indirect immunofluorescence microscopy / Frank R. Wettey and Antony P. Jackson -- METHOD 22. Quantification of receptor-mediated endocytosis / Frank R. Wettey and Antony P. Jackson -- METHOD 23. Measurement of DNA synthesis and strand breaks using alkaline sucrose density gradient centrifugation / Kouichi Yamada and Jun Takezawa -- METHOD 24. Fractionation of nuclear and cytoplasmic proteins from DT40 cell lines / Yan-Dong Wang and Randolph B Caldwell.
- 2012 Springer Protocolsedited by Julie A. Douthwaite and Ronald H. Jackson.Ribosome display : a perspective / Andreas Plückthun -- Preparation and testing of E. coli S30 in vitro transcirption translation extracts / James F. Zawada -- Eurkaryotic ribosome display selection using rabbit reticulocyte lysate / Julie A Douthwaite -- Stabilized ribosome display for in vitro selection / Shuta Hara [and others] -- Eukaryotic ribosome display with in situ DNA recovery / Mingyue He [and others] -- mRNA display using covalent coupling of mRNA to translated proteins / Rong Wang, Steve W. Cotten, and Rihe Liu -- SNAP display : in vitro rotein evolution in microdroplets / Miriam Kaltenbach and Florian Hollfelder -- cDNA display : rapid stabilization of mRNA display / Shingo Ueno and Naoto Nemoto -- Optimisation of antibody affinity by ribosome display using error-prone or site-directed mutagenesis / Leeanne Lewis and Chris Lloyd -- Affinity maturation of phage display antibody populations using ribosome display / Maria A. Groves and Adrian A. Nickson -- Evolution of protein stability using ribosome display / Andrew Buchanan -- Selection of lead antibodies from naive ribosome display antibody libraries / Peter Ravn -- Evolution of disulfide-rich peptide aptamers using cDNA display / Yuki Mochizuki and Naoto Nemoto -- Peptide screening using PURE ribosome display / Hiroyuki Ohashi [and others] -- Rapid selection of high-affinity binders using ribosome display / Birgit Dreier and Andreas Plückthun -- mRNA display-based selections using synthetic peptide and natural protein libraries / Steve W. Cotten [and others] -- Identification of candidate vaccine genes using ribosome display / Liancheng Lei -- Ribosome display for the selection of Sac7d scaffolds / Barbara Mouratou [and others] -- Charging of tRNAs using ribozymes and selection of cyclic peptides containing thioethers / Patrick C. Reid [and others] -- Update on pure translation display with unnatural amino acid incorporation / R. Edward Watts and Anthony C. Forster -- In vitro selection of unnatural cyclic peptide libraries via mRNA display / Zhong Ma and Matthew C.T. Hartman -- Optimization of CAT-354, a therapeutic antibody directed against interleukin-13, using ribosome display / George Thom and Ralph Minter -- Affinity maturation and functional dissection of a humanised anti-RAGE monoclonal antibody by ribosome display / Simon E. Hufton.
- 2013 Springer Protocolsedited by Yinong Yang.Rice artificial hybridization for genetic analysis / Xueyan Sha -- Fluorescence in situ hybridization techniques for cytogenetic and genomic analyses / Jason G. Walling, Wenli Zhang, and Jiming Jiang -- Generation of rice mutants by chemical mutagenesis / Thomas H. Tai -- TILLING and ecotilling for rice / Jennifer L. Cooper [and others] -- Functional characterization of rice genes using a gene-indexed T-DNA insertional mutant population / Ki-Hong Jung and Gynheung An -- QTL analysis and map-based cloning of salt tolerance gene in rice / Ji-Ping Gao and Hong-Xuan Lin -- Site-specific gene integration in rice / Vibha Srivastava -- Transcriptome profiling analysis using rice oligonucleotide microarrays / Ki-Hong Jung and Pamela C. Ronald -- Cloning of small RNAs for the discovery of novel microRNAs in plants / Guru Jagadeeswaran and Ramanjulu Sunkar -- Global identification of small RNA targets in plants by sequencing sliced ends of messenger RNAs / Yong-Fang Li and Ramanjulu Sunkar -- Artificial microRNAs for specific gene silencing in rice / Norman Warthmann [and others] -- Rice proteomic analysis : sample preparation for protein identification / Ganesh Kumar Agrawal [and others] -- Quantification of jasmonic and salicylic acids in rice seedling leaves / Kyoungwon Cho [and others] -- Analysis of insect-induced volatiles from rice / Nan Zhao [and others] -- Phenotypic and physiological evaluation for drought and salinity stress responses in rice / Utlwang Batlang [and others] -- Phenotypic, physiological, and molecular evaluation of rice chilling stress response at the vegetative stage / Benildo G. de los Reyes [and others] -- Analysis of rice root hair morphology using cryo-scanning electron microscopy / Zhiming Yu -- Inoculation and virulence assay for bacterial blight and bacterial leaf streak of rice / Bing Yang and Adam Bogdanove -- Inoculation and scoring methods for rice sheath blight disease / Yulin Jia [and others] -- Molecular approaches to improve rice abiotic stress tolerance / Junya Mizoi and Kazuko Yamaguchi-Shinozaki -- Molecular strategies to improve rice disease resistance / Emily E. Helliwell and Yinong Yang -- Molecular strategies to engineer transgenic rice seed compartments for large-scale production of plant-made pharmaceuticals / Trevor Greenham and Illimar Altosaar.
- 2008 Springer Protocolsedited by Henrik Nielsen.The transcriptional landscape -- Working with RNA -- Synthesis of RNA by in vitro transcription -- Efficient poly(A)+ RNA selection using LNA oligo(T) capture -- Genome browsers -- Web-based tools for studying RNA structure and function -- Northern blotting analysis -- Rapid amplification of cDNA ends (RACE) -- Fractionation of mRNA based on the length of the poly(A) tail -- Analysis of mutations that influence pre-mRNA splicing -- S1 nuclease analysis of alternatively spliced mRNA -- Promises and challenges in developing RNAi as a research tool and therapy -- Inhibition of gene function in mammalian cells using short-hairpin RNA (shRNA) -- Validation of RNAi by real time PCR -- Profiling RNA polymerase II using the fast chromatin immunoprecipitation method -- The post-transcriptional operon -- RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray (chip) profiling -- Isolation of RNP granules -- Electrophoretic mobility shift assay for characterizing RNA-protein interaction -- Polysome analysis and RNA purification from sucrose gradients -- Prediction of targets for microRNAs -- Outsourcing of experimental work.
- 2012 Springer Protocolsedited by Hailing Jin, Walter Gassmann.SuperSAGE : powerful serial analysis of gene expression / Hideo Matsumura [and others] -- Northern blot analysis for expression profiling of mRNAs and small RNAs / Ankur R. Bhardwaj [and others] -- Construction of RNA-seq libraries from large and microscopic tissues for the illumina sequencing platform / Hagop S. Atamian and Isgouhi Kaloshian -- Strand-specific RNA-seq applied to malaria samples / Nadia Ponts, Duk-Won D. Chung, and Karine G. Le Roch -- RNA in situ hybridization in Arabidopsis / Miin-Feng Wu and Doris Wagner -- Laser microdissection of cells and isolation of high-quality RNA after cryosectioning / Marta Barcala, Carmen Fenoll, and Carolina Escobar -- Detection and quantification of alternative splicing variants using RNA-seq / Douglas W. Bryant Jr, Henry D. Priest, and Todd C. Mockler -- Separating and analyzing sulfur-containing RNAs with Organomercury Gels / Elisa Biondi and Donald H. Burke -- RNAse mapping and quantitation of RNA isoforms / Lakshminarayan K. Venkatesh, Olufemi Fasina, and David J. Pintel -- Detection and quantification of viral and satellite RNAs in plant hosts / Sun-Jung Kwon, Jang-Kyun Seo, and A.L.N. Rao -- In situ detection of mature miRNAs in plants using LNA-modified DNA probes / Xiaozhen Yao, Hai Huang, and Lin Xu -- Small RNA isolation and library construction for expression profiling of small RNAs from neurospora and fusarium using illumina high-throughput deep sequencing / Gyungsoon Park and Katherine A. Borkovich -- Isolation and profiling of protein-associated small RNAs / Hongwei Zhao [and others] -- New virus discovery by deep sequencing of small RNAs / Kashmir Singh, Ravneet Kaur, and Wenping Qiu -- Global assembly of expressed sequence tags / Foo Cheung -- Computational analysis of RNA-seq / Scott A. Givan, Christopher A. Bottoms, and William G. Spollen -- Identification of microRNAs and natural antisense transcript-originated endogenous siRNAs from small-RNA deep sequencing data / Weixiong Zhang [and others].
- 2011 Springer Protocolsedited by Ruslan Aphasizhev.Three-dimensional reconstruction of trypanosoma brucei editosomes using single-particle electron microscopy / H.U. Goringer ... [et al.] -- Icoda: RNAi-based inducible knock-in system in trypanosoma brucei / G.E. Ringpis, R.H. Lathrop and R. Aphasizhev -- Perturbing a-to-i RNA editing using genetics and homologous recombination / C.J. Staber ... [et al.] -- Laser microdissection and pressure catapulting of single human motor neurons for RNA editing analysis / H. Sun ... [et al.] -- Biochemical identification of A-to-I RNA editing sites by the inosine chemical erasing (ice) method / M. Sakurai and T. Suzuki -- Identifying mRNA editing deaminase targets by RNA-seq / B.R. Rosenberg, S. Dewell and F.N. Papavasiliou -- Mouse and other rodent models of C to U RNA editing / V. Blanc and N.O. Davidson -- In vivo analysis of RNA editing in plastids / S. Ruf and R. Bock -- Identifying specific trans-factors of RNA editing in plant mitochondria by multiplex single base extension typing / M. Takenaka -- Complementation of mutants in plant mitochondrial RNA editing by protoplast transfection / M. Takenaka and A. Zehrmann -- A high-throughput assay for DNA deaminases / M. Wang, C. Rada and M.S. Neuberger -- Biochemical fractionation and purification of high-molecular-mass apobec3g complexes / Y.L. Chiu -- Analysis of tRNA editing in native and synthetic substrates / J.L. Spears, K.W. Gaston and J.D. Alfonzo -- Post-transcriptional modification of RNAs by artificial box h/aca and box c/d rnps / C. Huang, J. Karijolich and Y.T. Yu -- Functional analysis of noncoding RNAs in trypanosomes: RNA walk, a novel approach to study RNA-RNA interactions between small RNA and its target / C. Wachtel and S. Michaeli -- A post-labeling approach for the characterization and quantification of RNA modifications based on site-directed cleavage by dnazymes / M. Meusburger, M. Hengesbach and M. Helm.
- 2015 Springer Protocolsedited by Ernesto Picardi.Free energy minimization to predict RNA secondary structures and computational RNA design / Alexander Churkin, Lina Weinbrand, and Danny Barash -- RNA secondary structure prediction from multi-aligned sequences / Michiaki Hamada -- Simple protocol for the inference of RNA global pairwise alignments / Eugenio Mattei, Manuela Helmer-Citterich, and Fabrizio Ferrè -- De novo secondary structure motif discovery using RNA profile / Federico Zambelli and Giulio Pavesi -- Drawing and editing the secondary structure(s) of RNA / Yann Ponty and Fabrice Leclerc -- Modeling and predicting RNA three-dimensional structures / Jérôme Waldispühl and Vladimir Reinharz -- Fast prediction of RNA-RNA interaction using heuristic algorithm / Soheila Montaseri -- Quality control of RNA-Seq experiments / Xing Li ... [and 3 others] -- Accurate mapping of RNA-Seq data / Kin Fai Au -- Quantifying entire transcriptomes by aligned RNA-Seq data / Raffaele A. Calogero and Francesca Zolezzi -- Transcriptome assembly and alternative splicing analysis / Paola Bonizzoni ... [and 5 others] -- Detection of post-transcriptional RNA editing events / Ernesto Picardi ... [and 3 others] -- Prediction of miRNA targets / Anastasis Oulas ... [and 6 others] -- Using deep sequencing data for identification of editing sites in mature miRNAs / Shahar Alon and Eli Eisenberg -- NGS-trex : an automatic analysis workflow for RNA-seq data / Ilenia Boria ... [and 3 others] -- e-DNA meta-barcoding : from NGS raw data to taxonomic profiling / Fosso Bruno, Marzano Marinella, and Monica Santamaria -- Deciphering metatranscriptomic data / Evguenia Kopylova ... [and 6 others] -- RIP-seq data analysis to determine RNA-protein associations / Federico Zambelli and Giulio Pavesi -- ViennaRNA eeb services / Andreas R. Gruber, Stephan H. Bernhart, and Ronny Lorenz -- Exploring the RNA editing potential of RNA-Seq data by ExpEdit / Mattia D'Antonio ... [and 4 others] -- Guideline for the annotation of UTR regulatory elements in the UTRsite collection / Matteo Giulietti ... [and 3 others] -- Rfam : annotating families of non-coding RNA sequences / Jennifer Daub ... [and 3 others] -- ASPicDB : a database web tool for alternative splicing analysis / Mattia D'Antonio ... [and 5 others] -- Analysis of alternative splicing events in custom gene datasets by AStalavista / Sylvain Foissac and Michael Sammeth -- Computational design of artificial RNA molecules for gene regulation / Alessandro Laganà ... [and 6 others].
- 2012 SpringerNeocles Leontis, Eric Westhof, editors.Introduction / Michael Levitt -- Modeling RNA Molecules / Neocles Leontis and Eric Westhof -- Methods for Predicting RNA Secondary Structure / Kornelia Aigner, Fabian Dre€en and Gerhard Steger -- Why Can't We Predict RNA Structure At Atomic Resolution? / Parin Sripakdeevong, Kyle Beauchamp and Rhiju Das -- Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling / Kristian Rother, Magdalena Rother, Michał Boniecki, Tomasz Puton and Konrad Tomala, et al. -- The RNA Folding Problems: Different Levels of sRNA Structure Prediction / Fredrick Sijenyi, Pirro Saro, Zheng Ouyang, Kelly Damm-Ganamet and Marcus Wood, et al. -- Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus / Wojciech K. Kasprzak and Bruce A. Shapiro -- Methods for Building and Refining 3D Models of RNA / Samuel C. Flores, Magdalena Jonikas, Christopher Bruns, Joy P. Ku and Jeanette Schmidt, et al. -- Multiscale Modeling of RNA Structure and Dynamics / Feng Ding and Nikolay V. Dokholyan -- Statistical Mechanical Modeling of RNA Folding: From Free Energy Landscape to Tertiary Structural Prediction / Song Cao and Shi-Jie Chen -- Simulating Dynamics in RNA-Protein Complexes / John Eargle and Zaida Luthey-Schulten -- Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs / Jiří Šponer, Judit E. Šponer and Neocles B. Leontis -- Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking / Neocles B. Leontis and Craig L. Zirbel -- Ions in Molecular Dynamics Simulations of RNA Systems / Pascal Auffinger -- Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data / Joshua S. Martin, Paul Mitiguy and Alain Laederach -- A Top-Down Approach to Determining Global RNA Structures in Solution Using NMR and Small-Angle X-ray Scattering Measurements / Yun-Xing Wang, Jinbu Wang and Xiaobing Zuo -- RNA Structure Determination by Structural Probing and Mass Spectrometry: MS3D / A. E. Hawkins and D. Fabris.
- 2011 Springer Protocolsedited by Jeffrey E. Gerst.Single molecule imaging of RNA in situ / Mona Batish, Arjun Raj, and Sanjay Tyagi -- FISH and immunofluorescence staining in Chlamydomonas / James Uniacke, Daniel Colón-Ramos, and William Zerges -- High resolution fluorescent in situ hybridization in Drosophila / Eric Lécuyer -- Localization and anchorage of maternal mRNAs to cortical structures of ascidian eggs and embryos using high resolution in situ hybridization / Alexandre Paix, Janet Chenevert, and Christian Sardet -- Visualization of mRNA localization in Xenopus oocytes / James A. Gagnon and Kimberly L. Mowry -- Visualization of mRNA expression in the zebrafish embryo / Yossy Machluf and Gil Levkowitz -- High-resolution fluorescence in situ hybridization to detect mRNAs in neuronal compartments in vitro and in vivo / Sharon A. Swanger, Gary J. Bassell, and Christina Gross -- Localization of mRNA in vertebrate axonal compartments by in situ hybridization / José Roberto Sotelo-Silveira ... [et al.] -- Tiny molecular beacons for in vivo mRNA detection / Diana P. Bratu, Irina E. Catrina, and Salvatore A.E. Marras -- Delivery of molecular beacons for live-cell imaging and analysis of RNA / Antony K. Chen ... [et al.] -- Genetically-encoded fluorescent probes for imaging endogenous mRNA in living cells / Takeaki Ozawa and Yoshio Umezawa -- Visualization of induced RNA in single bacterial cells / Azra Borogovac and Natalia E. Broude -- Visualizing mRNAs in fixed and living yeast cells / Franck Gallardo and Pascal Chartrand -- In vivo visualization of RNA using the U1A-based tagged RNA system / Sunglan Chung and Peter A. Takizawa -- Visualizing endogenous mRNAs in living yeast using m-TAG, a PCR-based RNA aptamer integration method, and fluorescence microscopy / Liora Haim-Vilmovsky and Jeffrey E. Gerst -- Imaging mRNAs in living mammalian cells / Sharon Yunger and Yaron Shav-Tal -- Using the mRNA-MS2/MS2CP-FP system to study mRNA transport during Drosophila oogenesis / Katsiarina Belaya and Daniel St Johnston -- Genome-wide analysis of RNA extracted from isolated mitochondria / Erez Eliyahu, Daniel Melamed and Yoav Arava -- Analyzing mRNA localization to the endoplasmic reticulum via cell fractionation / Sujatha Jagannathan, Christine Nwosu and Christopher V. Nicchitta -- Isolation of mRNAs encoding peroxisomal proteins from yeast using a combined cell fractionation and affinity purification procedure / Gadi Zipor, Cecile Brocard and Jeffrey E. Gerst -- Profiling axonal mRNA transport / Dianna E. Willis and Jeffery L. Twiss -- RNA purification from tumor cell protrusions using porous polycarbonate filters / Jay Shankar and Ivan R. Nabi -- RNA-binding protein immunopurification-microarray (RIP-chip) analysis to profile localized RNAs / Alessia Galgano and André P. Gerber -- RaPID : an aptamer-based mRNA affinity purification technique for the identification of RNA and protein factors present in ribonucleoprotein complexes / Boris Slobodin and Jeffrey E. Gerst -- RIP : an mRNA localization technique / Sabarinath Jayaseelan ... [et al.] -- The dual use of RNA aptamer sequences for affinity purification and localization studies of RNAs and RNA-protein complexes / Scott C. Walker ... [et al.] -- Identifying and searching for conserved RNA localisation signals / Russell S. Hamilton and Ilan Davis -- Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes / Michal Rabani, Michael Kertesz, and Eran Segal.
- 2007 ScienceDirectedited by Jonatha M. Gott.
- 2008 SpringerH. Ulrich Göringer (ed.).Editing reactions from the perspective of RNA structure / Matthias Homann -- Editing of tRNA for structure and function / Juan D. Alfonzo -- RNA editing by adenosine deaminases that act on RNA (ADARs) / Michael F. Jantsch and Marie Öhman -- Insertion/deletion editing in Physarum polycephalum / Jonatha M. Gott and Amy C. Rhee -- RNA editing in plant mitochondria / Mizuki Takenaka ... [et al.] -- RNA editing in chloroplasts / Masahiro Sugiura -- Working together : the RNA editing machinery in Trypanosoma brucei / Jason Carnes and Kenneth Stuart -- RNA editing accessory factors : the example of mHel61p / H. Ulrich Göringer ... [et al.] -- The function of RNA editing in trypanosomes / Torsten Ochsenreiter and Stephen Hajduk -- Evolutionary aspects of RNA editing / Dave Speijer.
- 2011 Springeredited by Torben Heick Jensen."The diversity of RNAs inside living cells is amazing. We have known of the more "classic" RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of the book to introduce this fascinating protein complex and to give a timely and rich account of its many functions"--Provided by publisher.Also available: Print – 2011
- 2014 Springer Protocolsedited by Christina Waldsich.Predicting RNA Structure: Advances and Limitations -- Cis-Acting 5' Hammerhead Optimization for In Vitro Transcription of Highly Structured RNAs -- RNA Structural Analysis by Enzymatic Digestion -- A Mutate-and-Map Protocol for Inferring Base Pairs in Structured RNA -- Mapping RNA Structure In Vitro Using Nucleobase-Specific Probes -- Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-Seq Protocol -- Probing RNA Folding by Hydroxyl Radical Footprinting -- Monitoring Global Structural Changes and Specific Metal Binding Sites in RNA by In-Line Probing and Tb(III) Cleavage -- Chemical Probing of RNA in Living Cells -- A Chemogenetic Approach to Study the Structural Basis of Protein-Facilitated RNA Folding -- Applying UV Crosslinking to Study RNA-Protein Interactions in Multicomponent Ribonucleoprotein Complexes -- The Kinetics of Ribozyme Cleavage: A Tool to Analyze RNA Folding as a Function of Catalysis -- RNA Catalytic Activity as a Probe of Chaperone-Mediated RNA Folding -- Evaluation of RNA Chaperone Activity In Vivo and In Vitro Using Misfolded Group I Ribozymes -- RNA Conformational Changes Analyzed by Comparative Gel Electrophoresis -- Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation -- RNA Folding Dynamics Using Laser Assisted Single-Molecule Refolding -- RNA Refolding Studied by Light-Coupled NMR Spectroscopy -- Exploring RNA Oligomerization and Ligand Binding by Fluorescence Correlation Spectroscopy and Small Angle X-Ray Scattering.
- 2011 Springeredited by Lesley J. Collins.The RNA infrastructure : an introduction to ncRNA networks / Lesley J. Collins -- RNA interactions / Manja Marz and Peter F. Stadler -- Plant RNA silencing in viral defence / Vitantonio Pantaleo -- Micrornas as post-transcriptional machines and their interplay with cellular networks / Sarath Chandra Janga and Swathi Vallabhaneni -- Spatiotemporal aspects of microRNA-mediated gene regulation / Joris Pothof and Dik C. van Gent -- Spliceosomal RNA infrastructure : the network of splicing components and their regulation by miRNAs / Lesley J. Collins -- Construction, structure, and dynamics of post-transcriptional regulatory network directed by RNA binding proteins / Sarath Chandra Janga and Nitish Mittal -- Safe keeping the message : mRNP complexes tweaking after transcription / Said Hafidh, Věra Čapková, and David Honys -- Unexpected functions of tRNA and tRNA processing enzymes / Rebecca L. Hurto -- Programmed DNA elimination in tetrahymena : a small RNA mediated genome surveillance mechanism / Kensuke Kataoka and Kazufumi Mochizuki -- Long noncoding RNA and epigenomics / Chandrasekhar Kanduri -- Promoter associated long noncoding RNAs repress transcription through a RNA binding protein TLS / Riki Kurokawa -- RNA networks in prokaryotes I :CRISPRs and riboswitches / Patrick J. Biggs and Lesley J. Collins -- RNA networks in prokaryotes II : tRNA processing and small RNAs / Lesley J. Collins and Patrick J. Biggs -- Localization of the bacterial RNA infrastructure / Kenneth C. Keiler -- Small RNA discovery and characterisation in eukaryotes using high throughput approaches / Helio Pais ... [et al.] -- How old are RNA networks? / Toni Daly, X. Sylvia Chen, and David Penny.
- 2005 ScienceDirectedited by David R. Engelke, John J. Rossi.
- 2015 Springer Protocolsedited by Mouldy Sioud.RNA interference : mechanisms, technical challenges, and therapeutic opportunities / Mouldy Sioud -- Nanostructured RNAs for RNA interference / Yuko Nakashima [and others] -- One long oligonucleotide or two short oligonucleotides based shRNA construction and expression / Xue-jun Wang and Sheng-qi Wang -- PLGA microspheres encapsulating siRNA / Giuseppe De Rosa and Giuseppina Salzano -- Magnetic nanoparticle and magnetic field assisted siRNA delivery in vitro / Olga Mykhaylyk [and others] -- Cytoplasmic delivery of siRNAs to monocytes and dendritic cells via electroporation / Mouldy Sioud -- Delivery of siRNAs to cancer cells via bacteria / Omar Ahmed, Andrea Krühn, and Hermann Lage -- Microwell array-mediated delivery of lipoplexes containing nucleic acids for enhanced therapeutic efficacy / Yun Wu, Daniel Gallego-Perez, and L. James Lee -- Modulating the tumor microenvironment with RNA interference as a cancer treatment strategy / Karin Zins [and others] -- Targeted in vivo delivery of siRNA and an endosome- releasing agent to hepatocytes / Magdolna G. Sebestyén [and others] -- Cell-internalization SELEX : method for identifying cell- internalizing RNA aptamers for delivering siRNAs to target cells / William H. Thiel [and others] -- Strategies for siRNA navigation to desired cells / Mouldy Sioud -- Use of guanidinopropyl-modified siRNAs to silence gene expression / Maximilian C.R. Buff [and others] -- Therapy of respiratory viral infections with intranasal siRNAs / Sailen Barik and Patrick Lu -- Engineering therapeutic cancer vaccines that activate antitumor immunity / Per Ole Iversen and Mouldy Sioud -- Immunosuppressive factor blockade in dendritic cells via siRNAs results in objective clinical responses / Mouldy Sioud, Anne Mobergslien, and Stein Sæbøe-Larssen -- Targeting bcr-abl transcripts with siRNAs in an imatinib- resistant chronic myeloid leukemia patient : challenges and future directions / Michael Koldehoff -- Facile method for interfering with off-target silencing mediated by the sense strand / Anne Mobergslien and Mouldy Sioud -- Overcoming the challenges of siRNA activation of innate immunity : design better therapeutic siRNAs / Mouldy Sioud -- Gene silencing in vitro and in vivo using intronic microRNAs / Jia Han Deng [and others] -- In silico identification of novel endo-siRNAs / Andrew Schuster [and others] -- Computer-assisted annotation of small RNA transcriptomes / Nicole Ortogero [and others] -- miR-CATCH : microRNA capture affinity technology / Sebastian Vencken [and others] -- Roles of MicroRNAs in cancers and development / Shigeru Takasaki -- Targeting microRNAs to withstand cancer metastasis / Valentina Profumo [and others] -- Urinary microRNAs as a new class of noninvasive biomarkers in oncology, nephrology, and cardiology / Hana Mlcochova [and others] -- Magnetic bead-based isolation of exosomes / Morten P. Oksvold, Axl Neurauter, and Ketil W. Pedersen -- Modified 2'-ribose small RNAs function as toll-like receptor-7/8 antagonists / Mouldy Sioud.
- 2013 SpringerKenneth A. Howard, editor.The Nobel Prize winning discovery that small interfering RNA can be utilised to control cellular gene expression has propelled the field of RNA interference (RNAi) to the forefront of biomedical science as a potential molecular medicine set to revolutionalise disease treatment. Harnessing the molecular mechanisms of RNAi and development of delivery technologies is crucial for its transformation into a therapeutic modality, this dependency is the focus of "RNA Interference from Biology to Therapeutics" that gives a comprehensive overview of RNAi biology and state-of-the-art delivery methods relevant to clinical translation of RNAi therapeutics. Key players and shapers in the fields of RNAi and delivery science have been assembled in a single volume to produce a truly unique interdisciplinary text, making it a "must-read" for both students and experts in, and at the interface of, RNAi, pharmaceutical science and medicine. An attractive feature is the "future perspectives" section within each chapter that allows global leaders the opportunity to express their views on the direction the field is moving. Topics covered in the book include miRNA biology and therapeutic exploitation, exosome delivery and clinical translation."RNA Interference from Biology to Therapeutics" is an up-to-the-minute, highly informative and invaluable text for those actively involved or interested in this fascinating and high-impact field.
- 2011 Springer Protocolsedited by Scott Q. Harper.Designing hairpin-based RNAi shuttles / Yu Shen -- Rapid cloning and validation of microRNA shuttle vectors : a practical guide / Ryan L. Boudreau [and others] -- Use of small noncoding RNAs to silence transcription in human cells / Kevin V. Morris -- Delivery strategies for RNAi to the nervous system / Kevin D. Foust and Brian K. Kaspar -- Cloning small RNAs / Eric J. Devor and Lingyan Huang -- Profiling the miRNome : detecting global miRNA expression levels with DNA microarrays / Peter White -- High-throughput profiling of mature microRNA by real-time PCR / Jinmai Jiang [and others] -- In situ detection of microRNAs in paraffin-embedded, formalin-fixed tissues : different methodologies and co-localization with possible targets / Gerard J. Nuovo [and others] -- Tracing of siRNAs inside cells by FRET imaging / Markus Hirsch [and others] -- Application of RIP-chip for the identification of miRNA targets / Lu Ping Tan, Anke van den Berg, and Joost L. Kluiver.
- 2005 MyiLibraryedited by Krisharao Appasani ; forewords by Andrew Fire and Marshall Nirenberg.Chemical modifications to achieve increased stability and sensitive detection of siRNA -- RNA interference in postimplantation mouse embryos -- In ovo RNAi opens new possibilities for functional genomics in vertebrates -- Sect. 4. Gene silencing in model organisms. Practical applications of RNAi in C. elegans -- Inducible RNAi as a forward genetic tool in Trypanosoma brucei -- RNA-mediated gene silencing in fission yeast -- RNA silencing in filamentous fungi: Mucor ciccinelloides as a model organism -- RNAi and gene silencing phenomena mediated by viral suppressors in plants -- Sect. 1. Basic RNAi, siRNA, microRNAs and gene-silencing mechanisms. RNAi beginnings. Overview of the pathway in C. elegans -- Dicer in RNAi: its roles in vivo and utility in vitro -- Genes required for RNA interference -- MicroRNAs: a small contribution from worms -- miRNAs in the brain and the application of RNAi to neurons -- Sect. 2. Design, synthesis of siRNAs. Degign and synthesis of small interfering RNA (siRNA) -- Automated design and high throughput chemical synthesis of siRNA -- Rational design of siRNAs with the Sfold software -- Enzymatic production of small interfering RNAs -- Sect. 3. Vector development and in vivo, in vitro and in ovo delivery methods. Six methods of inducing RNAi in mammalian cells -- Viral delivery of shRNA -- siRNA delivery by lentiviral vectors: design and applications -- Liposomal delivery of siRNAs in mice -- Sect. 5. Drug target validation. Delivering siRNA in vivo for functional genomics and novel therapeutics -- The role of RNA interference in drug target validation: application to Hepatitis C -- RNAi in the drug discovery process -- RNA interference technology in the discovery and validation of druggable targets -- Sect. 6. Therapeutic and drug development. RNAi-mediated silencing of viral gene expression and replication -- RNAi in drug development: practical considerations -- RNA interference studies in liver failure -- RNAi applications in living animal systems -- Sect. 7. High-throughput genome-wide RNAi analysis. High-throughput RNAi by soaking in Caenorhabtis elegans -- Tools for integrative genomics: genome-wide RNAi and expression profiling in Drosophila -- Microarray analysis and RNA silencing to determine genes functionally important in mesothelioma -- High-throughput RNA interference -- Generation of highly specific vector-based shRNAi libraries directed against the entire human genome.
- 2014 Springer Protocolsedited by M. Lucrecia Alvarez, Mahtab Nourbakhsh.Part I Structural RNA mapping -- Full-length characterization of transcribed genomic region -- Rapid mapping of RNA 3 and 5 ends -- Single nucleotide mapping of RNA 5 and 3 ends -- Analysis of RNA secondary structure -- Tertiary structure mapping of the Pri-miRNA miR-17-92 -- In situ hybridization detection of miRNA using LNA [trademark] oligonucleotides -- Quantification of miRNAs by a simple and specific qPCR method -- RNA isolation for small RNA next-generation sequencing from acellular biofluids -- Sequencing small RNA : introduction and data analysis fundamentals -- Measuring expression levels of small regulatory RNA molecules from body fluids and formalin-fixed, paraffin-embedded samples -- MicroRNA profiling in plasma or serum using quantitative RT-PCR -- MicroRNA profiling of exosomes isolated from biofluids and conditioned media -- Isolation of urinary exosomes for RNA biomarker discovery using a simple, fast, and highly scalable method -- Part II Functional RNA mapping -- Identification of actively translated mRNAs -- Mapping of internal ribosome entry sites (IRES) -- Mapping of protein binding RNA elements -- Purification of RNA-binding proteins -- De novo approach to classify protein-coding and noncoding transcripts based on sequence composition -- Computational methods to predict long noncoding RNA functions based on co-expression network -- MicroRNA biogenesis : dicing assay -- Faster experimental validation of microRNA targets using cold fusion cloning and a dual firefly-Renilla luciferase reporter assay -- Experimental validation of predicted mammalian microRNAs of mirtron origin -- A guide for miRNA target prediction and analysis using web-based applications -- Tapping microRNA regulation networks through integrated analysis of microRNA-mRNA high-throughput profiles -- miRWalk database for miRNA-target interactions -- A schematic workflow for collecting information about the interaction between copy number variants and microRNAs using existing resources -- SYBR green and TaqMan quantitative PCR arrays : expression profile of genes relevant to a pathway or a disease state -- Comprehensive meta-analysis of microRNA expression using a robust rank aggregation approach.
- 2010 ScienceDirectRobert E. Farrell Jr.RNA and the cellular biochemistry revisited -- RNA isolation strategies -- The truth about tissues -- Going green : RNA and the molecular biology of plants -- Isolation of polyadenylated RNA -- Quality control for RNA preparations -- Resilient ribonucleases -- Stringency : conditions that influence nucleic acid structure -- Electrophoresis of RNA -- Photodocumentation and image analysis -- Northern analysis -- Nucleic acid probe technology -- Practical nucleic acid hybridization -- Principles of detection -- Quantifications of specific mRNAs by nuclease protection -- Analysis of nuclear RNA -- cDNA synthesis -- RT-PCR : a science and an art form -- Quantitative PCR techniques -- Functional genomics and transcript profiling -- High-throughput analysis of gene expression -- Non-array methods for global analysis of gene expression -- RNAi : take a RISC-role the dicer -- Genomes, transcriptomes, proteomes, and bioinformatics -- An RNA paradigm.
- 2007 ScienceDirectedited by Jonatha M. Gott.
- 2015 ScienceDirectedited by Chuan He.Methodology for the high-throughput identification and characterization of tRNA variants that are substrates for a tRNA decay pathway -- Nucleoside analysis by hydrophilic interaction liquid chromatography coupled with mass spectrometry -- A platform for discovery and quantification of modified ribonucleosides in RNA: application to stress-induced reprogramming of tRNA modifications -- Recogniion of specified RNA modifications by the innate immune system -- Kinetic analysis of tRNA methyltransferases -- Preparation of human nuclear RNA m6A methyltransferases and demethylases and biochemical characterization of their catalytic activity -- Transcriptome-wide mapping of N6-methyladenosine by m6A-Seq -- Probing RNA modification status at single-nucleotide resolution in total RNA -- High-resolution mapping of N6-methyladenosine in transcriptome and genome using a photo-crosslinking-assisted strategy -- Pseudouridine in mRNA: incorporation, detection, and recoding -- Pseudo-Seq: genome-wide detection of pseudouridine modifications in RNA -- Pseudouridine chemical labeling and profiling -- Experimental approaches for target profiling of RNA cytosine methyltranferases -- RNA 5-methylcytosine analysis by bisulfite sequencing -- Biochemical and transcriptome-wide identification of A-to-I RNA editing sites by ICE-Seq -- Radical SAM-mediated methylation of ribosomal RNA.
- pt. C-D, 2003. ScienceDirectpt. D ScienceDirectedited by Sankar Adhya, Susan Garges.Also available: Print – pt. C-D, 2003.
- 2015 Springer Protocolsedited by Frank J. Schmidt.Identifying RNA recombination events and non-covalent RNA-RNA interactions with the molecular colony technique / Helena V. Chetverina and Alexander B. Chetverin -- RNA-directed recombination of RNA in vitro / Niles Lehman, Nilesh Vaidya, and Jessica A.M. Yeates -- RNA-RNA SELEX / B. Cho -- Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system / Kazuo Harada -- Transactivation of large ribozymes / Matthew B. Martin, Thomas L. Leeper, and Frank J. Schmidt -- Native purification and labeling of RNA for single molecule fluorescence studies / Arlie J. Rinaldi, Krishna C. Suddala, and Nils G. Walter -- Single molecule studies of RNA-RNA interactions / Dongmei Yu, Peiwu Qin, and Peter V. Cornish -- Modification interference analysis of the ribosome / Simpson Joseph -- Assessing intermolecular RNA:RNA interactions within a ribonucleoprotein complex using heavy metal cleavage mapping / Keith T. Gagnon and E. Stuart Maxwell -- Electrophoretic mobility shift assays : analysis of tRNA binding to the T box riboswitch antiterminator RNA / R. Anupam, S. Zhou, and J.V. Hines -- Fluorescence anisotropy : analysis of tRNA binding to the T box riboswitch antiterminator RNA / S. Zhou, R. Anupam, and J.V. Hines -- Electrophoretic mobility shift assay of RNA-RNA complexes / Geunu Bak [and three others] -- Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering / Angela Criswell and Blaine H.M. Mooers -- Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing / Blaine H.M. Mooers.
- 2010 SpringerVolker A. Erdmann, Jan Barciszewski, editors.The key features of RNA silencing / Kuniaki Saito ... [et al.] -- Selected strategies for the delivery of siRNA in vitro and in vivo / Sandra D. Laufer ... [et al.] -- RNAi suppression and its application / Xiaoping Yi, Rui Lu -- Strategies to prevent siRNA-triggered cellular toxicity / Matthias Bauer -- RNAi in malignant brain tumors: relevance to molecular and translational research / Mitsutoshi Nakada ... [et al.] -- Silencing Huntington's disease gene with RNAi / Yu Zhang, Robert M. Friedlander -- Application of Dicer-substrate siRNA in pain research / Philippe Sarret ... [et al.] -- RNAi treatment of HIV-1 infection / Karin J. von Eije, Ben Berkhout -- Application of RNA interference to treat conditions associated with dysregulation of transient receptor potential vanilloid 1 channel / Vickram Ramkumar ... [et al.] -- Harnessing RNAi-based functional genomics to unravel the molecular complexity underlying skin pigment variation / Hsiang Ho ... [et al.] -- mRNA structure and its effects on posttranscriptional gene silencing / Stephen I. Rudnick, Veenu Aishwarya, Alan M. Gewirtz -- Antisense RNA-mediated regulation of the p53 tumor suppressor / Marianne Farnebo, Klas G. Wiman -- Antisense oligonucleotides: insights from preclinical studies and clinical trials / Doreen Kunze, Kai Kraemer, Susanne Fuessel -- What can the new hammerhead ribozyme structures teach us about design? / William G. Scott -- microRNA biogenesis and its impact on RNA interference / Stefanie Grund, Sven Diederichs -- MicroRNAs in epithelial antimicrobial immunity / Jun Liu ... [et al.] -- Emerging roles of long noncoding RNAs in gene expression and intracellular organization / Tetsuro Hirose -- Noncoding RNAs as therapeutic targets / Maciej Szymański, Jan Barciszewski -- Noncoding RNAs at H19/IGF2 locus: role in imprinting, gene expression, and associated pathologies / Nahalie Berteaux, Nathalie Spruyt, Eric Adriaenssens.
- 2008 ScienceDirectedited by Lynne E. Maquat, Cecilia M. Arraiano.Also available: Print – 2008
- 2008 ScienceDirectedited by Lynne E. Maquat, Megerditch Kiledjian.Also available: Print – 2008
- 2008 Springer Protocolsedited by Sailen Barik.
- 2011 Springer Protocolsedited by Hiroaki Kodama, Atsushi Komamine.Overview of plant RNAi / Yuichiro Watanabe -- Caveat of RNAi in plants : the off-target effect / Muthappa Senthil-Kumar and Kirankumar S. Mysore -- Plant gateway vectors for RNAi as a tool for functional genomic studies / Toshiya Muranaka -- Heat-inducible RNAi for gene functional analysis in plants / Frederic Masclaux and Jean-Philippe Galaud -- Gene function analysis by artificial microRNAs in Physcomitrella patens / Basel Khraiwesh [and others] -- Virus-induced gene silencing in ornamental plants / Cai-Zhong Jiang, Jen-Chih Chen, and Michael Reid -- Local RNA silencing mediated by agroinfiltration / Jutta Maria Helm, Elena Dadami, and Kriton Kalantidis -- Direct transfer of synthetic double-stranded RNA into protoplasts of Arabidopsis thaliana / Ha-il Jung, Zhiyang Zhai, and Olena K. Vatamaniuk -- Detection of long and short double-stranded RNAs / Toshiyuki Fukuhara [and others] -- Quantitative stem-loop RT-PCR for detection of microRNAs / Erika Varkonyi-Gasic and Roger P. Hellens -- Large-scale sequencing of plant small RNAs / William P. Donovan, Yuanji Zhang, and Miya D. Howell -- Computational prediction of plant miRNA targets / Ying-Hsuan Sun [and others] -- Bisulfite sequencing for cytosine-methylation analysis in plants / Nazmul Haque and Masamichi Nishiguchi -- Using nuclear run-on transcription assays in RNAi studies / Basel Khraiwesh -- Proteomic analysis of RNA interference induced knockdown plant / Sang Yeol Lee and Kyun Oh Lee -- Comparative analysis of phosphoprotein expression using 2D-DIGE / Tomoya Asano and Takumi Nishiuchi.
- 2011 CRCnetBASEeditors, R.K. Gaur, Yedidya Gafni, P. Sharma, V.K. Gupta."RNA interference (RNAi) is a system within living cells that helps to control active genes and their activity level. Two types of small RNA molecules--microRNA (miRNA) and small interfering RNA (siRNA)--are central to RNA interference. The discovery of RNAi was preceded first by observations of transcriptional inhibition by antisense RNA expressed in transgenic plants and more directly by reports of unexpected outcomes in experiments performed by plant scientists in the U.S. and The Netherlands in the early 1990s. RNAi technology are used for large-scale screens that systematically shut down each gene in the cell, which can help identify the components necessary for a particular cellular process or an event such as cell division. Exploitation of the pathway is also a promising tool in biotechnology and medicine. This book reviews the selective and robust effect of RNAi on gene expression which makes it a valuable research tool, both in cell culture and in living organisms because synthetic dsRNA introduced into cells can induce suppression of specific genes of interest. This book will introduce new technology in the study of RNA interference in microorganisms, plants and animals."--Provided by publisher.
- 2013Di Wu.First, we take a look at the function of a specific type of RNA editing mediated by ADAR (adenosine deaminase that acts on RNAs). We test our hypotheses on ADAR activity and target specificity through transcriptome analysis in the context of exogenous RNAi response pathway in C. elegans. By examining of small RNA and mRNA populations in adar mutants and additional RNAi defective mutants, we show that the activity and specificity of the ADAR enzyme likely precludes the detection of its targets through conventional methods of sequence capture and analysis. Based on this understanding, we develop novel computational approaches for analysis of small RNA and mRNA populations and identify a broader set of ADAR targets, leading to a deeper understanding of the ADAR pathway, the conserved functionalities of the ADAR enzyme, and its relationship with the exogenous RNAi pathway in C. elegans. Second, we examine the dynamics of the transcriptome upon and after exposure to extreme heat. We hypothesize that the recovery response after removal from heat exposure might involve alternations in transcription regulation that are more complex than a reversal of the heat-shock induced effects, and that one such form of long-term regulation might involve the endogenous RNAi pathway and regulation via synthesis of endogenous siRNAs. By examining the dynamics of the C. elegans transcriptome during time-course of heat exposure and recovery, we reach a deeper understanding of heat shock biology and explore the relationship between endogenous siRNAs and their sequence complementary mRNA targets in the context of environmentally induced perturbance.
- 2012Peggie Cheung.Epigenetics is the study of heritable changes in gene expression that occur independent of changes in the primary DNA sequence. Chromatin structure defines the state in which genetic information is organized in the cell. The organization of this structure greatly influences the abilities of genes to be activated or silenced. In eukaryotic cells, 146 base pairs of DNA is wrapped around the histone octamer (two H2A/H2B dimers and one H3/H4 tetramer) forming the nucleosomes, the basic unit of chromatin. The nucleosome cores are connected by linker DNA sequences to further package into higher-order chromatin structures. In addition to the core histones, each histone contains an unstructured N-terminal tail. The histone tails are the sites of most of the post-translational modifications (PTMs), such as acetylation, methylation and phosphorylation. These modifications regulate the structure and function of chromatin through two general mechanisms. In the first model, histone modifications may play a direct role in altering chromatin structure. For example, histone acetylation neutralizes the positive charge of lysine residues and thus, affecting the interactions of the histones with DNA, transcription factors and other nucleosomes. Secondly, histone modifications can indirectly affect chromatin functions by serving as a binding platform for modular proteins and complexes. For instance, the methylation of histone H3 at lysine 9 is recognized specifically by the chromatin organization modifier (Chromo) domain of heterochromatin protein 1 (HP1), which contributes to the induction and the propagation of heterochromatin structure. Ten years ago, Strahl and Allis proposed a general idea of "histone code" hypothesis, which states that histone modifications, distinct or in combination, to form a "code" to influence chromatin structure and lead to varied transcriptional outputs. In recent years, many chromatin regulators were identified, such as the proteins that "write" or "erase" or "read" the modifications. Some chromatin regulators are expressed in a tissue-specific manner and play important roles in physiology and disease pathogenesis. For instance, the H3K27 histone methyltransferase EZH2 is overexpressed in tumors such as prostate, breast, colon, skin and lung cancer. Disruption of normal patterns of covalent histone modifications is another hallmark of cancer. One of the most characterized examples is the global reduction of the trimethylation of H4K20 and acetylation of H4K16, along with hypomethylation, at repeat sequences in many tumors. Since post-translational modifications have been shown to be important for many biological processes such as gene expression, DNA damage and repair and apoptosis, disruption of these processes has been linked to carcinogenesis and other disease pathogenesis. The discovery of reversible mutations in the epigenetic machinery makes post-translational modifications as one of the most promising and expanding fields in the current biomedical research. Methylation does not neutralize the charge of the modified residue nor does addition of methyl groups add considerable bulk, this mark is believed to create a distinct molecular architecture on histones that is recognized by specialized binding domains present within chromatin-regulatory proteins. The proteins and domains that recognize histone modifications, named "effectors" or "readers", are thought to define the functional consequences of lysine methylation by transducing molecular events at chromatin into biological outcomes. Mutations in these "readers" proteins have been shown to link to many disease pathogenesis. However, relatively few effector domains have been identified in comparison to the number of modifications present on histones and non-histone proteins. Here we developed a human epigenome peptide microarray platform (HEMP) for high-throughput discovery of chromatin effectors. We probed this platform with modification-specific antibodies and known chromatin effector domains to test the integrity of the peptides on the slides. We also screened a library of Royal Domain family members and identified three effector proteins with novel modified-histone binding activity. Hence, the development of the HEMP facilitates the identification of effector proteins and understanding of chromatin signaling networks. Multiple Myeloma (MM) is a malignancy of bone marrow plasma cells that frequently results in bone marrow destruction, bone marrow failure and death. 15% of patients with multiple myeloma is diagnosed with an immunoglobin gene, t(4; 14), translocation. MM patients carrying the t(4; 14) translocation is associated with the overexpression of WHSC1/MMSET/NSD2. NSD2 is a protein lysine methylatransferase in the nuclear receptor binding SET domain protein family. However, the molecular mechanism by which NSD2 contributes to myeloma pathogenesis is not known. Here we show that the dimethylation of histone H3 at lysine 36 (H3K36) is the principal physiological activity of NSD2. In mammalian cells, H3K36me2 normally maps to gene bodies. In t(4; 14)+ myeloma cells, overexpression of NSD2 disrupts the physiologic genomic organization of H3K36me2 which is found being dispersed throughout the genome. NSD2 expression is linked to transcription activation and H3K36me2 location at gene bodies positively correlates with transcription levels. In Myeloma cells, NSD2-mediated localized elevation of H3K36me2 induces transcription at normally inert cancer-associated genes. Catalytic activity of NSD2 confers tumor formation in xenograft model and promotes oncogenic transformation of primary cells by regulating transcriptional programs that favor oncogenesis. The BAH domain is an evolutionarily conserved chromatin-associated motif. Utilizing the HEMP, we screened several BAH domains from yeast and human for binding activity. We found that the BAH domain of human ORC1 specifically bind to H4K20me2 peptides. Structural studies show that BAH domain has an aromatic dimethyl-lysine-binding cage that interacts with the bound peptide. ORC1 is dispensable for ORC complex assembly but is necessary for loading of the complex into chromatin. The ability of ORC1 BAH domain binding to H4K20me2 is required for the efficient stabilization of ORC complex at chromatin. H4K20me2 is enriched at replication origins. Abrogation in ORC1 and H4K20me2 interactions impairs cell-cycle progression. Mutations in ORC1 BAH domain have been implicated in aetiology of Meier-Gorlin syndrome (MGS), a form of primordial dwarfism. In a zebrafish model, orc1 morphants display an MGS-like dwarfism phenotype, which can be rescued by wild type Orc1 but not ORC1 binding mutants. Zebrafish depleted with H4K20me2 also displays the MGS-like phenotype. Together, our findings reveal a new function for histone methylation signaling at chromatin in the regulation of DNA replication and organismal growth. KDM2A is the first jumonjiC domain-containing demethylase identified. We solved the co-crystal structure of KDM2A and its substrate, H3K36me2. We found that KDM2A demethylation activity is required to maintain genomic stability. We also show that KDM2A is a tumor suppressor and its demethylation activity is required for suppressing cellular transformation.
- 2011 SpringerAntonio Costa de Oliveira, Rajeev K. Varshney, editors.With the predicted increase of the human population and the subsequent need for larger food supplies, root health in crop plants could play a major role in providing sustainable highly productive crops that can cope with global climate changes. While the essentiality of roots and their relation to plant performance is broadly recognized, less is known about their role in plant growth and development. "Root Genomics" examines how various new genomic technologies are rapidly being applied to the study of roots, including high-throughput sequencing and genotyping, Tilling, transcription.
- Scales of diversity in thermophilic microbial communities : from metagenomes to individual cells and viral metagenomes2013Michelle René Davison.Microbial diversity can be queried at several scales within natural environments. On a macroscopic scale, microbial communities are capable of incredible feats: from colonizing the most inhospitable habitats imaginable, to creating ancient stromatolites, or living in intimate symbioses with the human body, inside and out. These complex microbial assemblages are comprised of different microscopic populations, which interact as a whole to stabilize the community ecosystem: selective evolutionary pressures work to shape each population, exquisitely adapting it to succeed in the current environmental conditions. In turn, these populations are comprised of millions of individual cells, each struggling to survive a variety of environmental stressors, to outcompete their closely-related neighbours, and carve out a distinct niche. Single cells wage constant war against predators such as viruses, which exist in large numbers and can effect entire populations, and ultimately the community as a whole. With such a range of complexity within a microbial community, it is essential to view microbial diversity through several tiers, in order to achieve a more complete picture. Only when diversity is viewed from several hierarchical levels, can the connections be made between the biology that is occurring on very fine scales and its effect on the entire system. Thus, this thesis has characterized microbial diversity in the hot spring microbial mats of Yellowstone National Park at multiple scales. There are several reasons why the microbial mats represent the ideal model system in which to query microbial diversity (Chapter 1). The evolution and adaptation of thermophilic Synechococcus sp. across a temperature gradient is queried by the creation of a targeted deep sequencing dataset, revealing statistically significant SNPs that correlate with thermal adaptation (Chapter 2). A second targeted deep sequencing dataset of 90 loci was generated to investigate the microdiversity present between two closely related thermophilic Synechococcus species, confirming the presence of micro-niches in stabilizing diversity across several years (Chapter 3). Successful gene amplification of the T1B CRISPR loci from a single cyanobacterial cell was achieved with the goal of investigating diversity at the single cell level (Chapter 4). Lastly, host-virus co-evolution is characterized by creation of a virome and a novel pipeline to assemble and analyze viral sequences: matching potential host-viral pairs by using CRISPR spacers (Chapter 5).
- 2015 SpringerE. Scott Sills, editor.The Development of PGD -- Elements of Informed Consent for Preimplantation Genetic Diagnosis -- Follicular Recruitment & Oocyte Recovery in Assisted Reproduction -- Biomarker-based Flow-Cytometric Semen Analysis for Male Infertility Diagnostics and Clinical Decision Making in ART -- Comparison of Methods for Assessment of Sperm DNA Damage (Fragmentation) and Implications for the Assisted Reproductive Technologies -- Tweaking ICSI for a PGD program -- Comprehensive Chromosomal Screening from Polar Body Biopsy to Blastocyst Trophectoderm Sampling: Evidence and Considerations -- Polar Body Diagnosis -- An Alternative and Addition to Preimplantation Diagnosis -- Efficiency of Polar Body Biopsy for Aneuploidy Screening by DNA Microarray for Single Embryo Transfer -- Prediction of Embryo Viability by Morphokinetic Evaluation to Facilitate Single Transfer -- Comparison of PCR Techniques for Embryo Screening and Single Embryo Transfer -- Array CGH and Partial Genome Sequencing for Rapidly Karyotyping IVF Blastocysts Before Transfer -- Single Embryo Transfers Enabled by aCGH -- Current and Future Methodologies -- SNP array, qPCR, and next-generation sequencing based comprehensive chromosome screening -- Expanding PGD Applications to Non-traditional Genetic and Non-Genetic Conditions -- Should molecular cytogenetic techniques be applied to facilitate single embryo transfer in egg donation cases? Assessment of frequency and distribution of embryo aneuploidy after anonymous donor oocyte IVF -- Selecting the Single Embryo for Transfer in Mitochondrial Disorders -- Single Embryo Transfer: The Significance of the Embryo Transfer Technique -- The Vitrification Component: An Integral Part of a Successful eSET Program -- A Review of Luteal Support Protocols for Single Embryo Transfers -- Fresh and Frozen -- Cost effectiveness of single embryo transfers relative to higher embryo transfer policies in clinical practice: A population based analysis -- The Quebec experience -- One plus one equals two at once: Presenting cumulative pregnancy rates as the ideal outcome in elective SET programs -- Single Embryo Transfer in a State-Sponsored IVF Context: Current Experience from Israel -- Single Embryo Transfer: the Quebec Experience -- Regulatory Aspects of Embryo Testing: An American View -- Regulatory Challenges in Assisted Reproduction: A European Perspective -- Preimplantation Genetic Screening: Ethics & Policy -- Crossing Rubicons: Assisted Reproductive Therapies and Remaining Human.
- 2013David Stuart Lawrie.During my graduate career, my research has focused on studying signals of purifying selection, using the tools of population genomics and molecular evolution to elucidate the underlying function of sites across the genome. In this thesis, I first focus on the theoretical implications of the interplay between weak constraint and mutational biases for divergence data between species. By explicitly incorporating the selective fitness of nucleotides into DNA substitution models, weak selection and mutational biases under this model can together have unexpected effects on the pattern of DNA sequence evolution over a phylogeny. In the next chapter, I investigate the selective forces acting on the synonymous sites of D. melanogaster, taking advantage of the high quality, deep population sequencing data available for that species. Within-species polymorphism data can allow for the detection of strong purifying selection using a combination of SNP density and allele frequency. Synonymous sites are generally assumed to be subject to weak selective constraint. However, contrary to this expectation, I demonstrate in Chapter 2 that a substantial proportion of synonymous sites in D. melanogaster are evolving under very strong selective constraint while few, if any are evolving under weak or moderate constraint. I conclude by examining the power and properties of using divergence and polymorphism to search for functional elements in a genome. There is a large potential gain in power from having deep samples of population variation in multiple related species, which, combined with divergence data, should allow for the estimation of selection coefficients on relatively few sites. Comparative population genomics, the analysis of large-scale population data within and between species, represents a powerful extension to current approaches using the evolutionary signatures of purifying selection to detect functional elements and ascertain their functional importance.
- 2012Alex Pollen.Understanding the genetic changes responsible for the evolution of human traits is a major goal of biology. One of the most distinctive human traits is the dramatic expansion of the forebrain that has occurred over the last six million years. Whole genome sequencing projects have identified millions of genomic differences that separate human and chimpanzee (Chimpanzee Sequencing and Analysis Consortium, 2005). However, connecting particular mutations to evolved human traits such as brain size remains challenging due to the vast number of mutations that have accumulated (Varki and Altheide 2005; Sikela, 2006). Nonetheless, recent evolutionary genetic studies are identifying the most prevalent types of genetic mechanisms contributing to evolved traits in natural populations, and studies of comparative and molecular development are providing an emerging picture for mechanisms by which human brain expansion could have occurred. By combining insights from evolutionary genetics and developmental neurobiology, this thesis aims to identify genomic differences that are particularly likely to have contributed to the evolutionary expansion of the human brain. First, this thesis provides evidence for the role of cis-regulatory mutations in the evolution of natural populations of stickleback fish. Next, this thesis describes a genomic screen we conducted identifying 510 deletions likely to remove cis-regulatory enhancers from the human genome. One of these deletions removes a developmental ventral forebrain enhancer near the tumor suppressor gene GADD45g, the loss of which may release a brake on cell division in particular regions of the brain during neurogenesis. A second deletion removes a developmental dorsolateral neocortex enhancer demonstrating the specificity by which evolution can affect particular regions of the brain. Finally, this thesis identifies a human enhancer near the gene BDNF that drives expression in the nail bed of the digit tips and the stomach, and could influence the distribution and function of mechanoreceptors.
- 2003. NLMby Eugene V. Koonin and Michael Y. Galperin.
- 2009 Springerby Kun-Mao Chao, Louxin Zhang.
- 2008 Springer Protocolsedited by Kåre Lehmann Nielsen.SAGE and LongSAGE / Annabeth Laursen Høgh and Kåre Lehmann Nielsen -- Robust-LongSAGE (RL-SAGE) : an improved LongSAGE method for high-throughput transcriptome analysis / Malali Gowda and Guo-Liang Wang -- aRNA LongSAGE : SAGE with antisense RNA / Anna M. Heidenblut -- SuperSAGE / Hideo Matsumura ... [et al.] -- Low-cost-medium throughput Sanger dideoxy sequencing / Kåre Lehmann Nielsen -- DeepSAGE : higher sensitivity and multiplexing of samples using a simpler experimental protocol / Kåre Lehmann Nielsen -- High-resolution, genome-wide mapping of chromatin modifications by GMAT / Tae-Young Roh and Keji Zhao -- 5'- and 3'-RACEfrom LongSAGE tags / Kåre Lehmann Nielsen -- Extraction and annotation of SAGE tags using sequence quality values / Jeppe Emmersen -- Correction of technology-related artifacts in serial analysis of gene expression / Viatcheslav R. Akmaev -- Duplicate ditag analysis in LongSAGE / Jeppe Emmersen -- Statistical comparison of two or more SAGE libraries : one tag at a time / Gerben J. Schaaf ... [et al.] -- Scaling of gene expression data allowing the comparison of different gene expression platforms / Fred van Ruissen ... [et al.] -- Clustering analysis of SAGE transcription profiles using a Poisson approach / Haiyan Huang, Li Cai, and Wing H. Wong -- Identifying nonspecific SAGE tags by context of gene expression / Xijin Ge and San Ming Wang.
- 2013Alfonso Pedro Farruggio.The "integrase" enzyme of the bacterial virus phiC31 mediates the unidirectional fusion of the phiC31 and host-bacterium genomes. This recombination reaction occurs between two specific DNA sequences (att-sites), and can be performed by the enzyme without accessory factors in a wide variety of cellular environments, including human cells. Although its primary application to date in eukaryotes has been in organisms where the native phiC31 integrase (C31-int) att-sites have been pre-introduced, C31-int can also function on certain endogenous sequences (pseudosites) in animal genomes, albeit with significantly reduced activity. The ability of C31-int to perform pseudosite integration has made it the focus of several whole-animal and tissue-culture gene-therapy studies over the past decade, as there is currently no means to safely maintain the therapeutic DNA that is delivered for gene-therapy. The focus of my graduate work has been to assist these efforts to apply C31-int for gene-therapy. Specifically, I have sought to increase our basic scientific understanding of DNA recognition by C31-int through deletion and chimera studies (Chapters 2-3), and I have also attempted to improve the implementation of C31-int applications in mammals through my contributions to applied C31-int projects (Chapters 4-6). The results from my deletion and chimera studies have helped to clarify that C31-int employs DNA binding domains that are largely modular and have also helped to lay the groundwork for a potential means to derive serine integrases with novel specificities. The results from my contributions to applied C31-int projects have made it possible to reverse the wild-type reaction in mammalian cells (Chapter 4), to produce high-quality mouse induced-pluripotent-stem cells (iPSC) with C31-int (Chapter 5), and to genetically engineer mouse iPSCs (Chapter 6). Although C31-int will still require significant engineering before it is suitable for use in human gene therapy, and although additional work will be required to fully realize the potential of our iPSC-production and -engineering scheme in human cells, my experience with C31-int and related enzymes that I describe in this dissertation has left me optimistic that these are not unreasonable goals.
- 2007 Springer Protocolsedited by Alan Thornhill.Noninvasive metabolic assessment of single cells / David K. Gardner -- Laser capture microdissection for analysis of single cells / Nobuki Nakamura ... [et al.] -- Fluorescence in situ hybridization (FISH) on single cells (sex determination and chromosome rearrangements) / Paul N. Scriven and Caroline Mackie Ogilvie -- Single cell PCR for PGD : methods, strategies, and limitations / Karen Sermon and Martine De Rycke -- Real-time quantitative PCR measurement of male fetal DNA in maternal plasma / Bernhard Zimmermann ... [et al.] -- Cell-free fetal DNA plasma extraction and real-time PCR quantification / Jill L. Maron, Kirby L. Johnson, and Diana W. Bianchi -- LATE-PCR and allied technologies : real-time detection strategies for rapid, reliable diagnosis from single cells / Kenneth E. Pierce and Lawrence J. Wangh -- Efficient isothermal amplification of the entire genome from single cells / Karen V. Schowalter, Jolene R. Fredrickson, and Alan R Thornhill -- Comparative genomic hybridization on single cells / Lucille Voullaire and Leeanda Wilton -- Generation of amplified RNAs and cDNA libraries from single mammalian cells / James Adjaye -- Real-time PCR to measure gene expression in single cells / Dagan Wells -- Gender determination and detection of aneuploidy in single cells using DNA array-based comparative genomic hybridization (array CGH) / Dong Gui Hui, Xin Yuan Guan, and Nicole Hussey -- Microarray technology for mutation analysis of low template DNA samples / Chelsea Salvado and David Cram.
- Single-molecule fluorescence and super-resolution imaging of Huntington's disease protein aggregates2012Whitney Clara Duim.Single-molecule, super-resolution fluorescence microscopy is a powerful technique for studying biological systems because it reveals details beyond the optical diffraction limit (on the 20-100 nm scale) such as structural and conformational heterogeneity. Further, single-molecule imaging measures distributions of behaviors directly through the interrogation of many individual molecules and reports on the nanoscale environment of molecules. Sub-diffraction imaging adds increased resolution to the advantages of fluorescence imaging over the techniques of atomic force microscopy and electron microscopy for studying biological structures, which include imaging of large fields of view in aqueous environments, specific identification of protein(s) of interest by fluorescent labeling, low perturbation of the system, and the ability to image living systems in near real-time (limited by the time required for super-resolution sequential imaging). This dissertation describes the application of single-molecule and super-resolution fluorescence imaging to studying the huntingtin (Htt) protein aggregates that are a hallmark of Huntington's disease and that have been implicated in the pathogenesis of the disease. The intricate nanostructures formed by fibrillar Htt aggregates in vitro and the sub-diffraction widths of individual fibers mark the amyloids as important targets for high-resolution optical imaging. The characterization of Htt aggregate species is critical for understanding the mechanism of Huntington's disease and identifying potential therapies. Following an introduction to single-molecule, super-resolution imaging and Huntington's disease in Chapter 1, Chapter 2 describes the single-molecule methods, experimental techniques, Htt protein sample preparations, and data analysis performed in this dissertation. Chapter 3 discusses the development of super-resolution imaging of Htt protein aggregates and the validation of the images by atomic force microscopy. Chapter 4 continues the study of Htt by one- and two-color super-resolution with imaging of Htt protein aggregates over time from the initial protein monomers to the large aggregate assemblies of amyloid fibers. In Chapter 5, I detail our progress to-date in studying the earliest stages of Htt aggregation using zero-mode waveguide technology. Chapter 6 concludes the dissertation with a discussion of the results from additional projects comprising the effect of chaperonin proteins on Htt aggregation, extension of super-resolution Htt imaging to three dimensions, and cellular imaging of Htt aggregates. The future directions for these exciting projects are summarized with the expectation that research efforts directed in these areas will contribute to our understanding of Htt aggregation and Huntington's disease.
- 2012Kirsten Linnea Frieda.RNA--a ubiquitous and versatile type of biopolymer that is critically involved in many of life's molecular processes--is produced sequentially in single-stranded form during transcription by RNA polymerase and has the propensity to fold back on itself into interesting structures of functional import. In nature, riboswitches are elegant examples of structured RNA that adopt alternate conformations in response to ligand binding and thereby affect gene expression. We have been able to probe riboswitch conformations in novel detail using single-molecule optical-trapping techniques. These experimental approaches supply a unique perspective on folding since the ability to apply force provides an effective handle on the real-time state of individual RNA molecules and a means of modulating that state. In this dissertation, I focus on three studies that explore adenine riboswitch conformations and mechanisms. Specifically, in the first, we dissect the folding landscape of the aptamer (ligand-binding domain) of an adenine riboswitch. Extending this endeavor to full riboswitch sequences, we probe the interplay of a riboswitch aptamer with its downstream expression platform (which executes the switch's regulatory role), and develop methods to do so both during and after transcription. The second study takes full advantage of the latter ability: In a complete adenine riboswitch controlling transcription, we directly observe cotranscriptional folding of the nascent RNA in which the adopted conformation dictates whether or not to terminate transcription. Finally, in a different adenine riboswitch controlling translation, we investigate switch conformational changes and identify a series of competing structural elements that kinetically trap the riboswitch conformation, implying that the initial, cotranscriptional fold of the riboswitch may determine its gene regulatory state. These efforts enhance our understanding of folding architectures in riboswitches, specifically, and in RNA, more broadly. They further highlight the importance of cotranscriptional folding, providing a novel window into the nascent development of RNA conformations.
- 2012 Springer Protocolsedited by James L. Keck.Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair / Aimee H. Marceau -- Structural diversity based on variability in quaternary association. a case study involving eubacterial and related SSBs / S.M. Arif and M. Vijayan -- SSB binding to ssDNA using isothermal titration calorimetry / Alexander G. Kozlov and Timothy M. Lohman -- SSB-DNA binding monitored by fluorescence intensity and anisotropy / Alexander G. Kozlov, Roberto Galletto, and Timothy M. Lohman -- Single-molecule analysis of SSB dynamics on single-stranded DNA / Ruobo Zhou and Taekjip Ha -- Sample preparation methods to analyze DNA-induced structural changes in replication protein A / Chris A. Brosey, Susan E. Tsutakawa, and Walter J. Chazin -- Structural studies of SSB interaction with RecO / Mikhail Ryzhikov and Sergey Korolev -- Investigation of protein-protein interactions of single-stranded DNA-binding proteins by analytical ultracentrifugation / Natalie Naue and Ute Curth -- Ammonium sulfate co-precipitation of SSB and interacting proteins / Aimee H. Marceau -- Analyzing Interactions Between SSB and proteins by the use of fluorescence anisotropy / Duo Lu -- Far western blotting as a rapid and efficient method for detecting interactions between DNA replication and DNA repair proteins / Brian W. Walsh, Justin S. Lenhart, Jeremy W. Schroeder, and Lyle A. Simmons -- Methods for analysis of SSB-protein interactions by SPR / Asher N. Page and Nicholas P. George -- Use of native gels to measure protein binding to SSB / Jin Inoue and Tsutomu Mikawa -- Identification of small molecules that disrupt SSB-protein interactions using a high-throughput screen / Douglas A. Bernstein -- Detection of posttranslational modifications of replication protein A / Cathy S. Hass, Ran Chen, and Marc S. Wold -- Detecting posttranslational modifications of bacterial SSB proteins / Dusica Vujaklija and Boris Macek -- Fluorescent SSB as a reagentless biosensor for single-stranded DNA / Katy Hedgethorne and Martin R. Webb -- Fluorescent single-stranded DNA-binding proteins enable in vitro and in vivo studies / Piero R. Bianco, Adam J. Stanenas, Juan Liu, and Christopher S. Cohan -- Use of fluorescently tagged SSB proteins in in vivo localization experiments / Rodrigo Reyes-Lamothe.
- 2016 Springer Protocolsedited by Kato Shum and John Rossi.Synthesis and conjugation of small interfering ribonucleic neutral SiRNNs / Alexander S. Hamil and Steven F. Dowdy - - Liver-targeted SiRNA delivery using biodegradable poly(amide) polymer conjugates / Stephanie E. Barrett and Erin N. Guidry -- PepFect6 mediated SiRNA delivery into organotypic cultures / Suvarna Dash-Wagh, Ülo Langel, and Mats Ulfendahl -- Highly efficient SiRNA delivery mediated by cationic helical polypeptides and polypeptide-based nanosystems / Lichen Yin, Nan Zheng, and Jianjun Cheng -- Disulfide-bridged cleavable PEGylation of poly- L -lysine for SiRNA delivery / Min Tang ... [et al.] -- Preparation of a cyclic RGD : modified liposomal SiRNA formulation for use in active targeting to tumor and tumor endothelial cells / Yu Sakurai, Tomoya Hada, and Hideyoshi Harashima -- Multifunctional envelope-type nano device containing a pH-sensitive cationic lipid for efficient delivery of short interfering RNA to hepatocytes in vivo / Yusuke Sato, Hideyoshi Harashima, and Michinori Kohara -- Bioreducible poly (beta-amino ester)s for intracellular delivery of SiRNA / Kristen L. Kozielski and Jordan J. Green -- Preparation of polyion complex micelles using block copolymers for SiRNA delivery / Hyun Jin Kim ... [et al.] -- Delivery of small interfering RNAs to cells via exosomes / Jessica Wahlgren ... [et al.] -- Dendrimer nanovectors for SiRNA delivery / Xiaoxuan Liu and Ling Peng -- Chitosan nanoparticles for SiRNA delivery in vitro / Héloïse Ragelle ... [et al.] -- Non-covalently functionalized of single-walled carbon nanotubes by DSPE-PEG-PEI for SiRNA delivery / King Sun Siu ... [et al.] -- SiRNA in vivo-targeted delivery to murine dendritic cells by oral administration of recombinant yeast / Kun Xu ... [et al.] -- TLR9-targeted SiRNA delivery in vivo / Dewan Md Sakib Hossain ... [et al.] -- Aptamer-MiRNA conjugates for cancer cell-targeted delivery / Carla L. Esposito, Silvia Catuogno, and Vittorio de Franciscis -- Method for confirming cytoplasmic delivery of RNA aptamers / David D. Dickey ... [et al.] -- Hapten-binding bispecific antibodies for the targeted delivery of SiRNA and SiRNA-containing nanoparticles / Irmgard S. Thorey ... [et al.] -- Stable delivery of CCR5-directed shRNA into human primary peripheral blood mononuclear cells and hematopoietic stem/progenitor cells via a lentiviral vector / Saki Shimizu, Swati Seth Yadav, and Dong Sung An -- Hepatic delivery of artificial micro RNAs using helper- dependent adenoviral vectors / Carol Crowther, Betty Mowa, and Patrick Arbuthnot -- Intravascular AAV9 administration for delivering RNA silencing constructs to the CNS and periphery / Brett D. Dufour and Jodi L. McBride -- Efficient gene suppression in dorsal root ganglia and spinal cord using adeno-associated virus vectors encoding short-hairpin RNA / Mitsuhiro Enomoto ... [et al.] -- Synthetic SiRNA delivery : progress and prospects / Thomas C. Roberts ... [et al.].
- 2012 Springer Protocolsedited by Debra J. Taxman.What parameters to consider and which software tools to use for target selection and molecular design of small interfering RNAs / Olga Matveeva -- Methods for selecting effective siRNA target sequences using a variety of statistical and analytical techniques / Shigeru Takasaki -- Designing functional siRNA with reduced off-target effects / Yuki Naito and Kumiko Ui-Tei -- Design and screening of siRNAs against highly structured RNA targets / Neda Nasheri, John Paul Pezacki, and Selena M. Sagan -- Engineering small interfering RNAs by strategic chemical modification / Jesper B. Bramsen and Jørgen Kjems -- Design, selection, and evaluation of highly specific and functional siRNA incorporating unlocked nucleobase analogs / Narendra Vaish and Pinky Agarwal -- Design, preparation and evaluation of asymmetric small interfering RNA for specific gene silencing in mammalian cells / Chanil Chang [and others] -- Design of nuclease-resistant fork-like small interfering RNA (fsiRNA) / Elena L. Chernolovskaya and Marina A. Zenkova -- Designing dual-targeting siRNA duplexes having two active strands that combine siRNA and MicroRNA-like targeting / Pal Sætrom -- Strategies for designing and Validating immunostimulatory siRNAs / Michael P. Gantier -- Designing efficient and specific endoribonuclease-prepared siRNAs / Vineeth Surendranath [and others] -- Short hairpin RNA-mediated gene silencing / Luke S. Lambeth and Craig A. Smith -- Design of lentivirally expressed siRNAs / Ying Poi Liu and Ben Berkhout -- Bifunctional short hairpin RNA (bi-shRNA) : design and pathway to clinical application / Donald D. Rao [and others] -- Design and chemical modification of synthetic short shRNAs as potent RNAi triggers / Anne Dallas and Brian H. Johnston -- Production and application of long dsRNA in mammalian cells / Katerina Chalupnikova, Jana Nejepinska, and Petr Svoboda -- Design of RNAi reagents for invertebrate model organisms and human disease vectors / Thomas Horn and Michael Boutros -- Construction of shRNA expression plasmids for silkworm cell lines using single-stranded DNA and Bst DNA polymerase / Hiromitsu Tanaka -- Designing effective amiRNA and multimeric amiRNA against plant viruses / Muhammad Fahim and Philip J. Larkin -- Downregulation of plant genes with miRNA-induced gene silencing / Felipe Fenselau de Felippes.
- 2016 SpringerRiekelt H. Houtkooper, editor.1. Biochemistry and enzymology of sirtuins -- 2. NAD as a pharmacological tool to boost sirtuin activity -- 3. Protein lysine acylation: abundance, dynamics and function -- 4. SIRT1 in metabolic health and disease -- 5. Deacetylation by SIRT3 relieves inhibition of mitochondrial protein function -- 6. SIRT5 reveals novel enzymatic activities of sirtuins -- 7. Diverse roles of SIRT6 in mammalian healthspan and logevity -- 8. Sirtuins in cancer, emerging role as modulators of metabolic reprogramming -- 9. Sirtuins as metabolic modulators of muscle plasticity -- 10. Sirtuins and aging -- 11. Sirtuins and the circadian clock: epigenetic and metabolic crosstalk -- 12. Sirtuin activation by small molecules -- 13. Sirtuins: a future perspective -- Index.
- 2013 Springer Protocolsedited by Matthew D. Hirschey.Introduction: sirtuins in aging and diseases / Leonard Guarente -- Sirtuins in yeast: phenotypes and tools / Scott Tsuchiyama [and four others] -- C. elegans sirtuins / Mohan Viswanathan and Heidi A. Tissenbaum -- Genetic and biochemical tools for investigating sirtuin function in Drosophila melanogaster / Jason G. Wood, Rachel Whitaker, and Stephen L. Helfand -- Generating mammalian sirtuin tools for protein-interaction analysis / Kathleen A. Hershberger [and three others] -- Mass spectrometry-based detection of protein acetylation / Yu Li [and three others] -- SILAC-based quantification of Sirt1-responsive lysine acetylome / Yue Chen, Gozde Colak, and Yingming Zhao -- Targeted quantitation of acetylated lysine peptides by selected reaction monitoring mass spectrometry / Matthew J. Rardin, Jason M. Held, and Bradford W. Gibson -- Identification of deacetylase substrates with the biotin switch approach / J. Will Thompson, Alex Robeson, and Joshua L. Andersen -- Assaying chromatin sirtuins / Lei Zhong [and four others] -- Measurement of sirtuin enzyme activity using a substrate-agnostic fluorometric nicotinamide assay / Basil P. Hubbard and David A. Sinclair -- Detecting sirtuin-catalyzed deacylation reactions using 32P-labeled NAD and thin-layer chromatography / Anita Zhu, Xiaoyang Su, and Hening Lin -- Chemical acetylation and deacetylation / Kristofer S. Fritz -- Accurate measurement of nicotinamide adenine dinucleotide (NAD+) with high-performance liquid chromatography / Jun Yoshino and Shin-ichiro Imai -- In vivo measurement of the acetylation state of sirtuin substrates as a proxy for sirtuin activity / John Dominy, Pere Puigserver, and Carles Cantó -- Oxygen flux analysis to understand the biological function of sirtuins / Dongning Wang [and three others] -- The emerging links between sirtuins and autophagy / In Hye Lee, Jeanho Yun, and Toren Finkel -- Methods to study the role of sirtuins in genome stability / Paloma Martínez-Redondo and Alejandro Vaquero -- Circadian measurements of sirtuin biology / Kathryn Moynihan Ramsey [and five others] -- Utilizing calorie restriction to evaluate the role of sirtuins in healthspan and lifespan of mice / Jessica Curtis and Rafael de Cabo.
- Size-expanded ribonucleic acids (xRNAs) : a novel component in siRNAs for investigating the steric restrictions of RISC in RNAi2012Armando Ricardo Hernández.This thesis project describes the synthesis and use of size-expanded ribonucleic acids (xRNAs) as unnatural components in small interfering RNAs (siRNAs), which serve as a novel set of steric probes for investigating and identifying size restrictions that exist in the active site of the RNA-induced silencing complex (RISC), a critical protein complex in the RNA interference (RNAi) mechanism. xRNAs are analogous to natural RNAs, in which they retain canonical Watson Crick base-pairing groups, except their nucleobases are expanded linearly by 2.4 Å via benzo-fusion. In this report, the synthesis of the entire set of four xRNA nucleosides and their photophysical properties are described. Two of the xRNA nucleosides (i.e. rxA and rxU) are then converted to their corresponding phosphoramidites for use in automated RNA synthesis to synthesize various sets of xRNA-substituted siRNA strands for biophysical and biological studies. RNAi activity studies in HeLa cells using a firefly/Renilla luciferase dual reporter assay showed that xRNA substitutions in the antisense strand displayed poor RNAi activity in the middle of the sequence (positions 7-14) but were generally well tolerated near the 5'- and 3'-ends. Most significantly, single xRNA substitutions at the 3'-end showed RNAi activity that was more potent than that of unmodified siRNAs. Thermal denaturation studies revealed small changes in melting temperature (+1.4 to --5.0 °C); xRNA substitutions in the middle were found to be more thermodynamically destabilizing whereas the ends were shown to be stabilizing. Serum stability studies showed that xRNA-containing siRNAs have longer half-lives in human serum than unmodified siRNAs. Finally, xRNA-substituted siRNA strands and duplexes showed interesting position-dependent fluorescent properties, while CD spectroscopy experiments revealed that xRNA-substituted siRNAs does not greatly distort the native A-form helical structure of the duplexes. Taken together, the data demonstrate the utility of xRNA nucleobases as size-expanded mechanistic probes for RNAi research.
- 2015 Springer Protocolsedited by Mathieu Rederstorff.Small non-coding RNAs : a quick look in the rearview mirror / Guillaume Clerget, Yoann Abel, and Mathieu Rederstorff -- Alcoholic precipitation of small non-coding RNAs / Guillaume Clerget, Valérie Bourguignon-Igel, and Mathieu Rederstorff -- Quantification and quality control of a small non-coding RNA preparation / Virginie Marchand and Christiane Branlant -- Impact of RNA isolation protocols on RNA detection by Northern blotting / Katrin Damm [and seven others] -- Improved Northern blot detection of small RNAs using EDC crosslinking and DNA/LNA probes / Katrin Damm [and seven others] -- Direct cloning of double-stranded RNAs / Manli Shen [and three others] -- Detection and labeling of small non-coding RNAs by splinted ligation / Gabrielle Bourgeois [and three others] -- Fluorescence in situ hybridization of small non-coding RNAs / Valentin Vautrot [and three others] -- RT-qPCR-based quantification of small non-coding RNAs / Fjoralba Zeka, Pieter Mestdagh, and Jo Vandesompele -- Stem-loop RT-PCR based quantification of small non-coding RNAs / Véronique Salone and Mathieu Rederstorff -- miR-RACE : an effective approach to accurately determine the sequence of computationally identified miRNAs / Chen Wang and Jinggui Fang -- Probing small non-coding RNAs structures / Jean-Vincent Philippe [and three others] -- cDNA library generation for the analysis of small RNAs by high-throughput sequencing / Jennifer Gebetsberger, Roger Fricker, and Norbert Polacek -- CLIP-Seq to discover transcriptome-wide imprinting of RNA binding proteins in living cells / Jérôme Saulière and Hervé Le Hir -- Microarray analysis of small non-coding RNAs / Michael Karbiener and Marcel Scheideler -- RML-RACE, PPM-RACE, and qRT-PCR : an integrated strategy to accurately validate miRNA target genes / Chen Wang and Jinggui Fang -- Dual luciferase gene reporter assays to study miRNA function / Thomas Clément, Véronique Salone, and Mathieu Rederstorff -- Gene expression knockdown by transfection of siRNAs into mammalian cells / Yoann Abel and Mathieu Rederstorff -- Efficient and selective knockdown of small non-coding RNAs / Xue-Hai Liang, Wen Shen, and Stanley T. Crooke -- Cell-SELEX : in vitro selection of synthetic small specific ligands / Helena Dickinson [and three others] -- Small non-coding RNAs and aptamers in diagnostics and therapeutics / Marissa Leonard, Yijuan Zhang, and Xiaoting Zhang.
- 2006 SpringerWolfgang Nellen, Christian Hammann (eds.).
- 2006 Springeredited by Peter Sutovsky.Nuclear remodeling and nuclear reprogramming for making transgenic pigs by nuclear transfer / Randall S. Prather -- Somatic cell nuclei in cloning : strangers traveling in a foreign land / Keith E. Latham, Shaorong Gao, and Zhiming Han -- Cloning cattle : the methods in the madness / Bjørn Oback and David N. Wells -- Centrosome inheritance after fertilization and nuclear transfer in mammals / Qing-Yuan Sun and Heide Schatten -- Developmental, behavioral, and physiological phenotype of cloned mice / Kellie L.K. Tamashiro ... [et al.] -- Nucleolar remodeling in nuclear transfer embryos / Jozef Laurincik and Poul Maddox-Hyttel -- Somatic cell nuclear transfer (SCNT) in mammals : the cytoplast and its reprogramming activities / Josef Fulka, Jr. and Helena Fulka -- Mitochondrial DNA inheritance after SCNT / Stefan Hiendleder -- Activation of fertilized and nuclear transfer eggs / Christopher Malcuit and Rafael A. Fissore.Also available: Print – 2006
- 2014 CRCnetBASEedited by Kasirajan Ayyanathan, PhD.This new volume on gene expression and epigenetics discusses environmental effects related to specific gene expression. The book also shows methods for bioinformatic analysis of the epigenome. The book is broken into two sections: the first looks at eukaryotic DNA methylation and the second addresses how to integrate genomic medicine into clinical practice. The book includes chapters on these topics: Gene expression in colon cancer tissue Epigenetics in human acute kidney injury Embryologically relevant candidate genes in MRKH patients DNA methylation in common skeletal disorders Causal relat.
- 2014 Springer Protocolsedited by Klemens J. Hertel.The pre-mRNA splicing reaction / Somsakul Pop Wongpalee and Shalini Sharma -- Diversity and evolution of spliceosomal systems / Scott William Roy and Manuel Irimia -- Mechanisms of spliceosomal assembly / Ni-ting Chiou and Kristen W. Lynch -- Alternative pre-mRNA splicing / Stacey D. Wagner and J. Andrew Berglund -- Regulation of alternative pre-mRNA splicing / Miguel B. Coelho and Christopher W.J. Smith -- Introduction to cotranscriptional RNA splicing / Evan C. Merkhofer, Peter Hu, and Tracy L. Johnson -- Chromatin and splicing / Nazmul Haque and Shalini Oberdoerffer -- Preparation of splicing competent nuclear extracts / Chiu-Ho T. Webb and Klemens J. Hertel -- Preparation of yeast whole cell splicing extract / Elizabeth A. Dunn and Stephen D. Rader -- Efficient splinted ligation of synthetic RNA using RNA ligase / Martha R. Stark and Stephen D. Rader -- In vitro assay of pre-mRNA splicing in mammalian nuclear extract / Maliheh Movassat, William F. Mueller, and Klemens J. Hertel -- Kinetic analysis of in vitro pre-mRNA splicing in HeLa nuclear extract / William F. Mueller and Klemens J. Hertel -- In vitro systems for coupling RNAP II transcription to splicing and polyadenylation / Eric G. Folco and Robin Reed -- Isolation and accumulation of spliceosomal assembly intermediates / Janine O. Ilagan and Melissa S. Jurica -- Complementation of U4 snRNA in S. cerevisiae splicing extracts for biochemical studies of snRNP assembly and function / Martha R. Stark and Stephen D. Rader -- Expression and purification of splicing proteins from mammalian cells / Eric Allemand and Michelle L. Hastings -- Single molecule approaches for studying spliceosome assembly and catalysis / Eric G. Anderson and Aaron A. Hoskins -- Cell-based splicing of minigenes / Sarah A. Smith and Kristen W. Lynch -- Quantifying the ratio of spliceosome components assembled on pre-mRNA / Noa Neufeld, Yehuda Brody, and Yaron Shav-Tal -- Antisense methods to modulate pre-mRNA splicing / Joonbae Seo, Eric W. Ottesen, and Ravindra N. Singh -- Using yeast genetics to study splicing mechanisms / Munshi Azad Hossain and Tracy L. Johnson -- Medium throughput analysis of alternative splicing by fluorescently labeled RT-PCR / Ryan Percifield, Daniel Murphy, and Peter Stoilov -- Chromatin immunoprecipitation approaches to determine co-transcriptional nature of splicing / Nicole I. Bieberstein, Korinna Straube, and Karla M. Neugebauer -- Computational approaches to mine publicly available databases / Rodger B. Voelker, William A. Cresko, and J. Andrew Berglund -- Approaches to link RNA secondary structures with splicing regulation / Mireya Plass and Eduardo Eyras -- Methods to study splicing from high-throughput RNA sequencing data / Gael P. Alamancos, Eneritz Agirre, and Eduardo Eyras -- Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq / Chengguo Yao, Lingjie Weng, and Yongsheng Shi -- Predicting alternative splicing / Yoseph Barash and Jorge Vaquero Garcia.
- 2015 Cold Spring Harbor Lab PressCold Spring Harbor Laboratory.Symposium participants -- Foreword -- Gene control. Imaging transcription: past, present and future / Robert A. Coleman, Zhe Liu, Xavier Darzacq, Robert Tijan, Robert H. Singer, and Timothée Lionnet -- Visualizing the HoxD gene cluster at the nanoscale level / Pierre J. Fabre, Alexander Benke, Suliana Manley, and Denis Duboule -- Transcriptional enhancers: bridging the genome and phenome / Bing Ren and Feng Yue -- Regulatory principles governing tissue specificity of developmental enhancers / Emma K. Farley, Katrina M. Olson, and Michael S. Levine -- The importance of controlling transcription elongation at coding and noncoding RNA loci / Benjamin S. Scruggs and Karen Adelman -- Chromatin domains and nuclear position. Regulatory domains and their mechanisms / Nezha S. Benabdallah and Wendy A. Bickmore -- Large-scale chromatin structure-function relationships during the cell cycle and development: insights from replication timing / Vishnu Dileep, Juan Carlos Rivera-Mulia, Jiao Sima, and David M. Gilbert -- Prenucleosomes and active chromatin / Mai T. Khuong, Jia Fei, Haruhiko Ishii, and James T. Kadonaga -- HIPMap: a high-throughput imaging method for mapping spatial gene positions / Sigal Schachar, Gianluca, Pegoraro, and Tom Misteli -- Genome organization and chromosome architecture / Giorgio Bernardi -- Genome stability. A system to study aneuploidy in vivo / Sarah J. Pfau and Angelika Amon -- Resolution of recombination intermediates: mechanisms and regulation / Stephen C. West, Miguel G. Blanco, Ying Wait Chan, Joao Matos, Shriparna Sarbajna, and Haley D.M. Wyatt -- 21st century genetics: mass spectrometry of yeast telomerase / Kah Wai Lin and Virginia A. Zakian -- From mutational mechanisms in single cells to mutational patterns in cancer genomes / Cheng-Zhong Zhang and David Pellman -- The evolution of tumors in mice and humans with germline p53 mutations / Arnold J. Levine, Chang S. Chan, Crissy Dudgeon, Anna Puzio-Kuter, and Pierre Hainaut -- Germ cells and early development. Mechanism and reconstitution in vitro of germ cell development in mammals / Kazuki Kurimoto and Mitinori Saitou -- Erase-maintain-establish: natural reprogramming of the mammalian epigenome / Milena Leseva, Barbara B. Knowles, Daniel M. Messerschmidt, and Davor Solter -- Regulation of reprogramming and cellular plasticity through histone exchange and histone variant incorporation / Xavier Gaume and Maria-Elena Torres-Padilla -- ZFP57 and the targeted maintenance of postfertilization genomic imprints / Nozomi Takahashi, Dionne Gray, Ruslan Strogantsev, Angela Noon, Celia Delahaye, William C. Skarnes, Peri H. Tate, and Anne C. Ferguson-Smith -- Embryonic stem cells and development. Biological networks governing the acquisition, maintenance and dissolution of pluripotency: insights from functional genomics approaches / Kevin Andrew Uy Gonzales and Huck-Hui Ng -- Monitoring dynamics of DNA methylation at single-cell resolution during development and disease / Yonatan Stelzer and Rudolf Jaenisch -- Perturbing chromatin structure to understand mechanisms of gene expression / Caroline R. Bartman and Gerd A. Blobel -- Mechanisms underlying the selection and function of macrophage-specific enhancers / Verena M. Link, David Gosselin, and Christopher K. Glass -- Metabolism and signaling. Clock-talk: interactions between central and peripheral circadian oscillators in mammals / Ueli Schibler, Ivana Gotic, Camille Saini, Pascal Gos, Thomas Curie, Yann Emmenegger, Flore Sinturel, Pauline Gosselin, Alan Gerber, Fabienne Fleury-Olela, Gianpaolo Rando, Maud Demarque, and Paul Franken -- Dissecting the rev-erba cistrome and the mechanisms controlling circadian transcription in liver / Bin Fang and Mitchell A. Lazar -- Modulating the genomic programming of adipocytes / Anne Loft, Søren Fisker Schmidt, and Susanne Mandrup -- Targeting transcriptional and epigenetic reprogramming in stromal cells in fibrosis and cancer / Nasun Hah, Mara H. Sherman, Ruth T. Yu, Michael Downes, and Ronald M. Evans -- Regulation of RORyt in inflammatory lymphoid cell differentiation / Wendy Huang and Dan R. Littman -- Evolution. How transcription networks evolve and produce biological novelty / Isabel Nocedal and Alexander D. Johnson -- The African turquoise killifish: a model for exploring vertebrate aging and diseases in the fast lane / Itamar Harel and Anne Brunet -- Transposable elements, polydactyl proteins, and the genesis of human-specific transcription networks / Didier Trono -- Dorcas Cummings lecture. Svante Pääbo -- Conversations at the symposium. Geneviève Almouzni -- Angelika Amon -- Julius Brennecke -- Emmanuelle Charpentier -- Job Dekker -- Titia de Lange -- Jennifer Doudna -- Denis Duboule -- Ron Evans -- Anne Ferguson-Smith -- Edith Heard -- David Kingsley -- Arnold Levine -- Susan Lindquist -- Dan Littman -- Richard Morimoto -- David Page -- Wolf Reik -- Bing Ren -- Ueli Schibler -- Davor Solter -- Alexander Tarakhovsky -- Joanna Wysocka -- Rick Young -- Author index -- Subject index.
- 2012 Springer Protocolsedited by Robert C. Elston, Jaya M. Satagopan, Shuying Sun.Genetic terminology / Robert C. Elston, Jaya M. Satagopan, and Shuying Sun -- Identification of genotype errors / Yin Y. Shugart and Ying Wang -- Detecting pedigree relationship errors / Lei Sun -- Identifying cryptic relationships / Lei Sun and Apostolos Dimitromanolakis -- Estimating allele frequencies / Indra Adrianto and Courtney Montgomery -- Testing departure from Hardy-Weinberg proportions / Jian Wang and Sanjay Shete -- Estimating disequilibrium coefficients / Maren Vens and Andreas Ziegler -- Detecting familial aggregation / Adam C. Naj, Yo Son Park, and Terri H. Beaty -- Estimating heritability from twin studies / Karin J.H. Verweij [and others] -- Estimating heritability from nuclear family and pedigree data / Murielle Bochud -- Correcting for ascertainment / Warren Ewens and Robert C. Elston -- Segregation analysis using the unified model / Xiangqing Sun -- Design considerations for genetic linkage and association studies / Jérémie Nsengimana and D. Timothy Bishop -- Model-based linkage analysis of a quantitative trait / Audrey H. Schnell and Xiangqing Sun -- Model-based linkage analysis of a binary trait / Rita M. Cantor -- Model-free linkage analysis of a quantitative trait / Nathan J. Morris and Catherine M. Stein -- Model-free linkage analysis of a binary trait / Wei Xu [and others] -- Single marker association analysis for unrelated samples / Gang Zheng [and others] -- Single-marker family-based association analysis conditional on parental information / Ren-Hua Chung and Eden R. Martin -- Single marker family-based association analysis not conditional on parental information / Junghyun Namkung -- Allowing for population stratification in association analysis / Huaizhen Qin and Xiaofeng Zhu -- Haplotype inference / Xin Li and Jing Li -- Multi-SNP haplotype analysis methods for association analysis / Daniel O. Stram and Venkatraman E. Seshan -- Detecting rare variants / Tao Feng and Xiaofeng Zhu -- Analysis of ethnic mixtures / Xiaofeng Zhu -- Identifying gene interaction networks / Gurkan Bebek -- Structural equation modeling / Catherine M. Stein, Nathan J. Morris, and Nora L. Nock -- Genotype calling for the Affymetrix platform / Arne Schillert and Andreas Ziegler -- Genotype calling for the Illumina platform / Yik Ying Teo -- Comparison of requirements and capabilities of major multipurpose software packages / Robert P. Igo Jr. and Audrey H. Schnell.
- 2013 Springer Protocolsedited by Andrei Y. Yakovlev, Lev Klebanov, Daniel Gaile.What statisticians should know about microarray gene expression technology / Stephen Welle -- Where statistics and molecular microarray experiments biology meet / Diana M. Kelmansky -- Multiple hypothesis testing : a methodological overview / Anthony Almudevar -- Gene selection with the [delta]-sequence method / Xing Qiu and Lev Klebanov -- Using of normalizations for gene expression analysis / Peter Bubeliny -- Constructing multivariate prognostic gene signatures with censored survival data / Derick R. Peterson -- Clustering of gene expression data via normal mixture models / G.J. McLachlan [and others] -- Network-based analysis of multivariate gene expression data / Wei Zhi [and others] -- Genomic outlier detection in high-throughput data analysis / Debashis Ghosh -- Impact of experimental noise and annotation imprecision on data quality in microarray experiments / Andreas Scherer, Manhong Dai, and Fan Meng -- Aggregation effect in microarray data analysis / Linlin Chen, Anthony Almudevar, and Lev Klebanov -- Test for normality of the gene expression data / Bobosharif Shokirov.
- 2007 SpringerDavid Siegmund, Benjamin Yakir.
- 2015 ProQuest Ebook CentralSheldon Krimsky.Employing a series of Socratic dialogues, this study of the use of stem cells in medicine and medical research examines the ethical and public policy issues that confront scientists, clinicians, and the public health community.
- 2011 Springer Protocolsedited by James A. Williams.Bacterial genome reengineering / Jindan Zhou and Kenneth E. Rudd -- Targeted chromosomal gene knockout using PCR fragments / Kenan C. Murphy -- Scarless chromosomal gene knockout methods / Bong Hyun Sung, Jun Hyoung Lee, and Sun Chang Kim -- Random chromosomal gene disruption in vivo using transposomes / Les M. Hoffman -- Genome engineering using targeted oligonucleotide libraries and functional selection / Elie J. Diner, Fernando Garza-Sanchez, and Christopher S. Hayes -- Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries / Alison K. Hottes and Saeed Tavazoie -- Optimization of synthetic operons using libraries of post-transcriptional regulatory elements / Daniel E. Agnew and Brian F. Pfleger -- Marker-free chromosomal expression of foreign and native genes in Escherichia coli / Chung-Jen Chiang [and others] -- Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli / Mohan Babu [and others] -- Assembling new Escherichia coli strains by transduction using phage P1 / Sean D. Moore -- Yeast bioinformatics and strain engineering resources / Audrey L. Atkin -- Delete and repeat : a comprehensive toolkit for sequential gene knockout in the budding yeast Saccharomyces cerevisiae / Johannes H. Hegemann and Sven Boris Heick -- Genome-wide transposon mutagenesis in Saccharomyces cerevisiae and Candida albicans / Tao Xu, Nike Bharucha, and Anuj Kumar -- Signature-tagged mutagenesis to characterize genes through competitive selection of bar-coded genome libraries / Julia Oh and Corey Nislow -- Global strain engineering by mutant transcription factors / Amanda M. Lanza and Hal S. Alper -- Genomic promoter replacement cassettes to alter gene expression in the yeast Saccharomyces cerevisiae / Andreas Kaufmann and Michael Knop -- Microbial genome analysis and comparisons : web-based protocols and resources / Medha Bhagwat and Arvind A. Bhagwat -- Plasmid artificial modification : a novel method for efficient DNA transfer into bacteria / Tohru Suzuki and Kazumasa Yasui -- Broad-host-range plasmid vectors for gene expression in bacteria / Rahmi Lale, Trygve Brautaset, and Svein Valla -- Simple method for Introducing marker-free deletions in the Bacillus subtilis genome / Takuya Morimoto [and others] -- Transposon-mediated random mutagenesis of Bacillus subtilis / Adam C. Wilson and Hendrik Szurmant -- Integrative food grade expression system for lactic acid bacteria / Grace L. Douglas, Yong Jun Goh, and Todd R. Klaenhammer -- Clostron-mediated engineering of Clostridium / Sarah A. Kuehne [and others] -- High-throughput transposon mutagenesis of Corynebacterium glutamicum / Nobuaki Suzuki, Masayuki Inui, and Hideaki Yukawa -- Mini-mu transposon mutagenesis of ethanologenic Zymomonas mobilis / Katherine M. Pappas -- Engineering thermoacidophilic archaea using linear DNA recombination / Yukari Maezato, Karl Dana, and Paul Blum -- Targeted gene disruption in koji mold Aspergillus oryzae / Jun-ichi Maruyama and Katsuhiko Kitamoto -- Selectable and inheritable gene silencing through RNA interference in the unicellular alga Chlamydomonas reinhardtii / Karin van Dijk and Nandita Sarkar.
- 2016 Wileyedited by Frans J. de Bruijn.
- 2013 SpringerDavid Mittelman, editor.1. Stress-induced mutagenesis in bacteria / Ivan Matic -- 2. Mutagenesis associated with repair of DNA double-strand breaks under stress / Chandan Shee, P.J. Hastings, and Suman M. Rosenberg -- 3. Transcription-mediated mutagenic processes / Eduardo Robleto, Holly A. Martin, Carmen Vallin, Mario Pedraza-Reyes and Ronald Yasbin -- 4. Transposon mutagenesis in disease, drug discovery, and bacterial evolution / Zhongge Zhang, Jing Wang, Maksim A. Shlykov, and Milton H. Saier, Jr. -- 5. Hsp90 as a capacitor of both genetic and epigenetic changes in the genome during cancer progression and evolution / Xiangyi Lu, Luan Wang, Vincent E. Sollars, Mark D. Garfinkel, and Douglas M. Ruden -- 6. Inheritance of stress-induced epigenetic changes mediated by the ATF-2 family of transcription factors / Ki-Hyeon Seong, Toshio Maekawa and Shunsuke Ishii -- 7. Microsatellite repeats: canaries in the coalmine / Nimrat Chatterjee, Beatriz A. Santillan and John H. Wilson -- 8. Genetic instability induced by hypoxic stress / Susan E. Scanlon and Peter M. Glazer -- 9. Radiation-induced delayed genome instability and hypermutation in mammalian cells / Christopher P. Allen, Akira Fujimori, Ryuichi Okayasu and Jac A. Nickoloff -- 10. Radiation-induced bystander effects and stress-induced mutagenesis / Carmel Mothersill and Colin Seymour -- 11. Stress induced mutagenesis, genetic diversification, and cell survival via anastais, the reversal of late stage apoptosis / Ho Lam Tang, Ho Man Tang and Denise J. Mitchell -- 12. The transgenerational effects of parental exposure to mutagens in mammals / Yuri E. Dubrova -- 13. Revisiting mutagenesis in the age of High-throughput sequencing / Subhajyoti De and R. Matthew Ward.
- 2007 SpringerU. Bastolla ... [et al.] (eds.).Modeling conformational flexibility and evolution of structure : RNA as an example / P. Schuster and P.F. Stadler -- Gene3D and understanding proteome evolution / J.G. Ranea ... [et al.] -- The evolution of the globins : we thought we understood it / A.M. Lesk -- The structurally constrained neutral model of protein evolution / U. Bastolla ... [et al.] -- Towards unifying protein evolution theory / N.V. Dokholyan and E.I. Shakhnovich -- A twenty-first century view of evolution : genome system architecture, repetitive DNA, and natural genetic engineering / J.A. Shapiro -- Genomic changes in bacteria : from free-living to endosymbiotic life / F.J. Silva ... [et al.] -- Molecular phylogenetics : mathematical framework and unsolved problems / X. Xia -- Phylogenetics and computational biology of multigene families / P. Liò, M. Brilli and R. Fani -- SeqinR 1.0-2 : a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis / D. Charif and J.R. Lobry -- Evolutionary genomics of gene expression / I.K. Jordan and L. Mariño-Ramírez -- From biophysics to evolutionary genetics : statistical aspects of gene regulation / M. Lässig -- Drift and selection in evolving interacting systems / T. Ohta -- Adaptation in simple and complex fitness landscapes / K. Jain and J. Krug -- Genetic variability in RNA viruses : consequences in epidemiology and in the development of new strategies for the extinction of infectivity / E. Lázaro.
- 2014 Springer Protocolsedited by Yu Wai Chen.1. DisMeta : a meta server for construct design and optimization / Yuanpeng Janet Huang, Thomas B. Acton, and Gaetano T. Montelione -- 2. Stable expression clones and auto-induction for protein production in E. coli / F. William Studier -- 3. High-throughput expression screening and purification of recombinant proteins in E. coli / Natalie J. Saez and Renaud Vincentelli -- 4. Medium-throughput production of recombinant human proteins : ligation-independent cloning / Claire Strain-Damerell, Pravin Mahajam, Opher Gileadi and Nicola A. Burgess-Brown -- 5. Medium-throughput production of recombinant human proteins : protein production in E. coli / Nicola A. Burgess-Brown, Pravin Mahajan, Claire Strain-Damerell, Opher Gileadi and Susanne Gräslund -- 6. Medium-throughput production of recombinant human proteins : protein production in insect cells / Pravin Mahajan , Claire Strain-Damerell, Opher Gileadi and Nicola A. Burgess-Brown -- 7. OmniBac : universal multigene transfer plasmids for baculovirus expression vectors systems / Deepak B. Thimiri Govinda Raj, Lakshmi S. Vijayachandran, and Imre Berger -- 8. Multiprotein complex production in insect cells by using polyproteins / Yan Nie, Itxaso Bellon-Echeverria, Simon Trowitzch, Christoph Bieniossek and Imre Berger -- 9. Expression screening in mammalian suspension cells / Susan D. Chapple and Michael R. Dyson -- 10. Cell-free expression of protein complexes for structural biology / Takaho Terada, Takehi Murata, Mikako Shirouzu and Shigeyuki Yokoyama -- 11. Cell-free protein synthesis for functional and structural studies / Shin-ichi Makino, Emily T. Beebe, John L. Markley and Brian G. Fox -- 13. Insoluble protein purification with sarkosyl : facts and precautions / Ben Chisnall, Courtney Johnson, Yavuz Kulaberoglu and Yu Wai Chen -- 13. Estimation of crystallization likelihood through a fluorimetric thermal stability assay / Vincent Mariaule, Florine Dupeux, and José A. Márquez -- 14. CrystalDirect : a novel approach for automated crystal harvesting based on photoablation of thin films / José A. Márquez and Florent Cipriani -- 15. Methods to refine macromolecular structures in cases of severe diffraction anisotropy / Michael R. Sawaya -- 16. Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination / Yunhuang Yang, Theresa A. Ramelot, Shuisong Ni, Robert M. McCarrick and Michael A. Kennedy -- 17. Cost-effective protocol for the parallel production of libraries of 13CH3-specifically labeled mutants for NMR studies of high molecular weight proteins / Elodie Crublet, Rime Kerfah, Guillaume Mas, Marjolaine Noirclerc-Savoye, Violaine Lantez, Thierry Vernet and Jerome Boisbouvier -- 18. High-throughput SAXS for the characterization of biomolecules in solution : a practical approach / Kevin N. Dyer, Michael Hammel, Robert P. Rambo, Susan E. Tsutakawa, Ivan Rodic, Scott Classen, John A. Tainer and Greg L. Hura -- 19. Measuring spatial restraints on native protein complexes using isotope-tagged chemical cross-linking and mass spectrometry / Franz Herzog -- 20. Modeling of proteins and their assemblies with the integrative modeling platform / Benjamin Webb, Keren Lasker, Javier Velázquez-Muriel, Dina Schneidman-Duhovny, Riccardo Pellarin, Massimiliano Bonomi, Charles Greenberg, Barak Raveh, Elina Tjioe, Daniel Russel and Andrej Sali -- 21. Quality and validation of structures from structural genomics / Marcin J. Domagalski, Heping Zheng, Matthew D. Zimmerman, Zhigniew Dauter, Alexander Wlodawer and Wladek Minor -- 22. Navigating the global protein-protein interaction landscape using iRefWeb / Andrei L. Turinsky, Sabry Razick, Brian Turner, Ian M. Donaldson and Shoshana J. Wodak -- 23. Mespeus-a database of metal interactions with proteins / Marjorie M. Harding and Kun-Yi Hsin -- 24. High-quality macromolecular graphics on mobile devices : a quick starter's guide / Chin-Pang Benny Yiu and Yu Wai Chen.
- 2014 Springer Protocolsedited by Wayne F. Anderson.Data Management in the Modern Structural Biology and Biomedical Research Environment -- Structural Genomics of Human Proteins -- Target Selection for Structural Genomics of Infectious Diseases -- Selecting Targets from Eukaryotic Parasites for Structural Genomics and Drug Discovery -- High Throughput Cloning for Biophysical Applications -- Expression and Solubility Testing in a High Throughput Environment -- Protein Production for Structural Genomics Using E. coli Expression -- Eukaryotic Expression Systems for Structural Studies -- Automated Cell-free Protein Production Methods for Structural Studies -- Parallel Protein Purification -- Oxidative Refolding from Inclusion Bodies -- High throughput Crystallization Screening -- Screening Proteins for NMR Suitability -- Salvage or Recovery of Failed Targets by in situ Proteolysis -- Salvage of Failed Protein Targets by Reductive Alkylation -- Salvage or Recovery of Failed Targets by Mutagenesis to Reduce Surface Entropy -- Data Collection for Crystallographic Structure Determination -- Structure, Determination, Refinement, and Validation -- Virtual High-Throughput Ligand Screening -- Ligand Screening using Fluorescence Thermal Shift Analysis (FTS) -- Ligand Screening using Enzymatic Assays -- Ligand Screening using NMR -- Screening Ligands by X-ray Crystallography -- Case Study Structural Genomics and Human Protein Kinases.
- 2013Shanshan Tuo.This dissertation describes investigations of the machinery of cell polarization in the budding yeast Saccharomyces cerevisiae. Cell polarization is an essential feature of most, if not all, cell types. It occurs in two steps: (1) the selection of an axis and (2) the asymmetric organization of organelles, the cytoskeleton, and plasma-membrane components along this axis. The selection of an axis in S. cerevisiae is manifested as bud-site selection. S. cerevisiae cells select bud sites in either of two patterns, known as the axial and bipolar, depending on the mating type of the cells. Normal haploid cells use the axial pattern, whereas normal diploid cells use the bipolar pattern. Beginning with a re-analysis of the phenotypes of 38 mutants reported in a genome-wide screen to be defective in bipolar-bud-site selection, I focused on two groups of mutants with distinct phenotypes and tried to elucidate the molecular mechanisms underlying these phenotypes. The first group contains two mutants, bud13[Delta] and ist3[Delta]; the second group contains 14 endocytosis-related mutants. Each group has led to a separate story of how the corresponding proteins are involved in bipolar-bud-site selection. First, I found (Chapter 2) that Bud13 and Ist3 are responsible specifically for the efficient pre-mRNA splicing of MATa1, which encodes a cell-type-specific regulator for the expression of haploid-specific genes. One of these genes, AXL1, encodes a protein whose ectopic expression in diploid cells causes override of the bipolar-budding mechanism by the axial budding mechanism. Second, I found (Chapter 3) that endocytosis-related proteins are involved in maintaining the localization, and thus the function, of bipolar marker proteins including Bud8 and Bud9.
- 2011Kerri A. Spilker.Specification and assembly of synapses is a highly coordinated and regulated process. Knowledge of the position and connectivity of all C. elegans neurons makes it a highly useful organism for studying the underlying mechanisms that control synapse formation. Using cell-specific promoters and fluorescently-labeled synaptic vesicle proteins, we are able to monitor synapse formation in subsets of C. elegans neurons. Close observation of synapse formation in a single posterior motorneuron (DA9) led to the identification of a mutation in the alternative splicing regulator mbl-1 that changes the synaptic pattern. The cholinergic motorneuron DA9 is required for backwards locomotion and forms ~25 synapses onto both inhibitory neurons and body wall muscles in the dorsal nerve cord (DNC) of the worm. We found that the 10 most distal synapses of DA9 fail to form in mbl-1 mutants, visualized with the synaptic vesicle-associated protein RAB-3 and the active zone proteins SYD-2/liprin-[Alpha] and UNC-10/Rim. In addition, some RAB-3 mis-localizes to the dendrite of DA9 and animals have a backwards locomotion defect consistent with a loss of synapses onto dorsal body wall muscles. mbl-1 is a member of the conserved MBNL (Muscleblind like) family of CCCH zinc-finger RNA binding proteins that regulate alternative splicing of target genes by directly binding to target mRNA. In the human disease myotonic dystrophy type 1 (DM1), a progressive muscular dystrophy, sequestration of MBNL proteins in nuclear foci leads to altered splicing of downstream genes. Mis-splicing of several genes is responsible for the muscular and cardiac symptoms present in individuals with DM1. Most work on the MBNL proteins has focused on their role in muscle morphogenesis and maintenance. However, C. elegans mbl-1 is expressed in a subset of motorneurons including DA9 and is required cell autonomously in these neurons to regulate proper synapse formation. Post-synaptic and muscle markers were unaffected in mbl-1 mutant animals. Thus, our work demonstrates that mbl-1 also functions in neurons to regulate synapse formation. In a separate set of experiments, we identified a new mutation in the coding region of the touch cell-specific beta-tubulin, mec-7(wy116) that causes a defect in synapse formation in the mechanosensory neuron PLM. Previous studies have shown that mec-7 is expressed exclusively in the six touch neurons of C. elegans and is required for sensing light touch. Our mec-7 mutation leads to a loss of synaptic vesicle accumulation at PLM synaptic sites in the ventral nerve cord and synaptic vesicles are visible at ectopic locations along the lateral axon of PLM. Localization of the synaptic proteins VAMP and GIT-1 is also defective in our mutant, but neuronal morphology is wild-type. mec-7(wy116) is mildly Mec, but other alleles of mec-7 (e1506, e1527) do not phenocopy the synaptic vesicle localization defect. mec-7(wy116) is a missense mutation that alters a highly conserved Thr at position 409 to Ile. Crystal structures of tubulin indicate that this residue is on the face of tubulin that interacts with kinesin motor. Because we see synaptic vesicles along the lateral axon of PLM, we believe that kinesin-mediated vesicle transport is less efficient in mec-7(wy116) mutants.
- 2014 CRCnetBASEBor-Sen Chen, and Yu-Chao Wang.Mathematical models and design specifications in synthetic gene networks -- Robust synthetic biology designs based on system dynamic models -- Robust synthetic biology designs based on network evolutionary methods -- Construction of promoter and promoter-RBS libraries for synthesis of gene networks -- Robust synthetic gene network designs based on library-search method -- Robust design of synthetic biological filter and transistor based on promoter-RBS libraries -- Communication and synchronization of a population of coupled synthetic gene networks.
- 2013 Springer Protocolsedited by Peter M. Rabinovich.Cell engineering with synthetic messenger RNA / Peter M. Rabinovich and Sherman M. Weissman -- In vitro transcription of long RNA containing modified nucleosides / Norbert Pardi [and others] -- HPLC purification of in vitro transcribed long RNA / Drew Weissman [and others] -- Synthetic mRNAs with superior translation and stability properties / Ewa Grudzien-Nogalska [and others] -- Nonviral, cationic lipid-mediated delivery of mRNA / James G. Hecker -- Light-induced mRNA transfection / Sigurd Leinæs Bøe and Eivind Hovig -- Engineering B cells with mRNA / Jaewoo Lee, David Boczkowski, and Smita Nair -- Programming human dendritic cells with mRNA / Jaewoo Lee, David Boczkowski, and Smita Nair -- Large volume flow electroporation of mRNA : clinical scale process / Linhong Li [and others] -- Retrovirus-based mRNA transfer for transient cell manipulation / Melanie Galla, Axel Schambach, and Christopher Baum -- mRNA delivery to human dendritic cells by recombinant yeast and activation of antigen-specific memory T cells / Frank Breinig, Tanja Breinig, and Manfred J. Schmitt -- Nonviral RNA transfection to transiently modify T cells with chimeric antigen receptors for adoptive therapy / Tobias Riet [and others] -- Natural killer cell reprogramming with chimeric immune receptors / Noriko Shimasaki and Dario Campana -- Reprogramming to pluripotency and differentiation of cells with synthetic mRNA / Peizhe Wang and Jie Na -- Antitumor vaccination with synthetic mRNA : strategies for in vitro and in vivo preclinical studies / Mustafa Diken [and others] -- Mannosylated and histidylated LPR technology for vaccination with tumor antigen mRNA / Chantal Pichon and Patrick Midoux -- Analysis of survivin-specific T cells in breast cancer patients using human DCs engineered with survivin mRNA / Ozcan Met and Inge Marie Svane -- mRNA electroporation as a tool for immunomonitoring / Nathalie Cools [and others] -- mRNA PCR-based epitope chase method / Jean-Daniel Doucet, Dominique Gauchat, and Rejean Lapointe.
- 2015 Cambridgeedited by Sam Thiagalingam, Boston University School of Medicine.Part 1: Introduction to modular organization of the networks of gene functions and cancer -- Part 2: Alterations in the regulatory networks of cellular and molecular events -- Part 3: Events responsible for aberrant genetic and epigenetic codes in cancer -- Part 4: Functional networks of events that modulate phenotypic manifestation of cancer -- Part 5: Current state of the evolving MMMN cancer progression models of cancer -- Part 6: Applications of comprehensive cancer progression models in the fight against cancer.
- 2007 MyiLibraryedited by Isidore Rigoutsos and Gregory Stephanopoulos.
- 2015 Cambridgeedited by Florian Markowetz, Cancer Research UK, Cambridge Research Institute, Michael Boutros, German Cancer Research Center, Heidelberg.1. An introduction to systems genetics -- 2. Computational paradigms for analyzing genetic interaction networks -- 3. Mapping genetic interactions across many phenotypes in metazoan cells -- 4. Genetic interactions and network reliability -- 5. Synthetic lethality and chemoresistance in cancer -- 6. Joining the dots: network analysis of gene perturbation data -- 7. High-content screening in infectious diseases: new drugs against bugs -- 8. Inferring genetic architecture from systems genetics studies -- 9. Bayesian inference for model selection: an application to aberrant signalling pathways in chronic myeloid leukaemia -- 10. Dynamic network models of protein complexes -- 11. Phenotype state spaces and strategies for exploring them -- 12. Automated bahavioural fingerprinting of Caenorhabditis elegans mutants.
- 2015 Springer Protocolsedited by Ralf Kühn, Wolfgang Wurst, Benedikt Wefers.Xanthomonas and the TAL effectors: nature's molecular biologist -- TAL effector DNA-binding principles and specificity -- The development of TALE nucleases for biotechnology -- Online tools for TALEN design -- Assembly of customized TAL effectors through advanced ultimate system -- Engineering customized TALENs using the platinum gate TALEN kit -- Design, assembly, and characterization of TALE-based transcriptional activators and repressors -- A new approach to dissect nuclear organization: TALE-mediated genome visualization (TGV) -- TALEN-induced translocations in human cells -- Mutagenesis in newts: Protocol for Iberian ribbed newts -- Targeted mutagenesis in Bombyx mori using TALENs -- Geneknockout by targeted mutagenesis in a hemimetabolous insect, the two-spotted cricket Gryllus bimaculatus, using TALENs -- Methods for talen evaluation, use, and mutation detection in the mosquito Aedes aegypti -- Methods for TALEN-mediated genomic manipulations in drosophila -- Targeted mutagenesis in zebrafish by TALENs -- Mutagenesis in xenopus and zebrafish using TALENs -- Genome editing in mice using TALE nucleases -- Genome editing in rats using tale nucleases -- Designer nuclease-mediated generation of knockout THP1 cells.
- 2009 Springeredited by Uday Kishore.Macrophage pattern recognition receptors in immunity, homeostasis, and self tolerance / Subhankar Mukhopadhyay, Annette Plüddemann, and Siamon Gordon -- Pattern recognition by toll-like receptors / Stefan Bauer, Thomas Müller, and Svetlana Hamm -- Nod-like receptors : pivotal guardians of the immunological integrity of barrier organs / Philip Rosenstiel and Stefan Schreiber -- Toll-like receptors and nod-like receptors : domain architecture and cellular signalling / Tanja Langefeld ... [et al.] -- Humoral pattern recognition molecules : mannan-binding lectin and ficolins / Steffen Thiel and Mihaela Gadjeva -- Lung surfactant proteins A and D as pattern recognition proteins / Patrick Waters ... [et al.] -- Pattern recognition by pentraxins / Alok Agrawal ... [et al.] -- Target pattern recognition by complement proteins of the classical and alternative pathways / Yu-hoi Kang ... [et al.] -- Pattern recognition in phagocytic clearance of altered self / Yoshinobu Nakanishi, Peter M. Henson and Akiko Shiratsuchi -- Structural basis of pattern recognition by innate immune molecules / Eamon P. McGreal -- Lessons from the fly : pattern recognition in Drosophila melanogaster / Subhamoy Pal and Louisa P. Wu -- Immune recognition of plasmodium-infected erythrocytes / Damien V. Cordery and Britta C. Urban -- Innate immune recognition in tuberculosis infection / Anthony G. Tsolaki.Also available: Print – 2009
- 2011Junhee Seok.Translation of knowledge from basic science to medicine is essential to improving both clinical research and practice. In this translation, high-throughput genomic approaches can greatly accelerate our understanding of molecular mechanisms of diseases. A successful high-throughput genomic study of disease requires, first, comprehensive and efficient platforms to collect genomic data from clinical samples, and second, computational analysis methods that utilize databases of prior biological knowledge together with experimental data to derive clinically meaningful results. In this thesis, we discuss the development of a new microarray platform as well as computational methods for knowledge-based analysis along with their applications in clinical research. First, we and other colleagues have developed a new high-density oligonucleo-tide array of the human transcriptome for high-throughput and cost-efficient analysis of patient samples in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, and also pro-vides assays for coding SNP detection and non-coding transcripts. Compared with high-throughput mRNA sequencing technology, we show that this array is highly re-producible in estimating gene and exon expression, and sensitive in detecting expres-sion changes. In addition, the exon-exon junction feature of this array is shown to im-prove detection efficiency for mRNA alternative splicing when combined with an ap-propriate computational method. We implemented the use of this array in a multi-center clinical program and have obtained comparable levels of high quality and re-producible data. With low costs and high throughputs for sample processing, we antic-ipate that this array platform will have a wide range of applications in high-throughput clinical studies. Second, we investigated knowledge-based methods that utilize prior know-ledge from biology and medicine to improve analysis and interpretation of high-throughput genomic data. We have developed knowledge-based methods to enrich our prior knowledge, illustrate dynamic response to external stimulus, and identify distur-bances in cellular pathways by chemical exposure, as well as discover hidden biological signatures for the prediction of patient outcomes. Finally, we applied a knowledge-based approach in a large scale genomic study of trauma patients. Cooperating with clinical information, prior knowledge improved the interpretation of common and dif-ferential genomic response to injury, and provided efficient risk assessment for patient outcomes. The clinical and genomic data as well as analysis results in this trauma study were systematically organized and provided to research communities as new knowledge of traumatic injury. The microarray platform and knowledge-based methods presented in this thesis provide appropriate research tools for high-throughput translational medicine in a large clinical setting. This thesis is expected to advance understanding and treatment for dis-eases, and finally, improve public health.
- 2011 Springer Protocolsedited by Zhou Songyang.Introduction to telomeres and telomerase / Z. Songyang -- Analysis of average telomere length in cultured human cells / D. Liu -- Telomere length analysis by quantitative fluorescent in situ hybridization (Q-FISH) / I. Ourliac-Garnier and A. Londono-Vallejo -- Telomere strand-specific length analysis by fluorescent in situ hybridization (Q-CO-FISH) / I. Ourliac-Garnier and A. Londono-Vallejo -- Telomere G-overhang length measurement method 1: The DSN method / Y. Zhao, J.W. Shay and W.E. Wright -- Telomere G-overhang length measurement method 2: G-tail telomere HPA / H. Tahara -- Telomere terminal G/C strand synthesis: Measuring telomerase action and C-RICH fill-in / Y. Zhao, J.W. Shay and W.E. Wright -- G-quadruplex structures and G-quadruplex-interactive compounds / R.I. Mathad and D. Yang -- Analysis of yeast telomerase by primer extension assays / M. Hsu and N.F. Lue -- Telomeric repeat amplification protocol: Measuring the activity of the telomerase / H. Xin -- CO-FISH, COD-FISH, ReD-FISH, SKY-FISH / E.S. Williams [and others] -- Visualization of human telomerase localization by fluorescence microscopy techniques / E. Abreu, R.M. Terns and M.P. Terns -- Cytogenetic analysis of telomere dysfunction / A.S. Multani and S. Chang -- Probing the telomere damage response / R. Rai and S. Chang -- Analysis of telomere proteins by chromatin immunoprecipitation (CHIP) / W. Ma -- Studying of telomeric protein-protein interactions by bi-molecular fluorescence complementation (BIFC) and peptide array-based assays / W. Ma, H. Kim and Z. Songyang -- Human telomere POT1-TPP1 complex and its role in telomerase activity regulation / F. Wang and M. Lei.
- Telomeres and telomerase in aging, disease, and cancer : molecular mechanisms of adult stem cell ageing2008 SpringerK. Lenhard Rudolph, editor.
- 2009 SpringerKewal K. Jain.Basics of Personalized Medicine -- Molecular Diagnostics as Basis of Personalized Medicine -- Role of Biomarkers in Personalized Medicine -- Pharmacogenetics -- Pharmacogenomics -- Role of Pharmacoproteomics -- Role of Metabolomics in Personalized Medicine -- Personalized Biological Therapies -- Development of Personalized Medicine -- Personalized Therapy for Cancer -- Personalized Management of Neurological Disorders -- Personalized Therapy of Cardiovascular Diseases -- Personalized Management of Miscellaneous Disorders -- Personalized Preventive Medicine -- Organization of Personalized Medicine -- Ethical and Regulatory Aspects of Personalized Medicine -- Economics of Personalized Medicine -- Future of Personalized Medicine.
- 2014 SpringerThomas Boehm, Yousuke Takahama, editors.The thymus is an evolutionarily ancient primary lymphoid organ common to all vertebrates in which T cell development takes place. Failing thymus function is associated with immunodeficiency and/or autoimmunity. In this volume, leading experts provide a comprehensive overview of recent advances in thymopoiesis research. The chapters cover the development of the thymic epithelial microenvironment, address the formation of a diverse and self-tolerant repertoire of T cell receptors as the basis for cellular immunity, discuss the mechanisms by which progenitor cells colonize the thymus and detail the molecular basis for T lineage decisions. The reviews illustrate the important role of the multifaceted process of thymopoiesis for adaptive immunity.
- 2013 Springer Protocolsedited Tin-Lap Lee, Alfred Chun Shui Luk.A Brief Introduction to Tiling Microarrays: Principles, Concepts, and Applications -- Design of Tiling Arrays and their Application to Bacterial Transcriptome Analysis -- Transcript Profiling in Arabidopsis with Genome Tiling Microarrays -- Genome-wide Analysis of Transcription Factor Binding Sites in Skeletal Muscle Cells using ChIP-seq -- Analysis of Allele-Specific Gene Expression Using a Target-Oriented Tiling Microarray Assay -- Detection of Epigenetic Alterations Using Tiling Arrays -- Investigating Gene Promoter Methylation in a Mouse Model of Status Epilepticus -- Integrative Analysis of ChIP-chip and ChIP-seq Dataset -- HAT: A Novel Statistical Approach to Discover Functional Regions in the Genome -- Inference of Alternative Splicing from Tiling Array Data -- Analysis of in vivo Occupancy of Aebp1, a Transcription Factor, using High Resolution Tiling Array -- Application of the Simple and Efficient MPeak Modeling in Binding Peak Identification in CHIP-CHIP Studies -- Evaluation of MeDIP-chip in the Context of Whole Genome Bisulphite Sequencing (WGBS-seq) in Arabidopsis -- Mapping Genomic Features of Tiling Microarray Data by TileMapper.
- 2013Feng Chen.While there has been great progress in identifying stem and progenitor cells and the signals that control their proliferation and differentiation, how stem/progenitor cells exit their niche and how they form new tissue is not well understood. Unlike in the embryo, tissue formation in an adult animal faces new challenges such as longer distances to migrate and a complex milieu of differentiated tissue to migrate around and/or coordinate with. To restore function to a tissue, stem/progenitor cells must also integrate into healthy tissue and coordinate growth with decaying tissue. In this thesis, I examine how tracheal progenitor cells exit their niche to form tracheal tissue during Drosophila melanogaster metamorphosis. Tracheal progenitors exit the niche in two waves. During the first wave, progenitors migrate onto the basal surface of larval tracheal branches destined for destruction, and track along the decaying branches. Progenitor outgrowth requires the embryonic tracheal branch inducer, Breathless FGFR, and surprisingly, the Branchless FGF ligand is expressed in larval branches along which progenitors crawl. In this way, outgrowth is coordinated with tissue decay. Progenitors that remain within the niche during the first wave exit later. However, instead of moving onto the basal surface of larval branches, progenitors exiting the niche during this second wave move along the apical surface, displacing larval cells, and repopulating the tracheal branch. This latter process does not resemble branching morphogenesis in the embryo and does not require Bnl/Btl FGF signaling, demonstrating that progenitor outgrowth does not always require embryonic guidance cues.
- Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines2013Joseph William Foley.The human genome's nucleotide sequence contains a small amount of information relative to the complexity of the organism. The diversity of developmental programs and stimulus responses is instead enabled by a vast regulatory network of chemical modifications and protein interactions that determine the activity level of each genome element dynamically. Recent advances in molecular profiling techniques have led to the creation of large data sets that assay each regulatory interaction across the entire genome at once, with high sensitivity and precision. Here I introduce a new computational method, UniPeak, that synthesizes the output from any number of these experiments into a single straightforward analysis with rigorous quantitative measures. I then apply this method to the largest available data sets of genome regulation experiments, and integrate them with parallel experiments on genome activity. I discover and characterize novel regulatory interactions, and model how these interactions regulate the activity of genes.
- 2014 Springer Protocolsedited by Etsuko Miyamoto-Sato [and four others].
- 2012 Springer Protocolsedited by Ales Vancura.Genome-wide in vivo cross-linking of sequence-specific transcription factors / Xiao-Yong li and Mark D. Biggin -- Characterization of complex regulatory networks and identification of promoter regulatory elements in yeast : "in silico" And "wet-lab" approaches / Nuno P. Mira, Miguel C. Teixeira, and Isabel Sá-Correia -- Electrophoretic mobility shift assay analysis of NF[kappa]B transcriptional regulation by nuclear I[kappa]B[alpha] / Ashish Juvekar [and others] -- Probing endogenous RNA polymerase II pre-initiation complexes by electrophoretic mobility shift assay / Emmanuelle Wilhelm, Christopher Takacs, and Brendan Bell -- Elucidating protein : DNA complex by oligonucleotide DNA affinity purification / Teddy T.C. Yang and Chi-Wing Chow -- Chromatin immunoprecipitation assay as a tool for analyzing transcription factor activity / Padmaja Gade and Dhan V. Kalvakolanu -- Two-step cross-linking for analysis of protein-chromatin interactions / Bing Tian, Jun Yan, and Allan R. Brasier -- Chromatin immunoprecipitation analysis of NF[kappa]B transcriptional regulation by nuclear I[kappa]B[alpha] in human macrophages / Sitharam Ramaswami [and others] -- In vivo ChIP for the analysis of microdissected tissue samples / Chris Murgatroyd, Anke Hoffmann, and Dietmar Spengler -- Quantification of protein-DNA interactions by in vivo chromatin immunoprecipitation in yeast / Amparo Pascual-Ahuir and Markus Proft -- Mapping protein-DNA interactions using ChIP-sequencing / Charles E. Massie and Ian G. Mils -- ChIP and re-ChIP assays : investigating interactions between regulatory proteins, histone modifications, and the DNA sequences to which they bind / Agnieszka D. Truax and Susanna F. Greer -- Transcriptional regulation of genes via hypoxia-inducible factor / Olga Roche and Michael Ohh -- Exchange protein directly activated by cyclic AMP-1-regulated recruitment of CCAAT/enhancer-binding proteins to the suppressor of cytokine signaling-3 promoter / William A. Sands [and others] -- Computational analysis of promoter elements and chromatin features in yeast / John J. Wyrick -- Chromatin affinity purification / Ryoko Harada and Alain Nepveu -- Determination of histone acetylation status by chromatin immunoprecipitation / Luciano Galdieri, John Moon, and Ales Vancura -- Immunostaining of Drosophila polytene chromosomes to investigate recruitment of chromatin-binding proteins / Magdalena Murawska and Alexander Brehm -- Detection of transcriptional activators, co-activators, and chromatin remodeling by chromatin immunoprecipitation coupled with real-time PCR / Tamara Y. Erkina and Alexandre M. Erkine -- Chromatin endogenous cleavage and psoralen crosslinking assays to analyze rRNA gene chromatin in vivo / Joachim Griesenbeck [and others] -- UV-induced DNA damage and DNA repair in ribosomal genes chromatin / Julie Pelloux [and others] -- Analysis of SUC2 promoter structure by nucleosome scanning / Jennifer Chang and Ales Vancura -- Chromatin immunoprecipitation of mouse embryos / Anne K. Voss [and others] -- Chromatin immunoprecipitation in mouse hippocampal cells and tissues / Badi Sri Sailaja, Takumi Takizawa, and Eran Meshorer -- Approaches for studying nucleosome movement by ATP-dependent chromatin remodeling complexes / Swetansu K. Hota and Blaine Bartholomew -- Mapping protein-DNA and protein-protein interactions of ATP-dependent chromatin remodelers / Swetansu K. Hota [and others] -- Evaluation of histone-modifying enzymes in stem cell populations / Leanne Stalker and Christopher Wynder -- Purification of multiprotein histone acetyltransferase complexes / Yuan-Liang Wang, Francesco Faiola, and Ernest Martinez -- Reconstitution of active and stoichiometric multisubunit lysine acetyltransferase complexes in insect cells / Kezhi Yan [and others] -- Affinity purification of MLL3/MLL4 histone H3K4 methyltransferase complex / Young-Wook Cho, SunHwa Hong, and Kai Ge -- Methods for analyzing histone citrullination in chromatin structure and gene regulation / Pingxin Li, Jing Hu, and Yanming Wang -- Analysis of mRNA abundance and stability by ribonuclease protection assay / Cristina Romero-López [and others] -- Array-based nuclear run-on analysis / Jinshui Fan [and others] -- In vivo run-on assays to monitor nascent precursor RNA transcripts / Piergiorgio Percipalle and Emilie Louvet -- Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET) / Xiaoan Ruan and Yijun Ruan -- Analysis of co-transcriptional RNA processing by RNA- ChIP assay / Danielle Bittencourt and Didier Auboeuf -- Quantitative analysis of transcription elongation by RNA polymerase I in vitro / David Alan Schneider -- Detection and characterization of transcription termination / Ghada Ghazal, Jules Gagnon, and Sherif Abou Elela -- Promoter-associated noncoding RNA from the CCND1 promoter / Xiaoyuan Song [and others].
- 2008 SpringerSerena M. Dudek, editor.
- 2013 Springer Protocolsedited by Baohong Zhang.Transgenic cotton : from biotransformation methods to agricultural application / Baohong Zhang -- Genetically modified cotton in India and detection strategies / Gurinder Jit Randhawa and Rashmi Chhabra -- Agrobacterium-mediated transformation of cotton / Baohong Zhang -- Biolistic transformation of cotton zygotic embryo meristem / Kanniah Rajasekaran -- Biolistic transformation of cotton embryogenic cell suspension cultures / Kanniah Rajasekaran -- Cotton transformation via pollen tube pathway / Min Wang, Baohong Zhang, and Qinglian Wang -- Silicon carbide whisker-mediated transformation of cotton (Gossypium hirsutum L.) / Muhammad Arshad, Yusuf Zafar, and Shaheen Asad -- Investigating transgene integration and organization in cotton (Gossypium hirsutum L.) genome / Jun Zhang and Yan Hong -- Estimating the copy number of transgenes in transformed cotton by real-time quantitative PCR / Chengxin Yi and Yan Hong -- Development of enzyme-linked immunosorbent assay for the detection of Bt protein in transgenic cotton / Suchitra Kamle, Abhishek Ojha, and Arvind Kumar -- DNA-based diagnostics for genetically modified cotton : decaplex PCR assay to Differentiate MON531 and MON15985 Bt cotton events / Gurinder Jit Randhawa, Monika Singh, and Rashmi Chhabra -- Simple and rapid method for determining transgenic cotton plants / Baohong Zhang [and others] -- Efficient grafting technique for recovery of transgenic cotton plants / Min Wang, Qinglian Wang, and Baohong Zhang -- Inheritance of transgenes in transgenic Bt lines resistance to Helicoerpa armigera in upland cotton / Baolong Zhang, Wangzhen Guo, and Tianzhen Zhang -- Agrobacterium rhizogenes-induced cotton hairy root culture as an alternative tool for cotton functional genomics / Hee Jin Kim -- Overexpression of miR 156 in cotton via Agrobacterium-mediated transformation / Baohong Zhang [and others] -- Development of transgenic CryIA(c) + GNA cotton plants via pollen tube pathway method confers resistance to Helicoverpa armigera and Aphis gossypii Glover / Zhi Liu, Zhen Zhu, and Tianzhen Zhang -- Agrobacterium-mediated transformation of cotton (Gossypium hirsutum) shoot apex with a fungal phytase gene improves phosphorus acquisition / Zhiying Ma, Jianfeng Liu, and Xingfen Wang -- Genetic transformation of cotton with a harpin-encoding gene hpaXoo confers an enhanced defense response against Verticillium dahliae kleb / Weiguo Miao and Jingsheng Wang -- Development of insect-resistant transgenic cotton with chimeric TVip3A* accumulating in chloroplasts / Jiahe Wu and Yingchuan Tian -- Determining gene flow in transgenic cotton / Xiaoping Pan.
- 2011 Springer Protocolsedited by Marten H. Hofker, Jan van Deursen.Introduction: strategies for developing genetically modified mice / Marten H. Hofker -- Genetic modification of the mouse: general technology - pronuclear and blastocyst injection / Jan Willem Voncken -- Generation of chimeras by aggregation of embryonic stem cells with diploid or tetraploid mouse embryos / Jérôme Artus and Anna-Katerina Hadjantonakis -- Cryopreservation of mouse spermatozoa and in vitro fertilization / Naomi Nakagata -- Autopsy and histological analysis of the transgenic mouse / Marion J.J. Gijbels and Menno P.J. de Winther -- Transgene design / Bart van de Sluis and Jan Willem Voncken -- Inducible transgenic mouse models / Thomas L. Saunders -- Lentiviral transgenesis / Terunaga Nakagawa and Casper C. Hoogenraad -- Transgenesis in mouse embryonic stem cells / Janine van Ree, Wei Zhou, Ming Li, and Jan M. van Deursen -- Engineering BAC reporter gene constructs for mouse transgenesis / Yu Fu and Peter Maye -- Targeting vector construction through recombineering / Liviu A. Malureanu -- Generating conditional knockout mice / Roland H. Friedel, Wolfgang Wurst, Benedikt Wefers, and Ralf Kühm -- Hypomorphic mice / Darren J. Baker -- MICER targeting vectors for manipulating the mouse genome / Chunbong Liu, Paul F. Szurek, and Y. Eugene Yu -- Knock-in approaches / Anton J.M. Roebroek, Philip L.S.M. Gordts, and Sara Reekmans -- Generation of a series of knock-in alleles using RMCE in ES cells / Anton J.M. Roebroek, Philip L.S.M. Gordts, and Sara Reekmans -- Selection of targeting mutants from a library of randomly mutagenized ES cells / Kyoji Horie, George Gaitanaris, and Alexander Gragerov -- Generation of genetically modified rodents using random ENU mutagenesis / Ruben van Boxtel and Edwin Cuppen -- Bone marrow transplantations of study gene function in hematopoietic cells / Menno P.J. de Winther and Peter Heeringa -- Adenovirus-mediated gene transfer / Ko Willems van Dijk, Kyriakos E. Kyreos, Frits J. Fallaux, and Jurre Hageman.
- 2012 Springer Protocolsedited by Jim M. Dunwell, Andy C. Wetten.Employment of cytokinin vectors for marker-free and backbone-free transformation -- Organophosphorus hydrolase: A multifaceted plant genetic marker which is selectable, scorable, and quantifiable in whole seed -- Use of northern blotting for specific detection of small RNA molecules in transgenic plants -- Genetic transformation of the model green alga Chlamydomonas reinhardtii -- A high-efficiency agrobacterium-mediated transformation system of rice (Oryza sativa L.) -- Selection of transgenic rice plants using a herbicide tolerant form of the acetolactate synthase gene -- Visual selection in rice: A strategy for the efficient identification of transgenic calli accumulating transgene products -- Characterization of rice genes using a heterologous full-length cCDNA expression system -- Bioactive bead-mediated transformation of plants with large DNA fragments -- Agrobacterium-mediated transformation of sorghum bicolor using immature embryos -- Split-transgene expression in wheat -- Agrobacterium-mediated transformation of brachypodium distachyon -- Transformation of barley (Hordeum vulgare L.) by agrobacterium tumefaciens infection of in vitro cultured ovules -- Biolistic-mediated production of transgenic oil palm -- Transformation of oil palm using agrobacterium tumefaciens -- Highly efficient transformation protocol for plum (Prunus domestica L.) -- Co-transformation of grapevine somatic embryos to produce transgenic plants free of marker genes -- Initiation and transformation of grapevine embryogenic cultures -- Development of highly efficient genetic transformation protocols for table grape sugraone and crimson seedless -- Cotton pistil drip transformation method -- Enhanced agrobacterium-mediated transformation of embryogenic calli of upland cotton -- Targeted biolistics for improved transformation of impatiens balsamina -- A protocol for transformation of torenia -- Efficient modification of floral traits by heavy-ion beam irradiation on transgenic torenia -- Expression of artificial micrornas in physcomitrella patens -- High frequency of single-copy t-DNA transformants produced after floral dip in CRE-expressing arabidopsis plants -- A developmentally regulated cre-lox system to generate marker-free transgenic Brassica napus plants -- Exploiting multisite gateway and pENFRUIT plasmid collection for fruit genetic engineering -- A one-time inducible transposon to create knockout mutants in rice -- Marker-free gene targeting by recombinase-mediated cassette exchange -- Targeting DNA to a previously integrated transgenic locus using zinc finger nucleases -- Double-strand break-induced targeted mutagenesis in plants -- Combinatorial genetic transformation of cereals and the creation of metabolic libraries for the carotenoid pathway -- Production of a his-tagged canecystatin in transgenic sugarcane -- Plastid transformation as an expression tool for plant-derived biopharmaceuticals -- Use of a callus-specific selection system to develop transgenic rice seed accumulating a high level of recombinant protein -- How to grow transgenic arabidopsis in the field.
- 2009 Springer Protocolsedited by Huw D. Jones and Peter R. Shewry.Transgenic wheat, barley and oats : production and characterization / Paul A. Lazzeri and Huw D. Jones -- Selection of transformed plants / Huw D. Jones and Caroline A. Sparks -- Reporter genes / Alison Huttly -- Biolistics transformation of wheat / Caroline A. Sparks and Huw D. Jones -- Agrobacterium-mediated transformation of bread and durum wheat using freshly isolated immature embryos / Huixia Wu, Angela Doherty and Huw D. Jones -- Floral transformation of wheat / Sujata Agarwal ... [et al.] -- Highly efficient agrobacterium-mediated transformation of wheat via in planta inoculation / Thierry Risacher ... [et al.] -- Barley transformation using biolistic techniques / Wendy A. Harwood and Mark A. Smedley -- Barley transformation using agrobacterium-mediated techniques / Wendy A. Harwood ... [et al.] -- Transformation of oats and its application to improving osmotic stress tolerance / Shahina B. Maqbool ... [et al.] -- Promoter sequences for defining transgene expression / Huw D. Jones and Caroline A. Sparks -- Down-regulation of gene expression by RNA-induced gene silencing / Silvia Travella and Beat Keller -- Gene insertion patterns and sites / Philippe Vain and Vera Thole -- Fluorescent in situ hybridization to detect transgene integration into plant genomes / Trude Schwarzacher -- Establishing substantial equivalence : transcriptomics / María Marcela Baudo ... [et al.] -- Establishing substantial equivalence : proteomics / Alison Lovegrove, Louise Salt, and Peter R. Shewry -- Establishing substantial equivalence : metabolomics / Michael H. Beale, Jane L. Ward, and John M. Baker -- Design and management of field trials of transgenic cereals / Zoltán Bedő, Mariann Rakszegi, and László Láng -- GM risk assessment / Penny A.C. Sparrow -- Transgenic wheat, barley and oats : future prospects / Jim M. Dunwell.
- 2007 ScienceDirectedited by Jon Lorsch.Purification of FLAG-tagged eukaryotic initation factor 2B complexes, subcomplexes, and fragments from Saccharomyces cerevisiae / Sarah S. Mohammad-Qureshi ... [et al.] -- In vivo deletion analysis of the architecture of a multiprotein complex of translation initiation factors / Klaus H. Nielsen and Leos̆ Valás̆ek -- An approach to studying the localization and dynamics of eukaryotic translation factors in live yeast cells / Susan G. Campbell and Mark P. Ashe -- In vitro and tissue culture methods for analysis of translation initiation on the endoplasmic reticulum / Samuel B. Stephens and Christopher V. Nicchitta -- Mammalian stress granules and processing bodies / Nancy Kedersha and Paul Anderson -- Methods to analyze micro-RNA-mediated control of mRNA translation / Jennifer L. Clancy ... [et al.] -- Methods for studying signal-dependent regulation of translation factor activity / Xuemin Wang and Christopher G. Proud -- Analysis of mRNA translation in cultured hippocampal neurons / Yi-Shuian Huang and Joel D. Richter -- Detecting ribosomal association with the 5' leader of mRNAs by ribosome density mapping (RDM) / Naama Eldad and Yoav Arava -- Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays / Danial Melamed and Yoad Arava -- Synthesis of anti-reverse cap analogs (ARCAs) and their applications in mRNA translation and stability / Ewa Grudzien-Nogalska ... [et al.] -- Methods for identifying compounds that specifically target translation / Letizia Brandi ... [et al.] -- Identifying small molecule inhibitors of eukaryotic translation initiation / Regina Cencic, Francis Robert, and Jerry Pelletier -- Isolation and identification of eukaryotic initiation factor 4A as a molecular target for the marine natural product pateamine A / Woon-Kai Low ... [et al.].
- 2007 ScienceDirectedited by Jon Lorsch.Use of reticulocyte lysates for mechanistic studies of eukaryotic translation initiation / William C. Merrick and Diane Barth-Baus -- Studying translational control in Drosophila cell-free systems / Fátima Gebauer and Matthias W. Hentze -- Use of in vitro translation extract depleted in specific initiation factors for the investigation of translational regulation / Daniel R. Gallie -- A highly efficient and robust in vitro translation system for expression of picornavirus and hepatitis C virus in RNA genomes / Yuri V. Svitkin and Nahum Sonenberg -- A practical approach to isolate 48S complexes : affinity purification and analyses / Nicolas Locker and Peter J. Lukavsky -- Yeast phenotypic assays on translational control / Bumjun Lee ... [et al.] -- Localization and characterization of protein-protein interaction sites / Chingakham Ranjit Singh and Katsura Asano -- In vivo stabilization of preinitiation complexes by formaldehyde cross-linking / Leos Valás̆ek ... [et al.] -- Molecular genetic structure-function analysis of translation initiation factor elF5B / Byung-Sik Shin and Thomas E. Dever -- The use of fungal in vitro systems for studying translational regulation / Cheng Wu ... [et al.] -- Investigating translation initiation using drosophila molecular genetics / Gritta Tettweiler and Paul Lasko -- Analysis of RNA:protein interactions in vivo : identification of RNA-binding partners of nuclear factor 90 / Andrew M. Parrott, Melissa R. Walsh, and Michael B. Mathews -- Approaches for analyzing the differential activities and functions of elF4E family members / Robert E. Rhoads, Tzvetanka D. Dinkova, and Rosemary Jagus -- Tethered function assays : an adaptable approach to study RNA regulatory proteins / Jeff Coller and Marv Wickens -- Analysis of ribosomal shunting during translation initiation in eukaryotic mRNAs / Vincent P. Mauro, Stephen A. Chappell and John Dresios.
- 2007 ScienceDirectedited by Jon Lorsch.Transient kinetics, flourescence, and FRET in studies of initiation and translation in bacteria / Pohl Milon ... [et al.] -- Binding of mRNA to the bacterial translation initiation complex / Sean M. Studer and Simpson Joseph -- Real-time dynamics of ribosome-ligand interaction by time-resolved chemical probing methods / Attilio Fabbretti ... [et al] -- Overexpression and purification of mammalian mitochondrial translational initiation factor 2 and initiation factor 3 / Domenick G. Grasso ... [et al.] -- In vitro studies of archaeal translational initiation / Dario Benelli and Paola Londei -- Reconstitution of yeast translation initiation / Michael G. Acker ... [et al.] -- Assembly and analysis of eukaryotic translation initiation complexes / Andrey V. Pisarev -- Reconstitution of mammalian 48S ribosomal translation initiation complex / Romit Majumdar, Jayanta Chaudhuri, and Umadas Maitra -- Biophysical approach to studies of Cap-elF4E interaction by synthetic cap analogs / Anna Niedzwiecka ... [et al.] -- Biophysical studies of the translation initiation pathway with immobilized mRNA analogs / John E. G. McCarthy, Steven Marsden, and Tobias von der Haar -- Protection-based assays to measure aminoacyl-tRNA binding to translation initiation factors / Yves Mechulam ... [et al.] -- NMR methods for studying protein-protein interactions involved in translation initiation / Assen Marintchev, Dominique Frueh, and Gerhard Wagner -- Structural methods for studying IRES function / Jeffrey S. Kieft ... [et al.].
- Translational modulation as a consequence of codon choice and miRNA regulation in Caenorhabditis elegans2012Michael Richard Stadler.The conversion of genetic information from the language of nucleic acids into that of proteins is fundamental to nearly every biological process. The regulation of this process of gene expression--when, where, and how much product is produced from each gene--is a crucial determinant of cell state and identity. Gene expression is tightly regulated at every metabolic step, including transcription of DNA into mRNA, splicing of introns, export from the nucleus, polypeptide synthesis, and post-translational modification and stability. Regulation of protein synthesis acts directly or indirectly through the ribosome, as it is the interaction of ribosomes with mRNAs and dozens of protein and RNA translation factors that determine the efficiency and fidelity of translation. Emerging technologies allow the analysis of translation in contexts that were previously inaccessible. In my thesis work, I employed a technique known as ribosome profiling to examine snapshots of the positions of millions of ribosomes on cellular mRNAs in vivo. In the first part of my thesis, I used ribosome profiling data from Caenorhabditis elegans and cultured human tumor cells to investigate the sequence determinants of the rate of ribosome elongation. The genetic code is redundant, meaning that a single amino acid can usually encoded by more than one trinucleotide sequence, or codon. The choice from among these "synonymous" codons has long been suspected to influence local ribosomal elongation rates, with possible consequences on the folding of nascent polypeptides. By examining "snapshots" of the in vivo positions of ribosomes on thousands of mRNAs, we were able to determine that mRNA positions featuring "wobble" codons in the ribosomal decoding center were associated with greater ribosome occupancy, and thus most likely with slower translation elongation. These wobble codons pair with cognate tRNA anticodons using alternative base-pairing strategies that are less energetically stable than canonical Watson-Crick interactions. The observed wobble retention was strong for codons that employ G:U pairing at the wobble position, and weaker for those using I:U pairs. Importantly, this property of translation elongation was observed in both C. elegans samples and human cells, indicating that wobble-related slowing is a conserved feature of metazoan translation. In the second part of my thesis, I used ribosome profiling, together with traditional, low-throughput methods to investigate the molecular consequences of regulation by C. elegans miRNAs. miRNAs are post-transcriptional regulators of gene expression that have been proposed to act by directing mRNA degradation, deadenylation, translation initiation, by interfering with a post-initiation stage of translation or by triggering proteolysis. C. elegans features several well-validated, natural miRNA::mRNA interactions that serve to reduce target protein levels at specific developmental time points as part of the so-called heterochronic pathway. mRNA-seq measurements confirmed earlier observations from other groups that the abundance of target mRNAs decreases only slightly upon the onset of miRNA regulation. Analysis of ribosome footprint abundance showed that miRNA regulation is often associated with decreased ribosome loading in later larval stages, but changes in ribosome loading are negligible at time points where miRNA inhibition becomes active. Additionally, profiles of ribosome footprints did not appreciably change, rendering several models of post-initiation translational regulation unlikely. These data suggest a model in which processes beyond mRNA degradation and translational repression contribute to regulation by this set of miRNAs, including a possible role for post- or peri-translational destruction of peptide products.
- 2009 Springervolume editors, Dirk-Henner Lankenau, Jean-Nicolas Volff.
- 2005 SpringerH.J. Senn, R. Morant (eds.).Lifestyle and Medical Approaches to Cancer Prevention / Peter Greenwald, p. 1-15 -- Application of Genetics to the Prevention of Colorectal Cancer / John Hopper, p. 17-33 -- Genetics and Prevention of Oesophageal Adenocarcinoma / Rebecca Fitzgerald, p. 35-46 -- Preclinical Models Relevant to Diet, Exercise, and Cancer Risk R. James Barnard and William Aronson, p. 47-62 -- Individualizing Interventions for Cancer Prevention / Michael Pollak, p. 63-70 -- Can Animal Models Help Us Select Specific Compounds for Cancer Prevention Trials? / Ernest Hawk, Asad Umar, Ronald Lubet, Levy Kopelovich and Jaye Viner, p. 71-88 -- Problems with Using Biomarkers as Surrogate End Points for Cancer: A Cautionary Tale / Arthur Schatzkin, p. 89-98 -- Can a Marker Be a Surrogate for Development of Cancer, and Would We Know It if It Exists? / William Armstrong, Thomas Taylor and Frank Meyskens, p. 99-112 -- How Should We Move the Field of Chemopreventive Agent Development Forward in a Productive Manner? / Frank Meyskens and Eva Szabo, p. 113-124 -- The Problems with Risk Selection; Scientific and Psychosocial Aspects / Anne-Renée Hartman, p. 125-144 -- Chemoprevention of Lung Cancer / Stéphane Vignot, Jean-Philippe Spano, Sylvie Lantuejoul, Fabrice André, Thierry Le Chevalier and Jean-Charles Soria, p. 145-165 -- Anti-nicotine Vaccination: Where Are We? / T. Cerny, p. 167-175 -- Primary Prevention of Colorectal Cancer: Lifestyle, Nutrition, Exercise / María Martínez, p. 177-211 -- Chemoprevention of Colorectal Cancer: Ready for Routine Use? / Nadir Arber and Bernard Levin, p. 213-230 -- Screening of Colorectal Cancer: Progress and Problems Sidney Winawer, p. 231-244 -- The Role of Endogenous Hormones in the Etiology and Prevention of Breast Cancer: The Epidemiological Evidence / Paola Muti, p. 245-256 -- Innovative Agents in Cancer Prevention / Margaret Manson, Peter Farmer, Andreas Gescher and William Steward, p. 257-275 -- The IARC Commitment to Cancer Prevention: The Example of Papillomavirus and Cervical Cancer / Silvia Franceschi, p. 277-297 -- Health Economics in the Genomic Age / Thomas Szucs, p. 299-313 -- Screening for Cancer: Are Resources Being Used Wisely? / Robert Kaplan, p. 315-334.
- Understanding the mechanis of mammalian damage tolerance proteins in suppressing damage-specific mutagenesis2012Jia-Ren Lin.Post-replication repair (PRR) pathways play important roles in restarting stalled replication forks and regulating mutagenesis. In yeast, Rad5-mediated damage avoidance and Rad18-mediated translesion synthesis (TLS) are two forms of PRR. Two Rad5-related proteins, SHPRH and HLTF, have been identified in mammalian cells, but their specific roles in PRR are unclear. Here, we show that HLTF and SHPRH suppress mutagenesis in a damage-specific manner, preventing mutations induced by UV and MMS, respectively. Following UV, HLTF enhances PCNA monoubiquitination and recruitment of TLS polymerase eta, while also inhibiting SHPRH function. In contrast, MMS promotes the degradation of HLTF and the interactions of SHPRH with Rad18 and polymerase kappa. Our data not only suggest that cells differentially utilize HLTF and SHPRH for different forms of DNA damage, but also, surprisingly, that HLTF and SHPRH may coordinate the two main branches of PRR to choose the proper bypass mechanism for minimizing mutagenesis. Though the degradation of HLTF is required for the SHPRH-Rad18 interaction in MMS-damaged cells, knockdown of HLTF is not sufficient to induce SHPRH-Rad18 binding in undamaged cells. Thus, an unidentified factor, in addition to HLTF degradation, is required to fully activate SHPRH and Rad18 upon MMS damage. We have noticed that Rad18 is deubiquitinated after MMS treatment, and that this de-ubiquitination is correlated with the degree of Rad18-SHPRH interaction. Moreover, we show that promoting the ubiquitination of Rad18 has an inverse effect on the interaction with SHPRH both in vitro and in cells. Surprisingly, though, the ubiquitinated Rad18 shows a stronger self-interaction than the wild-type Rad18, opposite from the SHPRH binding results. As the zinc-finger motif of Rad18 has been previously shown to bind ubiquitin, this may be a logical mechanism to control the switch between Rad18 dimerization and its interaction with other proteins. Interestingly, ubiquitinated Rad18 appears to be inactive, not only from loss of its ability to interact with SHPRH, but also through the inability to form damage foci and suppress MMS-induced mutagenesis. Altogether, our data reveal a unique regulation of Rad18 through self-ubiquitination and dimerization. In summary, our studies have revealed a number of new mechanistic insights into the post-replication repair pathways in human cells, including the interesting conclusion that protein degradation, deubiquitination, and other key cell processes may be controlled in a DNA damage-specific manner.
- 2013Alexis Jane Battle.Recent technological advances have allowed us to collect genomic data on an unprecedented scale, with the promise of revealing genetic variants, genes, and pathways disrupted in clinically relevant human traits. However, identifying functional variants and ultimately unraveling the genetics of complex disease from such data have presented significant challenges. With millions of genetic factors to consider, spurious associations and lack of statistical power are major hurdles. Further, we cannot easily assess functional roles even for known trait-associated variants, particularly for those that lie outside of protein-coding regions of the genome. To address these challenges in identifying the genetic factors underlying complex traits, we have developed probabilistic machine learning methods that leverage biological structure and prior knowledge. In this thesis, we describe four applications of such models. First, we present a method for reconstructing causal gene networks from interventional genetic interaction data in model organisms. Here, we are able to identify intricate functional dependencies among hundreds of genes affecting a complex trait. We have applied this method to understanding the genetics of protein folding in yeast, where we demonstrate ability to recapitulate the details, including ordering, of known pathways, and make novel functional predictions. Second, we present PriorNet, a method for incorporating gene network and path- way information into the analysis of population-level studies of genetic variation in human disease. PriorNet utilizes a flexible, Markov Random Field prior to propagate information between functionally related genes and related diseases, in order to improve statistical power in large-scale disease studies. We demonstrate a significant improvement in the discovery of disease-relevant genes in studies of three autoimmune diseases. Next, we extend the intuitions of PriorNet in a method for identifying interactions between genetic variants in human disease, to begin to understand how genes work together in complex disease processes. Our method, GAIT, leverages gene networks, network structure, and other patterns to adaptively prioritize candidate in- teractions for testing, and dramatically reduce the burden of multiple hypothesis correction to identify a large number of interactions in diverse human disease studies. Finally, we discuss the identification of functional variants on a large scale through the use of gene expression as a high-resolution cellular phenotype. We have sequenced RNA from 922 genotyped individuals to provide a direct window into the distribution, properties, and consequences of thousands of regulatory variants affecting diverse gene expression traits including splicing and allelic expression. From the identified variants, we also train a model, LRVM, for predicting regulatory consequences based on location and genomic properties of each variant.
- 2013 SpringerLucy W. Barrett, Sue Fletcher, Steve D. Wilton.There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as ""junk DNA"", it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal and spatial gene expression through the combinatorial effect of numerous mechanisms and interactions working together to fine-tune gene expression. The major regions involved in regulation of a particular gene are the 5' and 3' untranslated regions and introns.
- 2014 ScienceDirectedited by Jennifer A Doudna and Erik J Sontheimer.This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers recent research and methods development for changing the DNA sequence within the genomes of cells and organisms. Focusing on enzymes that generate double-strand breaks in DNA, the chapters describe use of molecular tools to introduce or delete genetic information at specific sites in the genomes of animal, plant and bacterial cells.
- 2009 Springeredited by Pierre Ferrier.Early steps of V(D)J rearrangement : insights from biochemical studies of RAG-RSS complexes / Patrick C. Swanson, Sushil Kumar, and Prafulla Raval -- Regulation of RAG transposition / Adam G.W. Matthews and Marjorie A. Oettinger -- Recent insights into the formation of RAG-induced chromosomal translocations / Vicky L. Brandt and David B. Roth -- V(D)J recombination deficiencies / Jean-Pierre de Villartay -- Large-scale chromatin remodeling at the immunoglobulin heavy chain locus : a paradigm for multigene regulation / Daniel J. Bolland, Andrew L. Wood, and Anne E. Corcoran -- Genetic and epigenetic control of V gene rearrangement frequency / Ann J. Feeney -- Dynamic aspects of TCRa gene recombination : qualitative and quantitative assessments of the TCRa chain repertoire in man and mouse / Evelyne Jouvin-Marche, Patrizia Fuschiotti, and Patrice Noël Marche -- Germline transcription : a key regulator of accessibility and recombination / Iratxe Abarrategui and Michael S. Krangel -- Dynamic regulation of antigen receptor gene assembly / Lance R. Thomas, Robin Milley Cobb, and Eugene M. Oltz -- Molecular genetics at the T-cell receptor b locus : insights into the regulation of V(D)J recombination / Marie Bonnet, Pierre Ferrier, and Salvatore Spicuglia -- Molecular pathways and mechanisms regulating the recombination of immunoglobulin genes during B-lymphocyte development / Kristen Johnson, Karen L. Reddy, and Harinder Singh -- Regulation of V(D)J recombinationby E-protein transcription factors / Mary Elizabeth Jones and Yuan Zhuang -- Temporal and spatial regulation of V(D)J recombination : interactions of extrinsic factors with the RAG complex / Yun Liu, Li Zhang, and Stephen Desiderio -- V(D)J recombination : of mice and sharks / Ellen Hsu -- Normal and pathological V(D)J recombination : contribution to the understanding of human lymphoid malignancies / Saïda Dadi ... [et al.].Also available: Print – 2009
- 2006. Kargervolume editor, Jean-Nicolas Volff.The human genome and its upcoming dynamics / M. Platzer -- Primate genomes / H. Herlyn, H. Zischler -- The mouse genome / S.D.M. Brown, J.M. Hancock -- The dog genome / F. Galibert, C. André -- The feline genome / W.J. Murphy -- The bovine genome / J.E. Womack -- The sheep genome / N.E. Cockett -- Cracking the genomic piggy bank : identifying secrets of the pig genome / B.E. Mote, M.F. Rothschild -- The horse genome / B.P. Chowdhary, T. Raudsepp -- Marsupial and monotreme genomes / E. Koina, J. Fong, J.A. Marshall Graves -- The chicken genome / D.W. Burt -- Insights from Xenopus genomes / N. Pollet, A. Mazabraud -- The Tetraodon genome / H. Roest Crollius -- The medaka genome : why we need multiple fish models in vertebrate functional genomics / H. Mitani ... [et al.] -- The zebrafish genome : a review and msx gene case study / J.H. Postlethwait -- Urochordate genomes / N. Satoh ... [et al.].
- 2013 Springer Protocolsedited by Riccardo Brambilla, Division of Neuroscience, Institute of Experimental Neurology, San Raffaele Scientific Institute, Milan, Italy.Lentiviral vectors as research tools in neurobiology: design and production / Alessandro Papale and Riccardo Brambilla -- Recombinant adenovirus in neurobiology / Qian Li and Tong-Chuan He -- Adeno-associated virus-based vectors / Nathalie Dutheil and Erwan Bezard -- Herpes simples virus 1 (HSV-1)-based vectors / Aldo Pourchet, Matias E. Melendez, Anna Greco, and Alberto L. Epstein -- Aphavirus-based vectors / Kenneth Lundstrom -- Viral vectors to study synaptic function / Hélène Marie -- Using viral vectors to study the memory trace in mice / Asim J. Rashid, Chen Yan, and Sheena A. Josselyn -- Development of cell-type-specific viral vectors to tease apart the neural circuitry that contributes to drug addiction / Susan M. Ferguson and John F. Neumaier -- Using viral-mediated gene transfer to study depressive-like behavior / Amy R. Furay and John F. Neumaier -- Gene therapy for parkinson's disease / Erika Elgstrand Wettergren, Luis Quintino, Giuseppe Manfré, and Cecilia Lundberg -- Lentiviral vectors in huntington's disease research and therapy / Aurélie Delzor, Noëlle Dufour, and Nicole Déglon -- Application of viral vectors to motor neuron disorders / Elisabeth Dirren and Bernard L. Schneider -- In vivo gene silencing by virally delivered MicroRNA / Eugenia V. Gurevich, Mohamed R. Ahmed, and Yonatan Carl -- Viral manipulation of neural stem/precursor cells / Nunzio Iraci, Giulia Elisabetta Tyzack, Chiara Cossetti, Clara Alfaro-Cervello, and Stefano Pluchino -- Viral vector-based techniques for optogenetic modulation in vivo / Mathias Mahn, Shiri Ron, and Ofer Yizhar -- Viral vectors for optogenetics of hypothalamic neuropeptides / H. Sophie Knobloch, Alexander Charlet, Ron Stoop, and Valery Grinevich -- Viral vectors in primate research: examples from parkinson's disease research / Grégory Porras, Benjamin Dehay, and Erwan Bezard.
- 2011 Springer Protocolsedited by Otto-Wilhelm Merten, Mohamed Al-Rubeai.Introduction to viral vectors -- Introduction to gene therapy : a clinical aftermath -- Host cells and cell banking -- Overview of current scalable methods for purification of viral vectors -- Methods to construct recombinant adenovirus vectors -- Manufacturing of adenovirus vectors : production and purification of helper dependent adenovirus -- Manufacturing of retroviruses -- Lentiviral vectors -- Adeno-associated viruses -- Manufacturing of adeno-associated viruses, for example: AAV2 -- Vector characterization methods for quality control testing of recombinant adeno-associated viruses -- Baculoviruses mediate efficient gene expression in a wide range of vertebrate cells -- Herpes simplex virus type 1-derived recombinant and amplicon vectors -- Manufacture of measles viruses -- In vivo gene delivery into hCD34+ cells in a humanized mouse model -- In vivo evaluation of gene transfer into mesenchymal cells (in view of cartilage repair) -- Ethical consideration -- Clinical trials of GMP products in the gene therapy field.
- 2013 Springer Protocolsedited by Annette Becker.Virus-induced gene silencing (VIGS) in plants : an overview of target species and the virus-derived vector systems -- Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing -- Virus-induced gene silencing for rice using agroinoculation -- Utilizing virus-induced gene silencing for the functional characterization of maize genes during infection with the fungal pathogen ustilago maydis -- Analysis of developmental control genes using virus-induced gene silencing -- Virus-induced gene silencing in the rapid cycling columbine aquilegia coerulea Origami -- Virus-induced gene silencing of the alkaloid-producing basal eudicot model plant eschscholzia californica (California poppy) -- Virus-induced gene silencing using artificial miRNAs in nicotiana benthamiana -- The use of vigs technology to study plant-herbivore interactions -- Virus-aided gene expression and silencing using TRV for functional analysis of floral scent-related genes -- Virus-induced gene silencing in soybean and common bean -- Functional genomic analysis of cotton genes with agrobacterium-mediated virus-induced gene silencing -- Highly efficient virus-induced gene silencing in apple and soybean by apple latent spherical virus vector and biolistic inoculation -- VIGS : a tool to study fruit development in Solanum lycopersicum -- A protocol for VIGS in arabidopsis thaliana using a one-step TYMV-derived vector -- Virus-induced gene silencing in strawberry fruit.
- 2012 SpringerGunther Witzany, editor."Viruses are now considered to play major roles in the evolution of life. Because they have genes that are not found in any cellular organism they seem to be remnants of early stages of life on earth. Besides their disease causing features and actions as genetic parasites viruses have lifestyles that are clearly symbiotic and even symbiogenetic. Increasing empirical data suggest that some viruses such as endogenous retroviruses and non-retroviral RNA viruses and even DNA viruses prefer cellular genomes as habitat. They determine genetic host (group) identity and genetic host features. Viruses and virus-related modules such as mobile genetic elements and other repeat sequences identified in intronic regions of host genomes play important roles in gene regulation and genetic content (re)arrangement. This book exemplifies some astonishing key features of viruses acting as essential agents of life."--Publisher.
- 2011 SpringerSteve Horvath.Networks and fundamental concepts -- Approximately factorizable networks -- Different types of network concepts -- Adjacency functions and their topological effects -- Correlation and gene co-expression networks -- Geometric interpretation of correlation networks using the singular value decomposition -- Constructing networks from matrices -- Clustering procedures and module detection -- Evaluating whether a module is preserved in another network -- Association measures and statistical significance measures -- Structural equation models and directed networks -- Integrated weighted correlation network analysis of mouse liver gene expression data -- Networks based on regression models and prediction methods -- Networks between categorical or discretized numeric variables -- Network based on the joint probability distribution of random varaibles.
- 2015 Springer Protocolsedited by Thomas Kroneis.Principles of whole-genome amplification / Zbigniew Tadeusz Czyz, Stefan Kirsch, and Bernhard Polzer -- Bias in whole genome amplification : causes and considerations / Jeffrey Sabina and John H. Leamon -- Single-cell lab or how to perform single-cell molecular analysis / Roland Kirchner and Marianna Alunni-Fabbroni -- Sample preparation methods following cellsearch approach compatible of single-cell whole-genome amplification : an overview / Joost F. Swennenhuis and Leon Terstappen -- Deterministic whole-genome amplification of single cells / Zbigniew Tadeusz Czyż and Christoph A. Klein -- Construction of a DNA library on microbeads using whole genome amplification / Takaaki Kojima, Bo Zhu, and Hideo Nakano -- Heat-induced fragmentation and adapter-assisted whole genome amplification using GenomePlex® single-cell whole genome amplification kit (WGA4) / Amin El-Heliebi, Shukun Chen , and Thomas Kroneis -- Whole genome amplification by isothermal multiple strand displacement using Phi29 DNA polymerase / Thomas Kroneis and Amin El-Heliebi -- Using multiplex PCR for assessing the quality of whole genome amplified DNA / Amin El-Heliebi, Shukun Chen, and Thomas Kroneis -- Quality control of isothermal amplified DNA based on short tandem repeat analysis / Thomas Kroneis and Amin El-Heliebi -- Laser microdissection of FFPE tissue areas and subsequent whole genome amplification by Ampli1 / Zbigniew Tadeusz Czyz, Nikolas H. Stoecklein, and Bernhard Polzer -- Whole genome amplification from blood spot samples / Karina Meden Sørensen -- Analysis of whole mitogenomes from ancient samples / Gloria Gonzales Fortes and Johanna L. A. Paijmans -- Copy number variation analysis by array analysis of single cells following whole genome amplification / Eftychia Dimitriadou, Masoud Zamani Esteki, and Joris Robert Vermeesch -- Whole genome amplification in genomic analysis of single circulating tumor cells / Christin Gasch, Klaus Pantel, and Sabine Riethdorf -- Whole genome amplification of labeled viable single cells suited for array-comparative genomic hybridization / Thomas Kroneis and Amin El-Heliebi -- Low-volume on-chip single-cell whole genome amplification for multiple subsequent analyses / Thomas Kroneis, Shukun Chen, and Amin El-Heliebi -- Detection and characterization of circulating tumor cells by the cellsearch approach / Frank Coumans and Leon Terstappen.
- [editor-in chief, Martin Chalfie ; editor, Lisa Girard]."WormBook is a comprehensive online review of C. elegans biology, containing over 100 original, peer-reviewed chapters on a wide range of topics related to the biology of C. elegans and related nematodes; as well as WormMethods, a collection of laboratory methods and protocols useful for nematode researchers."
- 2012 Springer Protocolsedited by Stefan Hoppler, Peter D. Vize.Xenopus tropicalis as a model organism for genetics and genomics : past, present, and future / Robert M. Grainger -- Husbandry of Xenopus tropicalis / Alan Jafkins [and others] -- Generating diploid embryos from Xenopus tropicalis / Florencia del Viso and Mustafa Khokha -- Navigating the Xenopus tropicalis genome / Ira L. Blitz -- Genetic analysis of Xenopus tropicalis / Timothy J. Geach, Derek L. Stemple, and Lyle B. Zimmerman -- Forward genetic screens in Xenopus using transposon-mediated insertional mutagenesis / Donald A. Yergeau [and others] -- Targeted gene disruption with engineered zinc-finger nucleases (ZFNs) / John J. Young and Richard M. Harland -- Reverse genetic studies using antisense morpholino oligonucleotides / Yanan Zhao, Shoko Ishibashi, and Enrique Amaya -- Chemical genetics and drug discovery in Xenopus / Matthew L. Tomlinson, Adam E. Hendry, and Grant N. Wheeler -- Maternal mRNA knock-down studies : antisense experiments using the host-transfer technique in Xenopus laevis and Xenopus tropicalis / David J. Olson, Alissa M. Hulstrand, and Douglas W. Houston -- Generating transgenic frog embryos by restriction enzyme mediated integration (REMI) / Shoko Ishibashi, Kristen L. Kroll, and Enrique Amaya -- Simple method of transgenesis using I-SceI meganuclease in Xenopus / Shoko Ishibashi, Nick R. Love, and Enrique Amaya -- Using [phi]C31 integrase to mediate insertion of DNA in Xenopus embryos / You E. Li, Bryan G. Allen, and Daniel L. Weeks -- Xenopus transgenics : methods using transposons / Clair M. Kelley [and others] -- Comparative genomics-based identification and analysis of cis-regulatory elements / Hajime Ogino [and others] -- Tet-On binary systems for tissue-specific and inducible transgene expression / Daniel R. Buchholz -- Chromatin immunoprecipitation analysis of Xenopus embryos / Robert C. Akkers, Ulrike G. Jacobi, and Gert Jan C. Veenstra -- Transcriptomics using next generation sequencing technologies / Dasfne Lee-Liu [and others] -- Databases of gene expression in Xenopus development / Michael J. Gilchrist and Nicolas Pollet -- Investigating alternative RNA splicing in Xenopus / Agnes Mereau and Serge Hardy -- Immunoisolation of protein complexes from Xenopus / Frank L. Conlon [and others] -- Complementary proteomic analysis of protein complexes / Todd M. Greco [and others] -- Antibody development and use in chromogenic and fluorescent immunostaining / Eamon Dubaissi [and others] -- Multiple fluorescent in situ mRNA hybridization (FISH) on whole mounts and sections / Robert Lea [and others] -- Methods to analyze microRNA expression and function during Xenopus development / Boyan Bonev and Nancy Papalopulu -- Bromodeoxyuridine (BrdU) based protocol for characterizing proliferating progenitors in Xenopus embryos / Hélène Auger [and others] -- Microscopy tools for quantifying developmental dynamics in Xenopus embryos / Sagar D. Joshi, Hye Young Kim, and Lance A. Davidson -- Mathematical modeling of gene regulatory networks in Xenopus development / Yasushi Saka -- Stem-cell-like embryonic explants to study cardiac development / Boni A. Afouda -- Studying regeneration in Xenopus / Caroline W. Beck -- On-line resources for Xenopus / Jeff Bowes.
- 2006 Springer Protocolsedited by Alasdair MacKenzie.Markers, selection, and media in yeast artificial chromosomes cloning / David Markie -- Construction of yeast artificial chromosome libraries from pathogens and nonmodel organisms / Cecilia P. Sanchez and Michael Lanzer -- Analysis and screening of yeast artificial chromosome libraries by filter hybridization / Cecilia P. Sanchez and Michael Lanzer -- Analysis of Yeast Artificial Chromosome DNA by restriction digestion, southern blotting nucleic acid hybridization and polymerase chain reaction / Sylvia Vasiliou and John Peter Quinn -- Postgenomic bioinformatic analysis of yeast artificial chromosome sequence / Kerry Miller, Scott Davidson, and Alasdair MacKenzie -- Transformation of yeast using bioactive beads with surface-immobilized yeast artificial chromosomes / Shigeki Kawakami ... [et al.] -- Modification and amplification of yeast artificial chromosomes / Sanbing Shen, Anthony Harmar, and Nick Hastie -- Modifying yeast artificial chromosomes to generate Cre/LoxP and FLP/FRT site-specific deletions and inversions / Gabriela G. Loots -- Selective isolation of large chromosomal regions by transformation-associated recombination cloning for structural and functional analysis of mammalian genomes / Natalay Kouprina, Vladimir N. Noskov, and Vladimir Larionov -- A polymerase chain reaction-mediated yeast artificial chromosome-splitting technology for generating targeted yeast artificial chromosomes subclones / Yeon-Hee Kim ... [et al.] -- Genomic reconstruction by serial mitotic recombination of yeast artificial chromosomes / David Markie, Emma Jones, and Jiannis Ragoussis -- Targeting vector construction by yeast artificial chromosome modification / Peter J. Murray -- Production of yeast artificial chromosomes transgenic mice by pronuclear injection of one-cell embryos / Alasdair MacKenzie -- Generation of yeast artificial chromosomes transgenic mice by intracytoplasmic sperm injection / Pedro N. Moreira ... [et al.] -- Establishment of cell lines that exhibit correct ontogenic stage-specific gene expression profiles from tissues of yeast artificial chromosome transgenic mice using chemically induced growth signals / C. Anthony Blau and Kenneth R. Peterson -- Application of yeast artificial chromosomes in fluorescence in situ hybridization / Thomas Liehr -- Contribution of yeast artificial chromosome-based physical maps to the final assembly of the trypanosoma cruzi genome / Marcia R.M. Santos ... [et al.].
- 2016 Springer Protocolsedited by Alberto Sanchez-Diaz, Pilar Perez.Time-lapse fluorescence microscopy of budding yeast cells / Arun Kumar and Manuel Mendoza -- Real-time visualization and quantification of contractile ring proteins in single living cells / Reshma Davidson ... [et al.] -- Fluorescence recovery after photo-bleaching (FRAP) and fluorescence loss in photo-bleaching (FLIP) experiments to study protein dynamics during budding yeast cell division / Alessio Bolognesi ... [et al.] -- High-speed super-resolution imaging of live fission yeast cells / Caroline Laplante ... [et al.] -- Monitoring chitin deposition during septum assembly in budding yeast / Irene Arcones and Cesar Roncero -- Imaging septum formation by fluorescence microscopy / Juan Carlos Ribas and Juan Carlos G. Cortés -- Visualization of cytokinesis events in budding yeast by transmission electron microscopy / Franz Meitinger and Gislene Pereira -- Visualization of fission yeast cells by transmission electron microscopy / Matthias Sipiczki -- Characterization of septin ultrastructure in budding yeast using electron tomography / Aurélie Bertin and Eva Nogales -- Isolation of cytokinetic actomyosin rings from Saccharomyces cerevisiae and Schizosaccharomyces pombe / Junqi Huang ... [et al.] -- Measurements of myosin-II motor activity during cytokinesis in fission yeast / Qing Tang, Luther W. Pollard, and Matthew Lord -- In vitro biochemical characterization of cytokinesis actin-binding proteins / Dennis Zimmermann ... [et al.] -- Characterization of cytokinetic F-BARs and other membrane-binding proteins / Nathan A. McDonald and Kathleen L. Gould -- Analysis of three-dimensional structures of exocyst components / Johannes Lesigang and Gang Dong -- Analysis of Rho-GTPase activity during budding yeast cytokinesis / Masayuki Onishi and John R. Pringle -- Detection of phosphorylation status of cytokinetic components / Franz Meitinger, Saravanan Palani, and Gislene Pereira -- Studying protein-protein interactions in budding yeast using co-immunoprecipitation / Magdalena Foltman and Alberto Sanchez-Diaz -- Conditional budding yeast mutants with temperature-sensitive and auxin-inducible degrons for screening of suppressor genes / Asli Devrekanli and Masato T. Kanemaki -- Synchronization of the budding yeast Saccharomyces cerevisiae / Magdalena Foltman, Iago Molist, and Alberto Sanchez-Diaz -- Fission yeast cell cycle synchronization methods / Marta Tormos-Pérez, Livia Pérez-Hidalgo, and Sergio Moreno -- Review of fluorescent proteins for use in yeast / Maja Bialecka-Fornal, Tatyana Makushok, and Susanne M. Rafelski -- Visualization and image analysis of yeast cells / Steve Bagley -- Toolbox for protein structure prediction / Daniel Barry Roche and Liam James McGuffin -- From structure to function : a comprehensive compendium of tools to unveil protein domains and understand their role in cytokinesis / Sergio A. Rincon and Anne Paoletti.
- 2015 Springer Protocolsedited by Frederic Devaux.Using RNA-seq for analysis of differential gene expression in fungal species / Can Wang ... [et al.] -- Enhancing structural annotation of yeast genomes with RNA-Seq data / Hugo Devillers, Nicolas Morin, and Cécile Neuvéglise -- Pathogen gene expression profiling during infection using a nanostring nCounter platform / Wenjie Xu ... [et al.] -- Comparative transcriptomics in yeasts / Dawn A. Thompson -- Mapping the transcriptome-wide landscape of RBP binding sites using gPAR-CLIP-seq : experimental procedures / Ting Han and John K. Kim -- Mapping the transcriptome-wide landscape of RBP binding sites using gPAR-CLIP-seq : bioinformatic analysis / Mallory A. Freeberg and John K. Kim -- Translation analysis at the genome scale by ribosome profiling / Agnès Baudin-Baillieu ... [et al. ] -- Biotin-genomic run-on (Bio-GRO) : a high-resolution method for the analysis of nascent transcription in yeast / Antonio Jordán-Pla ... [et al.] -- Genome-wide probing of RNA structures in vitro using nucleases and deep sequencing / Yue Wan ... [et al.] -- Genome-wide chromatin immunoprecipitation in Candida albicans and other yeasts / Matthew B. Lohse [et al.] -- ChIPseq in yeast species : from chromatin immunoprecipitation to high-throughput sequencing and bioinformatics data analyses / Gaëlle Lelandais, Corinne Blugeon, and Jawad Merhej -- Systematic determination of transcription factor DNA- binding specificities in yeast / Lourdes Peña-Castillo and Gwenael Badis -- Generation and analysis of chromosomal contact maps of yeast species / Axel Cournac ... [et al.] -- Versatile procedure to generate genome-wide spatiotemporal program of replication in yeast species / Nicolas Agier and Gilles Fischer -- Single-step affinity purification (ssAP) and mass spectrometry of macromolecular complexes in the yeast S. cerevisiae / Christian Trahan, Lisbeth-Carolina Aguilar, and Marlene Oeffinger -- Label-free quantitative proteomics in yeast / Thibaut Léger ... [et al.] -- Profiling of yeast lipids by shotgun lipidomics / Christian Klose and Kirill Tarasov -- Identification of links between cellular pathways by genetic interaction mapping (GIM) / Christophe Malabat and Cosmin Saveanu -- On the mapping of epistatic genetic interactions in natural isolates : combining classical genetics and genomics / Jing Hou and Joseph Schacherer -- Experimental evolution and resequencing analysis of yeast / Celia Payen and Maitreya J. Dunham -- Reconstruction and analysis of the evolution of modular transcriptional regulatory programs using arboretum / Sara A. Knaack, Dawn A. Thompson, and Sushmita Roy -- Predicting gene and genomic regulation in Saccharomyces cerevisiae, using the YEASTRACT database : a step-by-step guided analysis / Miguel C. Teixeira, Pedro T. Monteiro, and Isabel Sá-Correia.
- 2007 ScienceDirectedited by Ian Stansfield and Michael J.R. Stark.
- 2011 Springer Protocolsedited by Attila Becskei.Global estimation of mRNA stability in yeast / Julia Marin-Navarro [and others] -- Genomic-wide methods to evaluate transcription rates in yeast / Jose Garcia-Martinez, Vicent Pelechano, and Jose E. Perez-Ortin -- Construction of cis-regulatory input functions of yeast promoters / Prasuna Ratna and Attila Becskei -- Luminescence as a continuous real-time reporter of promoter activity in yeast undergoing respiratory oscillations or cell division rhythms / J. Brian Robertson and Carl Hirschie Johnson -- Linearizer gene circuits with negative feedback regulation / Dmitry Nevozhay, Rhys M. Adams, and Gabor Balazsi -- Measuring in vivo signaling kinetics in a mitogen-activated kinase pathway using dynamic input stimulation / Megan N. McClean, Pascal Hersen, and Sharad Ramanathan -- Stochastic analysis of gene expression / Xiu-Deng Zheng and Yi Tao -- Studying adaptation and homeostatic behaviors of kinetic networks by using MATLAB / Tormod Drengstig, Thomas Kjosmoen, and Peter Ruoff -- Biochemical systems analysis of signaling pathways to understand fungal pathogenicity / Jacqueline Garcia [and others] -- Clustering change patterns using fourier transformation with time-course gene expression data / Jaehee Kim -- Finding modulators of stochasticity levels by quantitative genetics / Steffen Fehrmann and Gael Yvert -- Functional mapping of expression quantitative trait loci that regulate oscillatory gene expression / Arthur Berg [and others] -- Evolutionary aspects of a genetic network : studying the lactose/galactose regulon of Kluyveromyces lactis / Alexander Anders and Karin D. Breunig -- Analysis of subtelomeric silencing in Candida glabrata / Alejandro Juarez-Reyes, Alejandro De Las Penas, and Irene Castano -- Morphological and molecular genetic analysis of epigenetic switching of the human fungal pathogen Candida albicans / Denes Hnisz, Michael Tscherner, and Karl Kuchler -- Quantitation of cellular components in Cryptococcus neoformans for system biology analysis / Arpita Singh, Asfia Qureshi, and Maurizio Del Poeta.
- 2011 ScienceDirectedited by H. William Detrich III, Monte Westerfield, Leonard I. Zon.Pt.1 Forward and reverse genetics : Generating conditional mutations in zebrafish using gene-trap mutagenesis / Lisette A. Maddison, Jianjun Lu, Wenbiao Chen -- Tol2-mediated transgenesis, gene trapping, enhancer trapping, and the Gal4-UAS system / Gembu Abe, Maximilliano L. Suster, Koichi Kawakami -- Engineering zinc finger nucleases for targeted mutagenesis of zebrafish / Jeffry D. Sander, J.-R. Joanna Yeh, Randall T. Peterson, J. Keith Joung -- Retroviral-mediated insertional mutagenesis in zebrafish / Adam Amsterdam, Gaurav Kumar Varshney, Shawn Michael Burgess -- Genetic screens for mutations affecting adult traits and parental-effect genes / Francisco Pelegri, Mary C. Mullins -- High-throughput target-selected gene inactivation in zebrafish / Ross N.W. Kettleborough, Ewart de Bruijn, Freek van Eeden, Edwin Cuppen, Derek L. Stemple -- Genetic suppressor screens in haploids / Xiaoying Bai, Zhongan Yang, Hong Jiang, Shuo Lin, Leonard I. Zon -- Transgenic zebrafish using transposable elements / Karl J. Clark, Mark D. Urban, Kimberly J. Skuster, Stephen C. Ekker -- Spatiotemporal control of embryonic gene expression using caged morpholinos / Ilya A. Shestopalov, James K. Chen -- Pt.2 Transgenesis : Advanced zebrafish transgenesis with Tol2 and application for Cre/lox recombination experiments / Christian Mosimann, Leonard I. Zion -- Use of phage PhiC31 integrase as a tool for zebrafish genome manipulation / James A. Lister -- Method for somatic cell nuclear transfer in zebrafish / Kannika Siripattarapravat, Jose B. Cibelli -- Pt.3 The zebrafish genome and mapping technologies : Single nucleotide polymorphism (SNP) panels for rapid positional cloning in zebrafish / Matthew D. Clark, Victor Guryev, Ewart de Bruijn, Isaac J. Nijman, Masazumi Tada, Catherine Wilson, Panos Deloukas, John H. Postlethwait, Edwin Cuppen, Derek L. Stemple -- Molecular cytogenetic methodologies and a BAC probe panel resource for genomic analyses in the zebrafish / Kimberly P. Dobrinski, Kim H. Brown, Jennifer L. Freeman, Charles Lee -- Conserved synteny and the zebrafish genome / Julian M. Catchen, Ingo Braasch, John H. Postlethwait -- The zon laboratory guide to positional cloning in zebrafish / Yi Zhou, Leonard I. Zon -- Pt.4 Informatics and comparative genomics : Data extraction, transformation, and dissemination through ZFIN / Douglas G. Howe, Ken Frazer, David Fashena, Leyla Ruzicka, Yvonne Bradford, Sridhar Ramachandran, Barbara J. Ruef, Ceri Van Slyke, Amy Singer, Monte Westerfield -- DNA methylation profiling in zebrafish / Shan-Fu Wu, Haiying Zhang, Saher Sue Hammond, Magdalena Potok, David A. Nix, David A. Jones, Bradley R. Cairns -- Chromatin immunoprecipitation in adult zebrafish red cells / Eirini Trompouki, Teresa Venezia Bowman, Anthony DiBiase, Yi Zhou, Leonard I. Zon -- Discerning different in vivo roles of microRNAs by experimental approaches in zebrafish / Luke Pase, Graham J. Lieschke -- Sequencing-based expression profiling in zebrafish / Jin Liang, Gabriel Renaud, Shawn M. Burgess -- Chromatin modification in zebrafish development / Jordi Cayuso Mas, Emily S. Noël, Elke A. Ober -- Pt.5 Infrastructure : Advances in zebrafish husbandry and management / Christian Lawrence -- Aquaculture and husbandry at the Zebrafish International Resource Center / Zoltán M. Varga.
- 2016 ScienceDirectedited by H. William Detrich, Monte Westerfield and Leonard I. Zon.
- Accurate methods for ancestry and relatedness inference — Epigenetics protocols. 2nd ed. (156)
- Epigenetics, the environment, and children's health across lifespans — Investigations in yeast functional genomics and molecular biology (156)
- Kallmann syndrome and hypogonadotropic hypogonadism — Proteins and proteomics of Leishmania and Trypanosoma (156)
- Proteogenomics — Zebrafish-- genetics, genomics, and transcriptomics. Fourth edition. [4th ed.] (155)
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Cochrane reviews are created through a strict process of compiling and analyzing data from multiple randomized control trials to ensure comprehensiveness and reliability.Provides systematic coverage of the psychological literature from the 1800s to the present through articles, book chapters and dissertations.BMJ Clinical Evidence. A clinical information tool built around systematic reviews summarizing the current state of knowledge about prevention and treatment of clinical conditions.PIER (Physicians' Information and Education Resource) is a Web-based decision-support tool designed for rapid point-of-care delivery of up-to-date, evidence-based guidance for primary care physicians.Cochrane Central Register of Controlled Trials (CENTRAL) provides access to 300,000 controlled trials that have been identified the Cochrane Collaboration.Provides drug information targeted for patients.A continually updating drug monograph.The National Guideline Clearinghouse (NGC): A comprehensive database of evidence-based clinical practice guidelines and related documents.MedlinePlus: A repository of health information from the National Library of Medicine. Links are from trusted sites. No advertising, no endorsement of commercial companies or productsLPCH CareNotes via MicroMedex: Patient education handouts customized by LPCH clinical staffMicromedex Lab Advisor: Evidence based laboratory test informationA drug database organized by generic name, trade name and drug class.LPCH / Stanford Hospital Formulary.A goldmine of trusted consumer health information from the world's largest medical library.A trusted source of expert advice for and about kids, providing the information necessary to help patients and parents understand their unique needs.Provides patient handouts from the American Academy of Family Physician.Access to the Stanford Health Library for patients.Lane provides access to over 5,000 eBooks many of which provide helpful background material that will prepare you to better tackle primary literature.
Largest, broadest eBook package; covers all sciences, as well as technology (including software), medicine, and humanities.
In addition to covering Wiley and Springer, MyiLibrary is also the only provider for Oxford and Cambridge University Press titles. No seat restrictions.A collection of biomedical books that can be searched directly by concept, and linked to terms in PubMed abstracts.
A web-based, decision support system for infectious diseases, epidemiology, microbiology and antimicrobial chemotherapy. The database, updated weekly, currently includes 337 diseases, 224 countries, 1,147 microbial taxa and 306 antibacterial (-fungal, -parasitic, -viral) agents and vaccines.
Over 10,000 notes outline the status of specific infections within each country.
Provides online, full-text access to Springer's journal titles as well as journals from other publishers.
Subjects include: life sciences, chemical sciences, environmental sciences, geosciences, computer science, mathematics, medicine, physics and astronomy, engineering and economics. Also includes eBooks.Collection of over 8 thousand fulltext titles in engineering, math, and basic and applied biomedical research. Coverage is from 1967 to the present.A library of ebooks on a wide array of topics, digitized and made available online in conjunction with the original publishers.