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Molecular Biology

  • Carcinogens and mutagens -- Whole animal carcinogenicity bioassays -- Molecular mechanisms of action of selected organic carcinogens -- Binding of carinogens to DNA and covalent adducts and DNA damage - PAH, aromatic amines, nitro-aromatic compounds, and halogenated compounds -- Cellular oncogenes and carcinogenesis -- Tumor suppressor genes -- Hepatitis B, Hepatitis C, and hepatocellular carcinoma -- Oncongenesis in transgenic and knockout mice -- Chemically induced morphological and neoplastic transformation in C3H/10T1/2 C1 8 mouse embryo cells -- Radiation carcinogenesis -- DNA microarrays and computational analysis of DNA microarray data in cancer research -- Application of proteomics in basic biological sciences and cancer -- Overview of human cancer induction and human exposure to carcinogens -- Complex mixtures of chemical carcinogens: principles of action and human cancer -- Lung cancer -- Breast cancer -- Cancer of the prostate - Mechanisms of molecular carcinogenesis -- Skin cancer: epidemiology, clinical manifestations, and genetic and molecular aspects -- Cell and molecular biology of cancer of the brain --Thyroid cancer: molecular biology and clinical aspects -- Chemoprevention of chemical carcinogenesis and human cancer -- Carcinogen biomarkers and exposure assessment -- Risk assessment for chemical carcinogens -- Prevention and regulation approaches to carcinogens.
  • Molecular Diagnostics: 12 Tests That Changed Everything focuses on specific laboratory tests and emphasizes how the availability of these tests has altered how clinicians treat their patients. Presented as a standard outline, each chapter focuses on a specific molecular test and provides background on the test and its clinical applications. Continuing with some discussion on how the test is done, interpreted, and used clinically, each chapter then concludes with a discussion of how that test has changed the way medicine is practiced with respect to the disease or condition in question. Authored by renowned experts in the field, Molecular Diagnostics: 12 Tests That Changed Everything is a valuable resource for pathologists, pathology residents, laboratory directors, development personnel, lab medicine fellows and those working in the broad area of oncology, infectious disease and genetics.
  • Advances in genomic and proteomic profiling of disease have transformed the field of molecular diagnostics, thus leading the way for a major revolution in clinical practice. While the range of tests for disease detection and staging is rapidly expanding, many physicians lack the knowledge required to determine which tests to order and how to interpret results. This handbook provides a complete guide to the use and interpretation of molecular testing in the clinical arena. No other available resource offers this emphasis, comprehensive scope, and practical utility in the clinical setting.
  • This unique book provides a thorough overview of developing molecular cancer diagnostic assays, which are the prerequisites for optimal solutions within personalized cancer medicine. The book takes the reader through definitions of the pharmacodiagnostic concept, historical perspectives of the early steps into molecular cancer diagnostics linked to therapy, the basis of different diagnostic molecular techniques, ongoing research, drug-diagnostic co-development, assay validation, clinical trial methodology, regulatory issues around pharmacodiagnostics and future aspects within personalized cancer medicine.The book is the first of its kind to cover relevant subjects around molecular cancer diagnostics when used as important drivers in personalized cancer medicine. The different chapters of the book are authored by key opinion leaders, each representing their specialized areas, which provide the reader with expertise knowledge in the field.
  • Chapter 1. Molecular Diagnostics: Past, Present, and Future / George P. Patrinos, Wilhelm J. Ansorge -- Chapter 2 . Allele-Specific Mutation Detection / Aglaia Athanassiadou, Eleana F. Stavrou, Adamandia Papachatzopoulou, George P. Patrinos -- Chapter 3. Enzymatic and Chemical Cleavage Methods to Identify Genetic Variation / Chinh T. Bui, Emmanuelle Nicolas, Georgina Sallmann, Maria Chiotis, Andreana Lambrinakos, Kylee Rees, Ian Trounce, Richard G.H. Cotton, Lauryn Blakesley, Andrew K. Godwin, Anthony T. Yeung -- Chapter 4. Mutation Detection by Single Strand Conformation Polymorphism and Heteroduplex Analysis / Panayiotis G. Menounos, George P. Patrinos -- Chapter 5. Capillary Electrophoresis / Anja Bosserhoff, Claus Hellerbrand -- Chapter 6. Temperature and Denaturing Gradient Gel Electrophoresis / Hartmut Peters, Peter N. Robinson -- Chapter 7. Real-Time Polymerase Chain Reaction / Lut Overbergh, Anna-Paula Giulietti, Dirk Valckx, Chantal Mathieu -- Chapter 8 - Pyrosequencing / Sharon Marsh -- Chapter 9. Application of Padlock and Selector Probes in Molecular Medicine / Mats Nilsson, Chatarina Larsson, Johan Stenberg, Jenny Göransson, Ida Grundberg, Magnus Isaksson, Tim Conze, Sara Henriksson -- Chapter 10. Molecular Cytogenetics in Molecular Diagnostics / Holger Tönnies -- Chapter 11. Analysis of Human Splicing Defects Using Hybrid Minigenes / Franco Pagani, Francisco E. Baralle -- Chapter 12. Detection of Genomic Duplications and Deletions / Graham R. Taylor, Carol A. Delaney -- Chapter 13. Multiplex Ligation-Dependent Probe Amplification (MLPA) and Methylation-Specific (MS)-MLPA: Multiplex Detection of DNA/mRNA Copy Number and Methylation Changes / Eline M. Sepers, Jan P. Schouten -- Chapter 14. Molecular Techniques for DNA Methylation Studies / Jörg Tost, Ivo G. Gut -- Chapter 15. High-Resolution Melting Curve Analysis for Molecular Diagnostics / Jared S. Farrar, Gudrun H. Reed, Carl T. Wittwer -- Chapter 16. DNA Microarrays and Genetic Testing / Lars Dyrskjøt, Karina Dalsgaard-Sørensen, Marie Stampe-Ostenfeld, Karin Birkenkamp-Demtroder, Kasper Thorsen, Claus L. Andersen, Mogens Kruhøffer, Jens L. Jensen, Torben F. Ørntoft -- Chapter 17. Arrayed Primer Extension Microarrays for Molecular Diagnostics / Neeme Tonisson, Eneli Oitmaa, Kaarel Krjutskov, Janne Pullat, Ilona Lind, Merike Leego, Ants Kurg, Andres Metspalu -- Chapter 18. Application of Proteomics to Disease Diagnostics / Samir Hanash, Ji Qiu, Vitor Faca -- Chapter 19. RNA-Based Variant Detection: The Protein Truncation Test / Johan T. den Dunnen -- Chapter 20. Protein Diagnostics by Proximity Ligation: Combining Multiple Recognition and DNA Amplification for Improved Protein Analyses / Karl-Johan Leuchowius, Ola Söderberg, Masood Kamali-Moghaddam, Malin Jarvius, Irene Weibrecht, Katerina Pardali, Ulf Landegren -- Chapter 21. Mass Spectrometry and its Applications to Functional Proteomics / Thomas Köcher, Giulio Superti-Furga -- Chapter 22. Pharmacogenetics and Pharmacogenomics: Impact on Drug Discovery and Clinical Care / Minoli Perera, Federico Innocenti -- Chapter 23. Nutrigenomics: Integrating Genomic Approaches into Nutrition Research / Lynette R. Ferguson, Martin Philpott, Matthew P.G. Barnett -- Chapter 24. Novel Next-Generation DNA Sequencing Techniques for Ultra High-Throughput Applications in Bio-Medicine / Wilhelm J. Ansorge -- Chapter 25. Locus-Specific and National/Ethnic Mutation Databases: Emerging Tools for Molecular Diagnostics / George P. Patrinos -- Chapter 26. Molecular Diagnostic Applications in Forensic Science / Bruce Budowle, John V. Planz, Rowan Campbell, Arthur J. Eisenberg -- Chapter 27. Mass Disaster Victim Identification Assisted by DNA Typing / Daniel Corach -- Chapter 28. Detection of Highly Pathogenic Viral Agents: Implications for Therapeutics, Vaccines and Biodefense / Kylene Kehn-Hall, Sina Bavari -- Chapter 29. Identification of Genetically Modified Organisms / Farid E. Ahmed -- Chapter 30. Molecular Diagnostics and Comparative Genomics in Clinical Microbiology / Alex van Belkum -- Chapter 31. Genetic Monitoring of Laboratory Rodents / Jean-Louis Guénet, Fernando J. Benavides -- Chapter 32. Safety Analysis in Retroviral Gene Therapy: Identifying Virus Integration Sites in Gene-Modified Cells / Stephanie Laufs, Luisa Schubert, Patrick Maier, W. Jens Zeller, Stefan Fruehauf -- Chapter 33. Preimplantation Genetic Diagnosis / Martine de Rycke, Karen Sermon -- Chapter 34. Automated DNA Hybridization and Detection / Bert Gold -- Chapter 35. The Use of Microelectronic-Based Techniques in Molecular Diagnostic Assays / Piotr Grodzinski, Michael Ward, Robin Liu, Kathryn Scott, Saul Surrey, Paolo Fortina -- Chapter 36. Human Gene Patents and Genetic Testing / Timothy Caulfield, Yann Joly -- Chapter 37. Genetic Counseling and Ethics in Molecular Diagnostics / Mary Petrou -- Chapter 38. Genetic Testing and Psychology / Andrea Farkas Patenaude -- Chapter 39. General Considerations Concerning Safety in Biomedical Research Laboratories / William E. Grizzle, Walter C. Bell, Jerry Fredenburgh -- Chapter 40. Quality Management in the Laboratory / David Burnett.
  • Molecular Genetic Pathology, Second Edition presents up-to-date material containing fundamental information relevant to the clinical practice of molecular genetic pathology. Fully updated in each area and expanded to include identification of new infectious agents (H1N1), new diagnostic biomarkers and biomarkers for targeted cancer therapy. This edition is also expanded to include the many new technologies that have become available in the past few years such as microarray (AmpliChip) and high throughput deep sequencing, which will certainly change the clinical practice of molecular genetic pathology. Part I examines the clinical aspects of molecular biology and technology, genomics. Poharmacogenomics and proteomics, while Part II covers the clinically relevant information of medical genetics, hematology, transfusion medicine, oncology, and forensic pathology. Supplemented with many useful figures and presented in a helpful bullet-point format, Molecular Genetic Pathology, Second Edition provides a unique reference for practicing pathologists, oncologists, internists, and medical genetisists. Furthermore, a book with concise overview of the field and highlights of clinical applications will certainly help those trainees, including pathology residents, genetics residents, molecular pathology fellows, internists, hematology/oncology fellows, and medical technologists in preparing for their board examination/certification.
  • This searchable database is a collection of in vivo molecular imaging agents developed for positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), ultrasound (US), computed tomography (CT), and optical imaging. MICAD, a key component of the "Molecular Libraries and Imaging" program of the NIH Roadmap, is being developed by NCBI, the National Center for Biotechnology Information".
  • Part 1. Introduction to Glyco-Experiences -- Serendipity in Scientific Discoveries: Some Examples in Glycosciences / Yuan-Chuan Lee -- My 30-Year Devotion to the N-Linked Oligosaccharide Structures / Noriko Takahashi -- Part 2. Blood Group ABH/Le-related Antigens -- Human Blood Group ABH/Ii, Lea,b,x,y, and Sialyl Lea,x Glycotopes; Internal Structures; and Immunochemical Roles of Human Ovarian Cyst Glycoproteins / Albert M. Wu -- Lewis Glyco-Epitopes: Structure, Biosynthesis, and Functions / Hui-Li Chen -- A Unique Endo-β-Galactosidase that Cleaves Both Blood Group A and B Glycotopes / Su-Chen Li, Kimberly M. Anderson and Yu-Teh Li -- Part 3. Lectins -- Recognition Roles of Mammalian Structural Units and Polyvalency in Lectin-Glycan Interactions / Albert M. Wu, Jia-Haw Liu, Tanuja Singh and Zhangung Yang -- Adhesion/Growth-Regulatory Galectins: Insights into Their Ligand Selectivity Using Natural Glycoproteins and Glycotopes / Albert M. Wu, Tanuja Singh, Jia-Hau Liu, Sabine André and Martin Lensch, et al. -- Glycotope Structures and Intramolecular Affinity Factors of Plant Lectins for Tn/T Antigens / Pierre Rougé, Willy J. Peumans, Els J. M. Van Damme, Annick Barre and Tanuja Singh, et al. -- The Five Bacterial Lectins (PA-IL, PA-IIL, RSL, RS-IIL, and CV-IIL): Interactions with Diverse Animal Cells and Glycoproteins / Nechama Gilboa-Garber, Keren D. Zinger-Yosovich, Dvora Sudakevitz, Batya Lerrer and Anne Imberty, et al. -- On the Differential Sialic Acid Specificity of Lectins from Different Parts of Saraca indica / Bishnu P. Chatterjee and Mainak Majumder -- Regulation of Lectin Production by the Human Pathogens Pseudomonas aeruginosa and Chromobacterium violaceum: Effects of Choline, Trehalose, and Ethanol / Nachman C. Garber, Keren D. Zinger-Yosovich, Dvora Sudakevitz, Itschak Axelrad and Nechama Gilboa-Garber -- Non-carbohydrate-Mediated Interaction of Lectins with Plant Proteins / Jared Q. Gerlach, Michelle Kilcoyne, Seron Eaton, Veer Bhavanandan and Lokesh Joshi -- Novel Concepts About the Role of Lectins in the Plant Cell / Els J. M. Van Dammes, Elke Fouquaert, Nausicaä Lannoo, Gianni Vandenborre and Dieter Schouppe, et al. -- Part 4. Structures and Functions of Glycolipids -- Role of Gangliosides and Plasma Membrane-Associated Sialidase in the Process of Cell Membrane Organization / Sandro Sonnino, Vanna Chigorno, Massimo Aureli, Anie Priscilla Masilamani and Manuela Valsecchi, et al. -- 9-O-Acetyl GD3 in Lymphoid and Erythroid Cells / Kankana Mukherjee, Suchandra Chowdhury, Susmita Mondal, Chandan Mandal and Sarmila Chandra, et al. -- GM3 Upregulation of Matrix Metalloproteinase-9 Possibly Through PI3K, AKT, RICTOR, RHOGDI-2, and TNF-A Pathways in Mouse Melanoma B16 Cells / Pu Wang, Xiaodong Wang, Peixing Wu, Jinghai Zhang and Toshinori Sato, et al. -- Pathological Roles of Ganglioside Mimicry in Guillain-Barré Syndrome and Related Neuropathies / Robert K. Yu, Toshio Ariga, Seigo Usuki and Ken-ichi Kaida -- Structure and Function of Glycolipids in Thermophilic Bacteria / Feng-Ling Yang, Yu-Liang Yang and Shih-Hsiung Wu -- Lipooligosaccharides of Neisseria Species: Similarity Between N. polysaccharea and N. meningitidis LOSs / Chao-Ming Tsai -- Part 5. Structures and Functions of Complex Carbohydrates -- Roles for N- and O-Glycans in Early Mouse Development / Suzannah A. Williams and Pamela Stanley -- Glycobiology in the Field of Gerontology (Glycogerontology) / Akira Kobata -- Galectins in Regulation of Apoptosis / Fu-Tong Liu, Ri-Yao Yang, Jun Saegusa, Huan-Yuan Chen and Daniel K. Hsu -- Avian and Human Influenza Virus Receptors and Their Distribution / Yasuo Suzuki -- Importance of a Factor VIIIc-Like Glycoprotein Expressed in Capillary Endothelial Cells (eFactor VIIIc) in Angiogenesis / Dipak K. Banerjee, Caroline M. Oliveira, José J. Tavárez, Viswa N. Katiyar and Subiman Saha, et al. -- Mucin O-Glycan Branching Enzymes: Structure, Function, and Gene Regulation / Pi-Wan Cheng and Prakash Radhakrishnan -- Studying Carbohydrate Self-Recognition in Marine Sponges Using Synthetic Aggregation Factor Epitopes / Johannis P. Kamerling and Adriana Carvalho de Souza -- Docking of Chitin Oligomers and Nod Factors on Lectin Domains of the LysM-RLK Receptors in the Medicago-Rhizobium Symbiosis / Pierre Rougé, Wim Nerinckx, Clare Gough, Jean-Jacques Bono and Annick Barre -- Part 6. Glycoimmunology -- O-Acetylated Sialic Acids and Their Role in Immune Defense / Roland Schauer, G. Vinayaga Srinivasan, Dirk Wipfler, Bernhard Kniep and Reinhard Schwartz-Albiez -- Sialylated and Sulfated Carbohydrate Ligands for Selectins and Siglecs: Involvement in Traffic and Homing of Human Memory T and B Lymphocytes / Reiji Kannagi, Katsuyuki Ohmori, Guo-Yun Chen, Keiko Miyazaki and Mineko Izawa, et al. -- Diversity of Natural Anti-α-Galactosyl Antibodies in Human Serum / Elwira Lisowska and Maria Duk -- Significance of Serum Glycoprotein Profiles in Spontaneous Tolerance After Liver Allograft Transplantation / Pei-Weng Wang and Tai-Long Pan -- Part 7. Glycobiology of Cancer -- Hematogenous Metastasis: Roles of CD44v and Alternative Sialofucosylated Selectin Ligands / Konstantinos Konstantopoulos and Susan N. Thomas -- Regulation of Glycosyltransferase Genes in Apoptotic Breast Cancer Cells Induced by l-PPMP and Cisplatin / Rui Ma, Elizabeth A. Hopp, N. Matthew Decker, Audrey Loucks and James R. Johnson, et al. -- Aberrant Glycosphingolipid Expression and Membrane Organization in Tumor Cells: Consequences on Tumor-Host Interactions / Alessandro Prinetti, Simona Prioni, Nicoletta Loberto, Massimo Aureli and Valentina Nocco, et al. -- Human KDN (Deaminated Neuraminic Acid) and Its Elevated Expression in Cancer Cells: Mechanism and Significance / Sadako Inoue, Ken Kitajima, Chihiro Sato and Shinji Go -- Polysialic Acid Bioengineering of Cancer and Neuronal Cells by N-Acyl Sialic Acid Precursor Treatment / Robert A. Pon, Wei Zou and Harold J. Jennings -- Part 8. Glyco Applications -- Synthesis of Hemagglutinin-Binding Trisaccharides / Cheng-Chung Wang, Suvarn S. Kulkarni, Medel Manuel L. Zulueta and Shang-Cheng Hung -- Fabrication and Applications of Glyconanomaterials / Po-Chiao Lin, Avijit Kumar Adak and Chun-Cheng Lin -- Glycan Arrays to Decipher the Specificity of Plant Lectins / Els J. M. Van Damme, David F. Smith, Richard Cummings and Willy J. Peumans -- Targeting C-Type Lectin for the Treatment of Flavivirus Infections / Szu-Ting Chen, Yi-Ling Lin, Ming-Ting Huang, Ming-Fang Wu and Shie-Liang Hsieh.
  • Speakers at the Symposium / Hartmann, D. -- Hematopoietic stem cell aging and fate decision / Illing, A., Ju, Z. -- Alterations of systemic environment impair stem cell function during aging / Song, Z., Ju, Z. -- Novel insights into regulation of stem cell aging by aging of the niche and alterations in systemic factors / Geiger, H. -- Aging and hematopoietic malignancies / Gompf, A. -- Intestinal stem cell aging / Sperka, T., Rudolph, K.L. -- Molecular mechanisms of aging in muscle stem cells / Tümpel, S. -- Free radicals and stem cell aging / Guachalla, L.M. -- DNA damage, checkpoint responses, and cell cycle control in aging stem cells / Sperka, T., Nalapareddy, K., Rudolph, K.L.
  • Theories of carcinogenesis -- Physioloigic correlates of malignancy -- Cell division and survival -- Cellular senescence -- Invasiveness -- DNA repair -- Epigenetic regulation of cancer-associated gene products -- Interaction of the groups of cancer-related gene products -- Structural growth control -- The organ preference of metastasis formation -- Angiogenesis -- Interactions with the immune system -- Endocrine dysregulation -- Dormancy and minimal residual disease -- Epithelial tumors -- Hematologic malignancies -- Mesenchymal tumors -- Neurologic tumors -- Tumors of serous cavities -- Embryonic tumors.
  • Sect. I. Molecular Biology -- Ch. 1. Parasite genomics -- Ch. 2. RNA processing in parasitic organisms: trans-splicing and RNA editing -- Ch. 3. Transcription -- Ch. 4. Post-transcriptional regulation -- Ch. 5. Antigenic variation in African trypanosomes and malaria -- Ch. 6. Genetic and genomic approaches to the analysis of leishmania virulence -- Sect. II. Biochemistry and Cell Biology: Protozoa -- Ch. 7. Energy metabolism -- Ch. 8. Amino acid and protein metabolism -- Ch. 9. Purine and pyrimidine transport and metabolism -- Ch. 10. Trypanosomatid surface and secreted carbohydrates -- Ch. 11. Intracellular signaling -- Ch. 12. Plastids, mitochondria, and hydrogenosomes -- Sect. III. Biochemistry and Cell Biology: Helminths -- Ch. 13. Helminth surfaces: structural, molecular and functional properties -- Ch. 14. Carbohydrate and energy metabolism in parasitic helminths -- Ch. 15. Neurotransmitters -- Sect. IV. Medical Applications -- Ch. 16. Drug resistance in parasites -- Ch. 17. Medical implications of molecular parasitology.
  • 2012 ClinicalKey
    Molecular Medicine is the application of genetic or DNA-based knowledge to the modern practice of medicine. Molecular Medicine, 4e, provides contemporary insights into how the genetic revolution is influencing medical thinking and practice. The new edition includes recent changes in personalized medicine, new growth in omics and direct-to-consumer DNA testing, while focusing on advances in the Human Genome project and implications of the advances in clinical medicine. Graduate students, researchers, clinicians and allied health professionals will appreciate the background history and clinical application of up-to-date molecular advances. Extensively revised to incorporate the results of the Human Genome Project, it provides the latest developments in molecular medicineThe only book in Molecular Medicine to reach its fourth edition Identifies current practice as well as future developmentsPresents extensive tables, well presented figures and resources for further understanding.
  • Genetic analysis of bacterial pathogenesis -- Genetic exchance in bacteria and the modular stucture of mobile DNA elements -- Genomics and the use of genomic tools to study pathogenic bacteria -- Pathogenicity islands and bacterial virulence -- Capsules -- Bacterial cell walls -- Mechanisms of bacterial adhesion and consequences of attachment -- Bacterial invasion into non-phagocytic cells -- Bacterial protein secretion mechanisms -- Toxins as host cell modulators -- Quorum sensing: coordinating group behavior through intercellular signals -- The role of sigma factors in regulating bacterial stress responses and pathogenesis -- Two-component regulatory systems -- Oxidative stress systems in bacteria: four model organisms -- Bacterial biowarfare agents.
  • Basics of molecular biology -- Molecular pathology methods -- Genetic counseling -- Pedigree analysis and risk assessment -- Bayesian analysis -- Developmental disabilities -- Neuromuscular diseases -- Molecular genetic testing for metabolic disorders -- Fibroblast growth factor receptor-related skeletal disorders -- Cystic fibrosis -- Deafness -- Coagulation disorders -- Hematologic disorders : hemochromatosis, hemoglobinopathies, and Rh incompatibility -- Cardiovascular disease -- Neurodegenerative disorders -- Skin and connective tissue disorders -- Inherited breast cancer -- Familial adenomatous polyposis and Turcot and Peutz-Jeghers syndromes -- Hereditary nonpolyposis colorectal cancer -- Multiple endocrine neoplasia syndromes -- The neurofibromatoses -- TP53 mutation and Li-Fraumeni syndrome -- von Hippel-Lindau disease -- Breast cancer -- Urothelial carcinoma -- Sarcomas -- Gliomas -- Molecular detection of occult tumor cells -- Microarray studies (Beyond histology) -- Acute myeloid leukemia -- Acute lymphoblastic leukemia -- B-cell lymphomas -- T-cell lymphomas -- Lymphoproliferations of immunodeficiency -- Myeloproliferative disorders and myelodysplastic syndromes -- Human immunodeficiency virus type 1 -- Hepatitis B and C viruses -- Viral infections in transplant patients -- Viral infections of the central nervous system -- Sexually transmitted diseases -- Respiratory pathogens -- Bacterial pathogens -- Mycobacterial infections -- Forensic DNA typing -- Parentage and relationship testing -- Assessment of chimerism in the setting of allogenic hematopoietic cell transplantation -- Specimen identification through DNA analysis -- Molecular HLA typing -- Molecular pathology laboratory management -- From research to clinical practice.
  • "This book reviews the latest developments in pharmacognosy, introduces a series of new views and insights, presents the hotspots and focus of the field of study on molecular pharmacognosy, and predicts a new direction of study on the resource science of TCM. Furthermore, the book also provides an open communications platform for the development of molecular pharmacognosy."--Publisher.
  • The application of modern molecular genetic and biologic techniques to infectious disease epidemiology dramatically improves measurement of disease and putative risk factors increasing our ability to detect and track outbreaks, identify risk factors and detect new infectious agents. However, integration of these techniques into epidemiologic studies also poses new challenges in the design, conduct, and analysis. We examine these opportunities and methodologic challenges giving specific examples. The book will be written for the reader with limited understanding of genetics, biology and epidemiology. *Presents the key points of consideration when integrating molecular biology and epidemiology *Discusses how using molecular tools in epidemiologic research affects program design and conduct *Considers the ethical concerns that arise in molecular epidemiologic studies *Provides a context for understanding and interpreting scientific literature as a foundation for subsequent practical experience in the laboratory and in the field.
  • Part 1. General consideration on microorganism typing methods -- Molecular Epidemiology / Amy E. Seitz and D. Rebecca Prevots -- Part 2. Gastrointestinal Pathogens -- Enterococcus / Lúcia Martins Teixeira and Vânia Lúcia Carreira Merquior -- Listeria monocytogenes / Todd J. Ward -- Enterobacteriaceae / Steven L. Foley, Aaron M. Lynne and Rajesh Nayak -- Molecular Typing of Vibrio cholerae: Imprints in the Epidemiology of Cholera / T. Ramamurthy, A. K. Mukhopadhyay, R. K. Nandy and G. Balakrish Nair -- Molecular Typing of Clostridium difficile / Andrej Weintraub and Carl Erik Nord -- Oral and Intestinal Bacteroidetes / Marina C. Claros and Georg Conrads -- Part 3. Oral and Respiratory Pathogens -- Streptococci / Lesley McGee and Bernard Beall -- Molecular Typing of Streptococcus mutans / Kazuhiko Nakano, Ichiro Nakagawa, Satu Alaluusua and Takashi Ooshima -- Genotyping of Periodontal Anaerobic Bacteria in Relationship to Pathogenesis / Masae Kuboniwa and Atsuo Amano -- Molecular Typing of Nontuberculous Mycobacteria / Jakko van Ingen and Dick van Soolingen -- Molecular Typing of Neisseria meningitidis / Muhamed-Kheir Taha and Ala-Eddine Deghmane -- Molecular Typing in Bacterial Infections Haemophilus spp. / Marina Cerquetti -- Moraxella / Nevada M. Pingault and Thomas V. Riley -- Legionella pneumophila Typing / Christophe Ginevra -- Mycoplasma and Ureaplasma / Ken B. Waites, Li Xiao, Vanya Paralanov, Rose M. Viscardi and John I. Glass -- Corynebacterium diphtheriae / Igor Mokrousov -- Burkholderia / Pavel Drevinek and Eshwar Mahenthiralingam -- Part 4. Urogenital Pathogens -- Treponema / Allan Pillay -- Chlamydiaceae / Troy Skwor and Deborah Dean -- Part 5. Vector borne Pathogens -- Borreliae / Dionysios Liveris, Klára Hanincová and Ira Schwartz -- Erysipelothrix / Yumiko Imada -- Part 6. Pathogens causing Healthcare-Associated Infection -- Staphylococci / Jodi A. Lindsay -- Molecular Typing Methods for the Genus Pseudomonas / Balázs Libisch -- Part 7. Emerging and Reemerging Pathogens -- Acinetobacter baumannii / Lenie Dijkshoorn -- Molecular Typing of Coxiella burnetii: A Review of Available Methods with Major Focus on PCR-Based Techniques / V. Boldis, E. Spitalska and R. Toman.
  • "Written for chemists, physicists, molecular biologists, and students in related fields, this reference covers information presently available on the specific properties of metallic nanoparticles, and compares their properties with those related to nanoobjects formed by biological molecules. It also discloses details of formation and physic-chemical peculiarities of the DNA nanostructures and DNA-based nanoconstructions. Timely in publication, the reference contains more DNA physics and molecular biology than other published titles. Authors discuss how nucleic acid molecules and their complexes with chemical and biologically active compounds are of great interest in the development of various nanoscale systems and devices of practical importance"-- Provided by publisher.
  • Neurofibromatosis type 1 (NF1), caused by mutational inactivation of the NF1 tumour suppressor gene, is one of the most common dominantly inherited human disorders, affecting 1 in 3000 individuals worldwide. This book presents in concise fashion, but as comprehensively as possible, our current state of knowledge on the molecular genetics, molecular biology and cellular biology of this tumour predisposition syndrome. Written by internationally recognized experts in the field, the 44 chapters that constitute this edited volume provide the reader with a broad overview of the clinical features of the disease, the structure and expression of the NF1 gene, its germ line and somatic mutational spectra and genotype-phenotype relationships, the structure and function of its protein product (neurofibromin), NF1 modifying loci, the molecular pathology of NF1-associated tumours, animal models of the disease, psycho-social aspects and future prospects for therapeutic treatment.Neurofibromatosis Type 1: Molecular and Cellular Biology will be of great value to medical geneticists, molecular and cellular biologists, oncologists, dermatologists, neurologists, genetic counsellors and general practitioners alike.
  • Methods and tools in molecular epidemiology -- Molecular typing of bacterial pathogens: a tool for the epidemiological study and control of infectious diseases -- Contribution of population genetics -- Molecular epidemiology and evolutionary genetics of infectious diseases -- Population genetics and molecular epidemiology of infectious diseases -- Contribution of population and evolutionary epidemiology -- Modelling the dynamics of host-parasite interactions: basic principles -- Evolution of virulence: intuitions and models -- Case studies -- Molecular epidemiology of tuberculosis -- Pneumocystis molecular phylogeny: a way to understand both pneumocystosis natural histry and host taxonomy -- Hantavirus genetic diversity -- New integrations -- Nasal carriage of methicillin-resistant coagulase-negative staphylocococci: a reservoir of mecA gene for Staphylococcus aureus -- Molecular knowledge of mechanisms of helminth resistance: importance for diagnostic and epidemiology -- Molecular epidemiology of disease resistance genes with perspectives for researches on biological invasions and hybrid zones -- How does biodiversity influence the ecology of infectious disease? -- Epidemiological interaction at the wildlife/livestock/human interface: can we anticipate emerging infectious diseases in their hotspots? A framework for understanding emerging diseases processes in their hot spots.
  • Introduction: next generation sequencing technology and cancer research -- The majority of total nuclear-encoded non-ribosomal RNA in a human cell is dark matter unannotated RNA -- Total RNA-seq of breast cancer in hypoxia -- Altered antisense-to-sense transcript ratios in breast cancer -- Identification of piRNAs in Hela cells by massive parallel sequencing -- Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia -- Whole-Exome Sequencing Identifies FAM20A Mutations as a Cause of Amelogenesis Imperfecta and Gingival Hyperplasia Syndrome -- Whole-exome sequencing in CIC and IDH1/2 contributing to human oligodendroglioma -- Genetic and structural variation in the gastric cancer kinome revealed through targeted deep sequencing -- Tumour evolution inferred by single-cell sequencing -- Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq -- Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNASeq analysis -- Whole genome DNA methylation analysis based on high throughput sequencing technology -- Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors -- High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq -- MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action -- Genome-wide identification of polycomb-associated RNAs by RIP-seq -- Single-molecule sequencing: sequence methods to enable accurate quantisation -- Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells -- Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA -- The genome information process for cancer research: the challenge and perspective.
  • Nitric oxide methods and protocols 2011
    Springer Protocols
    Nitric oxide physiology and pathology / David G. Hirst and Tracy Robson -- Ionizing radiation-induced DNA strand breaks and [gamma]-H2AX foci in cells exposed to nitric oxide / Kai Rothkamm and Susanne Burdak-Rothkamm -- Determination of S-nitrosothiols in biological fluids by chemiluminescence / Enika Nagababu and Joseph M. Rifkind -- Measurement of nitrite in blood samples using the ferricyanide-based hemoglobin oxidation assay / Barbora Piknova and Alan N. Schechter -- Selective fluorescent activation for bioimaging the expression of nitric oxide in cellular and in vivo systems / Junfeng Zhang and Hao Hong -- Real-time measurement of murine hippocampus NO levels in response to cerebral ischemia/reperfusion / Xiaoxiang Zheng, Kezhou Liu, and Yong Yang -- Detection of low levels of nitric oxide using an electrochemical sensor / Yong Chool Boo ... [et al.] -- Determination of the scavenging capacity against reactive nitrogen species by automatic flow injection-based methodologies / Marcela A. Segundo ... [et al.] -- Aqueous measurement of nitric oxide using membrane inlet mass spectrometry / David N. Silverman and Chingkuang Tu -- Quantum cascade laser technology for the ultrasensitive detection of low-level nitric oxide / Angela Elia ... [et al.] -- Determination of in vivo nitric oxide levels in animal tissues using a novel spin trapping technology / Anatoly F. Vanin and Alexander A. Timoshin -- [Beta] cell protection by inhibition of iNOS through lentiviral vector-based strategies / Sean O. Hynes, Cillian McCabe, and Timothy O'Brien -- Characterization of nitric oxide delivery systems produced by various nanotechnologies / Chi H. Lee -- Nitric oxide releasing nanoparticle synthesis and characterization / George Han, Adam J. Friedman, and Joel M. Friedman -- NOS antagonism using viral vectors as an experimental strategy : implications for in vivo studies of cardiovascular control and peripheral neuropathies / Beihui Liu ... [et al.]
  • Nuclear organization and function 2010
    Cold Spring Harb Lab Press
    Chromatin modifications and gene expressions -- Transcription and beyond -- DNA replication and genome integrity -- Reprogramming and differentiation -- Heterochromatin formation and gene silencing -- Nuclear bodies and RNA biology -- Chromosome structure and mitosis -- Chromatin structure and organization -- Nuclear periphery.
  • Ch. 1. Molecular biology of Omega-3 chains as structural lipids : many central questions remain unanswered -- Ch. 2. Darwinian selection of the fittest membrane lipids : from archaeal isoprenoids to DHA-enriched rhodopsin disks -- Ch. 3. Coevolution of DHA membranes and their proteins -- Ch. 4. Convergent evolution of DHA/EPA biosynthetic pathways -- Ch. 5. Membrane evolution in a marine bacterium : capitalizing on DHA for energy conservation in seawater -- Ch. 6. Evolution of DHA membranes in human neutrons -- Ch. 7. DHA/EPA chains as powerful membrane antifreeze -- Ch. 8. DHA as a mediocre permeability barrier against cations : water wire theory -- Ch. 9. DHA/EPA membranes as targets of oxidative damage -- Ch. 10. Bacteria : environmental modulation of membrane lipids for bioenergetic gain -- Ch. 11. Chloroplasts : harnessing DHA/EPA for harvesting light in the sea -- Ch. 12. Mitochondria : DHA-cardiolipin boosts energy output -- Ch. 13. Sperm : essential roles of DHA lead to development of a mechanical stress hypothesis -- Ch. 14. DHA/EPA mutualism between bacteria and marine animals -- Ch. 15. Membrane adaptations for an oily environment : lessons from a petroleum-degrading bacterium -- Ch. 16. Lessons from yeast : phospholipid conformations are important in winemaking -- Ch. 17. DHA principle applied to global warming -- Ch. 18. DHA principle applied to molecular farming -- Ch. 19. DHA/unsaturation theory of aging -- Ch. 20. DHA principle applied to neurodegenerative diseases -- Ch. 21. Dietary DHA in prevention of colon cancer : how a risk to the cell benefits the organism.
  • Organelle proteomics 2008
    Springer Protocols
    Analysis of organelles by on-line two-dimensional liquid chromatography-tandem mass spectrometry / Edwin P. Romijn and John R. Yates III -- Purification and proteomic analysis of chloroplasts and their sub-organellar compartments / Daniel Salvi ... [et al.] -- Proteomic analysis of the stacked golgi complex / Mark S. Lowenthal, Kathryn E. Howell, and Christine C. Wu -- Purification of Saccharomyces cerevisiae mitochondria by zone electrophoresis in a free flow device / Hans Zischka ... [et al.] -- Preparation of respiratory chain complexes from Saccharomyces cerevisiae wild-type and mutant mitochondria : activity measurement and subunit composition analysis / Claire Lemaire and Geneviève Dujardin -- Mitochondrial proteomics : analysis of a whole mitochondrial extract with two-dimensional electrophoresis / Thierry Rabilloud -- Purification and proteomic analysis of the mouse liver mitochondrial inner membrane / Sandrine Da Cruz and Jean-Claude Martinou -- Subcellular fractionation and proteomics of nuclear envelopes / Laurence Florens, Nadia Korfali, and Eric C. Schirmer -- Purification and proteomic analysis of a nuclear-insoluble protein fraction / Tsuneyoshi Horigome, Kazuhiro Furukawa, and Kohei Ishii -- Preparation methods of human metaphase chromosomes for their proteome analysis / Kiichi Fukui, Hideaki Takata, and Susumu Uchiyama -- Purification and proteomic analysis of plant plasma membranes / Erik Alexandersson ... [et al.] -- Protocol to enrich and analyze plasma membrane proteins from frozen tissues / Jacek R. Wiśniewski -- Proteomic characterization of membrane protein topology / Adele R. Blackler and Christine C. Wu -- Free flow isoelectric focusing : a method for the separation of both hydrophilic and hydrophobic proteins of rat liver peroxisomes / Markus Islinger and Gerhard Weber -- Use of gas-phase fractionation to increase protein identifications : application to the peroxisome / Jacob Kennedy and Eugene C. Yi -- Purification and proteomic analysis of lysosomal integral membrane proteins / Huiwen Zhang ... [et al.] -- Affinity purification of soluble lysosomal proteins for mass spectrometric identification / Sylvie Kieffer-Jaquinod ... [et al.] -- Purification and proteomic analysis of synaptic vesicles / Holly D. Cox and Charles M. Thompson -- Purification and proteomics analysis of pancreatic zymogen granule membranes / Xuequn Chen and Philip C. Andrews -- Isolation and proteomic analysis of chlamydomonas centrioles / Lani C. Keller and Wallace F. Marshall -- Purification and proteomic analysis of 20S proteasomes from human cells / Marie-Pierre Bousquet-Dubouch ... [et al.] -- Characterization of E. coli ribosomal particles : combined analysis of whole proteins by mass spectrometry and of proteolytic digests by liquid chromatography-tandem mass spectrometry / Isabelle Iost ... [et al.] -- Assessment of organelle purity using antibodies and specific assays : the example of the chloroplast envelope / Daniel Salvi ... [et al.] -- Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes / Marcello Marelli, Alexey I. Nesvizhskii, and John D. Aitchison -- Determination of genuine residents of plant endomembrane organelles using isotope tagging and multivariate statistics / Kathryn S. Lilley and Tom P.J. Dunkley -- Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins / Wei Yan, Daehee Hwang, and Ruedi Aebersold -- Use of transcriptomic data to support organelle proteomic analysis / Wallace F. Marshall.
  • A brief overview of molecular genetics -- An overview of information theory -- More on molecular genetics -- More on information theory -- An outline of error-correcting codes -- DNA is an ephemeral memory -- A toy living world -- Subsidiary hypothesis, nested system -- Soft codes -- Biological reality conforms to the hypotheses -- Identification of genomic codes.
  • p53 2011
    TP53 mutations in human cancers : selection versus mutagenesis / Magali Olivier, Audrey Petitjean, Claude Caron de Fromentel, and Pierre Hainaut -- Lessons on p53 from mouse models / Dadi Jiang and Laura D. Attardi -- TP63, TP73 : the guardian's elder brothers / Stephanie Courtois, Pierre Hainaut and Claude Caron de Fromentel -- The regulation of p53 protein function by phosphorylation / Nicola J. Maclaine and Theodore Hupp -- The p53-Mdm2 loop : a critical juncture of stress response / Yaara Levav-Cohen, Zehavit Goldberg, Osnat Alsheich Bartok, Valentina Zuckerman, Sue Haupt and Ygal Haupt -- Cooperation between MDM2 and MDMX in the regulation of p53 / Jeremy Blaydes -- Regulation and function of the original p53-inducible p21 gene / Jennifer A. Fraser -- p53 localization / Carl G. Maki -- Modes of p53 interactions with DNA in the chromatin context / Vladana Vukojevic, Tatiana Yakovleva, and Georgy Bakalkin -- p53's dilemma in transcription : analysis by microarrays / Karuppiah Kannan, Gideon Rechavi and David Givol -- Tumor viruses and p53 / Nobuo Horikoshi -- p53 and immunity / Vikram Narayan, Sarah E. Meek and Kathryn L. Ball.
  • PCR cloning protocols. 2nd ed. 2002
    Springer Protocols
  • PCR mutation detection protocols 2002
    Springer Protocols
  • Purification of PDE6 isozymes from mammalian retina / Dana C. Pentia ... [et al.] -- Cyclic guanosine 5'-monophosphate binding to the regulatory GAF domains of photoreceptor phosphodiesterase / Rick H. Cote -- Renaturation of the catalytic domain of PDE4A expressed in escherichia coli as inclusion bodies / Wito Richter, Thomas Hermsdorf, and Dietrich Dettmer -- Determining the subunit structure of phosphodiesterases using gel filtration and sucrose density gradient centrifugation / Wito Richter -- Crystallization of cyclic nucleotide phosphodiesterases / Hengming Ke, Qing Huai, and Robert X. Xu -- Generation of PDE4 knockout mice by gene targeting / S.-L. Catherine Jin, Anne M. Latour, and Marco Conti -- Immunoprecipitating PDE2 phosphorylated and inactivated by an associated protein kinase / J. Kelley Bentley -- Investigation of extracellular signal-regulated kinase 2 mitogen-actived protein kinase phosphorylation and regulation of activity of PDE4 cyclic adenosine monophosphate-specific phosphodiesterases / Elaine V. Hills, Miles D. Houslay, and George S. Baillie -- Radiolabeled ligand binding to the catalytic or allosteric sites of PDE5 and PDE11 / James L. Weeks ... [et al.] -- Analysis of dimerization determinants of the PDE6 catalytic subunits / Khakim G. Muradov, Kimberley K. Boyd, and Nikolai O. Artemyev -- Interaction between catalytic and inhibitory subunits of PDE6 / Nikolai O. Artemyev -- Purification, reconstitution on lipid vesciles and assays of PDE6 and its activator G protein, transducin -- Theodore G. Wensel, Feng He, and Justine A. Malinski. Study of cyclic adenosine monophosphate microdomains in cells / Marco Mongillo ... [et al.] -- High-resolution measurements of cyclic adenosine monophosphate signals in 3D microdomains / Jeffrey W. Karpen and Thomas C. Rich -- Cygnets : in vivo characterization of novel cGMP indicators and in vivo imaging of intracellular cGMP / Akira Honda ... [et al.] -- High-throughput screening of phosphodiesterase activity in living cells / Thomas C. Rich and Jeffrey W. Karpen -- Assessment of phosphodiesterase isozyme contribution in cell and tissue extracts / Thèrése Keravis, Rima Thaseldar-Roumié, and Claire Lugnier -- Localization of the cyclic guanosine 3', 5'-monophosphate-hydrolysing phosphodiesterase type 9 in rat brain by nonradioactive in situ hybridization / Wilma C.G. Van Staveren and Marjanne Markerink-Van Ittersum -- Determination of Ca2+/calmodulin-stimulated phosphodiesterase activity in intact cells / Chen Yan -- Adenovirus-mediated overexpression of murine cyclic nucleotide phosphodiesterase 3B / Faiyaz Ahmad ... [et al.] -- Identification of promoter elements in the 5'-flanking region of the murine cyclic nucleotide phosphodiesterase 3B gene / Hanguan Liu ... [et al.] --
  • Phylogenomics 2008
    Springer Protocols
    From gene-scale to genome-scale phylogenetics : the data flood in, but the challenges remain / Antonis Rokas and Stylianos Chatzimanolis -- Phylogenomic analysis of chromosome sorting and painting / Roscoe Stanyon and Gary Stone -- FISH for mapping single copy genes / Terje Raudsepp and Bhanu P. Chowdhary -- Construction of radiation hybrid panels / John E. Page and William J. Murphy -- Survey sequencing and radiation hybrid mapping to construct comparative maps / Christophe Hitte ... [et al.] -- Construction of high-resolution comparative maps in mammals using BAC-end sequences / Denis M. Larkin and Harris A. Lewin -- Amniote phylogenomics : testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale sequences from reptiles / Andrew M. Shedlock, Daniel E. Janes, and Scott V. Edwards -- Comparative physical mapping : universal overgo hybridization probe design and BAC library hybridization / James W. Thomas -- Phylogenomic resources at the UCSC Genome Browser / Kate Rosenbloom ... [et al.] -- Computational tools for the analysis of rearrangements in mammalian genomes / Glenn Tesler and Guillaume Bourque -- Computational reconstruction of ancestral DNA sequences / Mathieu Blanchette ... [et al.] -- Sequencing and phylogenomic analysis of whole mitochondrial genomes of animals / Rafael Zardoya and Mónica Suárez -- Retroposons : genetic footrpints on the evolutionary paths of life / Hidenori Nishihara and Norihiro Okada -- LINE-1 elements : analysis by FISH and nucleotide sequences / Paul D. Waters ... [et al.] -- Identification of cryptic sex chromosomes and isolation of X- and Y-borne genes / Paul D. Waters ... [et al.]
  • pt. 1. Principles of biophysical inquiry -- pt. 2. Foundations -- pt. 3. Building a model of biomolecular structure -- pt. 4. Function and action biological state space -- pt. 5. Methods for the measuring structure and function -- pt. 6. Physical constants.
  • Part I. Overview of Chloride Transporters and Channels -- Part II. Current Methods for Studying Chloride Regulation -- Part III. From Cloning to Structure, Function and Regulation of Chloride Transporters and Channels -- Part IV. Cation-Chloride Cotransporters in Neural Function and Dysfunction -- Part V. Cation-Chloride Cotransport in Choroid Plexus and Blood-Brain Barrier.
  • Drs. Gerhard Meisenberg and William H. Simmons covers the latest developments in the field, including genome research, the molecular basis of genetic diseases, techniques of DNA sequencing and molecular diagnosis, and more. An updated and expanded collection of figures and access to the fully searchable text, USMLE test questions, clinical case studies and more makes this the resource for understanding all aspects of biochemistry needed in medicine. Tap into the most up-to-date coverage of new developments in genome research, the molecular basis of genetic diseases, techniques of DNA sequencing and molecular diagnosis, RNA interference as a mechanism both for regulation of gene expression and for anti-viral defense, and more. Gain a clear visual understanding through new and updated figures that provide current and relevant guidance. Make the link between basic science and clinical medicine with new Clinical Example boxes in nearly every chapter. Focus on the most essential biochemistry principles and how they apply to clinical medicine.
  • Section I. Introduction of cancer biology and cancer genetics -- Section II. Molecular techniques -- Section III. Molecular tests and cancer management -- Section IV. Molecular diagnostics of common malignancies -- Section V. Molecular basis of cancer therapeutics -- Section VI. Personalized medicine and targeted therapy of cancer -- Section VII. Future of molecular diagnostics and personalized cancer medicine.
  • Prion protein protocols 2008
    Springer Protocols
    Cell culture models to unravel prion protein function and aberrancies in prion diseases / Katarina Bedecs -- Investigation of PrPc metabolism and function in live cells : methods for studying individual cells and cell populations / Cathryn L. Haigh and David R. Brown -- Immunodetection of PrPsc using western and slot blotting techniques / Hanny Gyllberg and Kajsa Löfgren -- Assaying prions in cell culture : the standard scrapie cell assay (SSCA) and the scrapie cell assay in end point format (SCEPA) / Sukhvir P. Mahal ... [et al.] -- Generation of cell lines propagating infectious prions and the isolation and characterization of cell-derived exosomes / Laura J. Vella and Andrew F. Hill -- Neurotoxicity of prion peptides on cultured cerebellar neurons / Giuseppe D. Ciccotosto, Roberto Cappai, and Anthony R. White -- Understanding the nature of prion diseases using cell-free assays / Victoria A. Lawson -- Methods for conversion of prion protein into amyloid fibrils / Leonid Breydo, Natallia Makarava, and Ilia V. Baskakov -- Amplification of purified prions in vitro / Surachai Supattapone, Nathan R. Deleault, and Judy R. Rees -- Expression and purification of full-length recombinant PrP of high purity / Natallia Makarava and Ilia V. Baskakov -- Analysis of PrP conformation using circular dichroism / Sen Han and Andrew F. Hill -- Effect of copper on the de novo generation of prion protein expressed in Pichia pastoris / Carina Treiber -- Biophysical investigations of the prion protein using electron paramagnetic resonance / Simon C. Drew and Kevin J. Barnham -- Molecular diagnosis of human prion disease / Jonathan D.F. Wadsworth ... [et al.] -- Analysis of endogenous PrPc processing in neuronal and non-neuronal cell lines / Victoria Lewis and Steven J. Collins -- Molecular typing of PrPres in human sporadic CJD brain tissue / Victoria Lewis ... [et al.] -- Transgenic mouse models of prion diseases / Glenn C. Telling -- Quantitiative bioassay of surface-bound prion infectivity / Victoria A. Lawson.
  • Introduction -- Type I Toxin - Antitoxin Systems: Hok/Sok and Fst -- Novel Type I Toxin - Antitoxin Systems -- Type II TA Loci: The Ccdab and Parde Families -- Type II TA Loci: The Relbe Family -- Type II TA Loci: The Unusual Mqsra Locus -- Type II TA Loci: The Mazef Family -- Type II TA Loci: Vapbc and Other TA Loci In Mycobacteria -- Type II TA Loci: Phd Doc Family -- Type II TA Loci: The Fic Family -- Type II TA Loci, Hipab And Persisters -- Type II TA Loci: Zeta/Pezt Family -- Type II Loci: Phylogeny -- Type III TA Loci -- TA Loci Encoded By Plasmids -- TA Loci in Archaea -- TA Loci in Mycobacterium Tuberculosis -- TA Loci in Streptococcus Pneumoniae -- Biotechnological and Medical Exploitations Of TA Genes and Their Components.
  • A digest of protein purification -- Gel-filtration chromatography -- Immunoaffinity chromatography -- Avoiding proteolysis during protein chromatography -- Scale-up of protein purification : Downstream processing issues -- Phage display : A powerful technology for the generation of high specificity affinity reagents from alternative immune sources -- Engineering protein stability -- Microfluidics in protein chromatography -- Tagging recombinant proteins to enhance solubility and aid purification -- Storage and lyophilisation of pure proteins -- Differential precipitation and solubilization of proteins -- Ion-exchange chromatography : Basic principles and application to the partial purification of soluble mammalian prolyl oligopeptidase -- Protein quantitation and analysis of purity -- Purification of proteins fused to glutathione S-transferase -- Purification of proteins fused to maltose-binding protein -- Purification of proteins from baculovirus-infected insect cells -- Purification of poly-histidine-tagged proteins -- Immobilized metal affinity chromatography/reversed-phase enrichment of phosphopeptides and analysis by cid/etd tandem mass spectrometry -- Tag removal by site-specific cleavage of recombinant fusion proteins -- Purification of antibodies using affinity chromatography -- Optimized generation of high-affinity, high-specificity single-chain Fv antibodies from multiantigen immunized chickens -- Measuring protein-protein interactions using biacore -- Ultra-performance liquid chromatography-mass spectrometry of proteins -- Hydrophobic interaction chromatography -- Fast protein liquid chromatography -- Shotgun proteomics : A qualitative approach applying isoelectric focusing on immobilized pH gradient and LC-MS/MS -- Shotgun proteomics : A relative quantitative approach using off-gel electrophoresis and LC-MS/MS -- Clinical proteomics : Liquid chromatography-mass spectrometry purification systems -- Strategies for the purification of membrane proteins -- A multi-step chromatographic strategy to purify three fungal endo-[beta]-glucanases.
  • "This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression"--Publisher's description.
  • Design of structural elementary motifs. Structure and stability of the [alpha]-helix: lessons for design / Neil Errington, Teuku Iqbalsyah, and Andrew J. Doig. De novo design of monomeric [beta]-hairpin and [beta]-sheet peptides / David Pantoja-Uceda, Clara M. Santiveri, and M. Angeles Jiménez. De novo proteins from binary-patterned combinatorial libraries / Luke H. Bradley, Peter P. Thumfort, and Michael H. Hecht. Non-protein amino acids in the design of secondary structure scaffolds / Radhakrishnan Mahalakshmi and Padmanabhan Balaram. Design and synthesis of [beta]-peptides with biological activity / Marc J. Koyack and Richard P. Cheng -- Design of entire proteins and protein complexes. Design of miniproteins by the transfer of active sites onto small-size scaffolds / Franc̦ois Stricher, Loïc Martin, and Claudio Vita. Consensus design as a tool for engineering repeat proteins / Tommi Kajander, Aitziber L. Cortajarena, and Lynne Regan. Multiple sequence alignment as a guideline for protein engineering strategies / Alan R. Davidson. Sequence search methods and scoring functions for the design of protein structures / Hocine Madaoui, Emmanuelle Becker, and Raphael Guerois. Prediction of protein-protein interaction based on structure / Gregorio Fernandez-Ballester and Luis Serrano. Electrostatic design of protein-protein association rates / Gideon Schreiber, Yossi Shaul, and Kay E. Gottschalk -- Design of amyloidogenic polypeptides and amyloid inhibitors. Peptide model systems for amyloid fiber formation: design strategies and validation methods / Alexandra Esteras-Chopo, María Teresa Pastor, and Manuela López de la Paz. Protein misfolding disorders and rational design of antimisfolding agents / Lisbell D. Estrada, June Yowtak, and Claudio Soto.
  • Protein engineering protocols 2006
    Springer Protocols
  • Protein folding protocols 2006
    Springer Protocols
  • Protein misfolding and celluar stress : an overview / Niels Gregersen and Peter Bross -- Protein aggregation diseases : toxicity of soluble prefibrillar aggregates and their clinical significance / Massimo Stefani -- Consequences of stress in the secretary pathway : the ER stress response and its role in the metabolic syndrome / Martin Schröder and Louise Sutcliffe -- What role does mitochondrial stress play in neurodegenerative diseases? / Alicia Mae Pickrell and Carlos Torres Moraes -- Autophagy in disease / Dalibor Mijaljica, Mark Prescott, and Rodney J. Devenish -- Mitophagy and mitoptosis in disease processes / Dalibor Mijaljica, Mark Prescott, and Rodney J. Devenish -- Cellular stress and protein misfolding during aging / Rajiv Vaid Basaiawmoit and Suresh I.S. Rattan -- Measuring consequences of protein misfolding and cellular stress using OMICS techniques / Peter Bross ... [et al.] -- Production of cells with targeted integration of gene variants of human ABC transporter for stable and regulated expression using the Flp recombinase system / Kanako Wakabayashi-Nakao ... [et al.] -- Stress response profile in human fribroblasts exposed to heat shock or oxidative stress / Christina Bak Pedersen and Niels Gregersen -- Examining ubiquitinated protein aggregates in tissue sections / Natalia A. Kaniuk and John H. Brumell -- Determination of proteasomal activities / Cristovao F. Lima and Suresh I.S. Rattan -- Measurement of autophagy in cells and tissues / Isei Tanida and Satoshi Waguri -- Transcription factor sequestration by polyglutamine proteins / Tomoyuki Yamanaka and Nobuyuki Nukina -- Biological membranes as protein aggregation matrices and targets of amyloid toxicity / Monica Bucciantini and Cristina Cecchi -- Measurement of mitochondrial ROS production / Anatoly A. Starkov -- In vivo detection of oxidized proteins : a practical approach to tissue-derived mitochondria / Francesca Maltecca and Giorgio Casari -- Measurement of oxidized/reduced glutathione ratio / Joshua B. Owen and D. Allan Butterfield -- Determination of altered mitochondria ultrastructure by electron microscopy / Shoichi Sasaki -- Assessing bad sub-cellular localization under conditions associated with prevention or promotion of mitochondrial permeability transition-dependent toxicity / Liana Cerioni and Orazio Cantoni -- A cellular viability assay to monitor drug toxicity / Jakob Hansen and Peter Bross -- Rescue of misfolded proteins and stabilization by small molecules / Raymond C. Stevens, javier Sancho, and Aurora Martinez.
  • Analysis of protein phosphatases / Shirish Shenolikar -- A brief introduction to the protein phosphatase families / Tomas Mustelin -- Small molecule inhibitors of Ser/thr protein phosphatases / Mark Swingle, Li Ni, and Richard E. Honkanen -- Synthesis and use of the protein phosphatase affinity matrices microcystin- and microcystin-biotin-sepharose / Greg Moorhead, Timothy A.J. Haystead, and Carol MacKintosh -- Utilizing protein phosphatase inhibitors to define PP2A as a regulator of ataxia-telangiectasia mutated (ATM) / Aaron A. Goodarzi ... [et al.] -- An automated, fluorescence-based method for continuous assay of PP2A activity / Adam M. Wegner ... [et al.] -- An in vivo assay to quantify stable protein phosphatase 2A (PP2A) heterotrimeric species / Matthew S. Gentry, Richard L. Hallberg, and David C. Pallas -- Mutagenesis and expression of the scaffolding Aa and Ab subunits of PP2A / Ralf Ruediger, Jin Zhou, and Gernot Walter -- Isolation and characterization of PP2A holoenzymes containing FLAG-tagged B subunits / Deanna G. Adams and Brian E. Wadzinski -- Purification of PP2A holoenzymes by sequential immunoprecipitation with anti-peptide antibodies / Gernot Walter, Jin Zhou, and Ralf Ruediger -- Purification of PP2Ac from bovine heart / Hue T. Tran ... [et al.] -- Visualization of intracellular PP1 targeting through transiently and stably expressed fluorescent protein fusions / Laura Trinkle-Mulcahy ... [et al.] -- Yeast two-hybrid screens to identify drosophila PP1-binding proteins / Daimark Bennett and Luke Alphey -- Identification of cellular protein phosphatase-1 regulators / David W. Roadcap, Matthew H. Brush, and Shirish Shenolikar -- Assay for 3-way interaction of protein phosphatase-1 (Glc7) with regulatory subunits plus phosphatase inhibitor-2 / Masumi Eto and David L. Brautigan -- Phosphorylation of the protein phosphatase type 1 inhibitor protein, CPI-17, by protein kinase C / Michael P. Walsh ... [et al.] -- Purification of smooth muscle myosin phosphatase using a thiophosphorylated myosin light chain-affinity resin / Merideth Borman and Justin MacDonald -- Proteins interacting with saccharomyces cerevisiae type 1 protein phosphatase catalytic subunit identified by single-step affinity purification and mass spectrometry / Edmund P. Walsh ... [et al.] -- Expression of protein histidine phosphatase in Escherichia coli, purification, and determination of enzyme activity / Nicole Bäumer .. [et al.] -- The use of RNA interference to analyze protein phosphatase function in mammalian cells / Iain Fraser ... [et al.] -- Recognition of a PP2C interaction motif in several plant protein kinases / Niranjan Chakraborty, Ohta Masaru, and Jian-Kang Zhu -- The use of yeast genetic tools to define biological roles of novel protein phosphatases / Joaquín Ariño ... [et al.] -- Targeting of PP2C in budding yeast / Irene Ota and James Mapes -- Phosphatase targets in TOR signaling / Estela Jacinto -- Functional characterization of the small CTD phosphatases (SCPs) / Michele Yeo and Patrick S. Lin -- Genome-scale discovery and characterization of class-specific protein sequences / David Kerk -- Yeast substrate-trapping system for isolating substrates of protein tyrosine phosphatases / Masahide Fukada and Masaharu Noda.
  • An introduction to protein sequencing using tandem mass spectrometry -- The primary structure of proteins and a historical overview of protein sequencing -- Fundamental mass spectrometry -- Collisionally induced dissociation of protonated peptide icons and the interpretation of product ion spectra -- Basic polyacrylamide gel electrophoresis -- The preparation of protein digests for mass spectrometric sequencing experiments -- Mass spectrometric analysis of tryptic digests -- Protein identification by database searching -- Sequence analysis of novel proteins -- The characterization of post-translationally modified proteins using tandem mass spectometry.
  • A historical perspective of template-based protein structure prediction / Jun-tao Guo, Kyle Ellrott, and Ying Xu -- The assessment of methods for protein structure prediction / Anna Tramontaro ... [et al.] -- Aligning sequences to structures / Liam James McGuffin -- Protein structure prediction using threading / Jinbo Xu, Feng Jiao, and Libo Yu -- Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment / Maxim Shatsky, Ruth Nussinov, and Haim J. Wolfson -- Indexing protein structures using suffix trees / Feng Gao and Mohammed J. Zaki -- Hidden Markov models for prediction of protein features / Christopher Bystroff and Anders Krogh -- The pros and cons of predicting protein contact maps / Lisa Bartoli ... [et al.] -- Roadmap methods for protein folding / Mark Moll, David Schwarz, and Lydia E. Kavraki -- Scoring functions for de novo protein structure prediction revisited / Shing-Chung Ngan ... [et al.] -- Protein-protein docking : overview and performance analysis / Kevin Wiehe ... [et al.] -- Molecular dynamics simulations of protein folding / Angel E. Garcia.
  • Immunofluorescent labeling of proteins in cultured cells with quantum dot secondary antibody conjugates / Richard L. Ornberg and Hongjian Liu -- Immunohistochemical detection with quantum dots / Rizwan S. Akhtar ... [et al.] -- Quantum dots for multicolor clinical pathology and multispectral imaging / Johbu Itoh and Robert Yoshiyuki Osamura -- Light and electron microscopic localization of multiple proteins using quantum dots / Thomas J. Deerinck ... [et al.] -- Human metaphase chromosome fluorescence in situ hybridization using quantum dot conjugates / Joan H.M. Knoll -- Biotin-ligand complexes with streptavidin quantum dots for in vivo cell-labeling of membrane receptors / Diane S. Lidke ... [et al.] -- Single quantum dot tracking of membrane receptors / Cødric Bouzigues ... [et al.] -- Optical monitoring of single cells using quantum dots / Jyoti K. Jaiswal and Sanford M. Simon -- Peptide-mediated intracellular delivery of quantum dots / B. Christoffer Lagerholm -- High-content analysis in multiple cell lines using quantum dots / Paul G. Wylie -- Measuring cell motility using quantum dot probes / Weiwei Gu ... [et al.] -- Quantum dots for in vivo molecular and cellular imaging / Xiaohu Gao, Leland W.K. Chung, and Shuming Nie -- Sentinel lymph node mapping with type II quantum dots / John V. Frangioni ... [et al.] -- Macrophage-mediated colocalization of quantum dots in experimental glioma / Osman Muhammad, Alexandra Popescu, and Steven A. Toms -- Applications of quantum dots to multicolor flow cytometry / Pratip K. Chattopadhyay and Mario Roederer -- Quantum dots in flow cytometry / Barnaby Abrams and Tim Dubrovsky -- Luminescent biocompatible quantum dots: a tool for immunosorbent assay design / Ellen R. Goldman ... [et al.] -- Fluorescence-based analysis of cellular protein lysate arrays using quantum dots / David H. Geho ... [et al.] -- Application of quantum dots to multicolor microarray experiments: four-color genotyping / George Karlin-Neumann ... [et al.].
  • Bioassays of quorum sensing compounds using Agrobacterium tumefaciens and Chromobacterium violaceum -- Detection of 2-alkyl-4-quinolones using biosensors -- FRET-based biosensors for the detection and quantification of AI-2 class of quorum sensing compounds -- Isolation of agr quorum sensing autoinducers -- Liquid chromatography/mass spectrometry for the detection and quantification of N-acyl-l-homoserine lactones and 4-hydroxy-2-alkylquinolines -- Detection of autoinducer (AI-2)-like activity in food samples -- Detection of bacterial signaling molecules in liquid or gaseous environments -- Determination of acyl homoserine lactone and tetramic acid concentrations in biological samples -- Luminescent reporters and their applications for the characterization of signals and signal-mimics that alter LasR-mediated quorum sensing -- Modulation of mammalian cell processes by bacterial quorum sensing molecules -- Imaging N-acyl homoserine lactone quorum sensing in vivo -- Defining the structure and function of acyl-homoserine lactone autoinducers -- Global expression analysis of quorum-sensing controlled genes -- Small RNA target genes and regulatory connections in the Vibrio cholerae quorum sensing system -- Quantifying pseudomonas aeruginosa quinolones and examining their interactions with lipids -- Linking quorum sensing regulation and biofilm formation by Candida albicans -- Design of synthetic mammalian quorum-sensing systems -- Qualitative and quantitative determination of quorum sensing inhibition in vitro -- Custom synthesis of autoinducers and their analogues -- Heterologous overexpression, purification, and in vitro characterization of ahl lactonases -- High-performance liquid chromatography analysis of N-acyl homoserine lactone hydrolysis by paraoxonases -- Generation of quorum quenching antibodies.
  • Receptor databases and computational websites for ligand binding -- Identification of orphan G protein-coupled receptor ligands using FLIPR assays -- Quantitative analysis of orphan G protein-coupled receptor mRNAs by TaqMan real-time PCR: G2A and GPR4 lysophospholipid receptor expression in leukocytes and in a rat myocardial infarction-heart failure model -- mRNA: detection by in situ and northern hybridization -- Radioligand-binding and molecular-imaging techniques for the quantitative analysis of established and emerging orphan receptor systems -- Measurement of radioligand binding by scintillation proximity assay -- Autoradiography of enzymes, second messenger systems, and ion channels -- Immunocytochemical localization of receptors using light and confocal microscopy with application to the phenotypic characterization of knock-out mice -- Live cell imaging of G protein-coupled receptors --Imaging and characterization of radioligands for positron emission tomography using quantitative phosphor imaging autoradiography -- Dynamic in vivo imaging of receptors in small animals using positron emission tomography.
  • "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.
  • 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.
  • 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.
  • Repetitive DNA 2012
    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..
  • Ribonuclease P 2010
    History of RNase P and Overview of Its Catalytic Activity -- The Evolution of RNase P and Its RNA -- Over a Decade of Bacterial Ribonuclease P Modeling -- Structural Studies of Ribonuclease P -- Folding of Bacterial RNase P RNA -- Kinetic Mechanism of Bacterial RNase P -- Roles of Metal Ions in RNase P Catalysis -- Challenges in RNase P Substrate Recognition: Considering the Biological Context -- Archaeal RNase P: A Mosaic of Its Bacterial and Eukaryal Relatives -- Eukaryote RNase P and RNase MRP -- RNase P from Organelles -- Human RNase P and Transcription -- RNase P as a Drug Target -- Ribonuclease P as a Tool.
  • RNA 2001
  • 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.
  • 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.
  • 1. RNA polymerases and transcription factors of trypanosomes / Arthur Günzl -- 2. SL RNA biogenesis in kinetoplastids: a long and winding road / Nancy R. Sturm, Jesse R. Zamudio, and David A. Campbell -- 3. Pre-mRNA splicing in trypanosoma brucei: factors, mechanisms, and regulation / Christian Preusser, Nicolas Jaé, Arthur Günzl, and Albrecht Bindereif -- 4. mRNA turnover in trypanosomes / Christine Clayton -- 5. tRNA biogenesis and processing / Jessica L. Spears, Mary Anne T. Rubio, Paul J. Sample, and Juan D. Alfonzo -- 6. rRNA biogensis in trypanosomes / Shulamit Michaeli -- 7. RNA editing in African trypanosomes: a U-ser's G-U-ide / H. Ulrich Göringer -- 8. The RNA interference pathway in trypanosoma brucei / Elisabetta Ullu, Nikolay G. Kolev, Rebecca L. Barnes, and Christian Tschudi -- 9. Translation in trypanosomatids -- 10. Mitochondrial translation in trypanosomatids / Dmitri A. Maslov and Rajendra K. Agrawal -- 11. RNA-Seq analysis of the transcriptome of trypanosoma brucei / Jan Mani, Kapila Gunasekera, and Isabel Roditi.
  • RNA methods and protocols 2008
    Springer Protocols
    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.
  • 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.
  • 1. Isolation of a sequence-specific RNA binding protein, polypyrimidine tract binding protein using RNA affinity chromatography / Shalini Sharma -- 2. An affinity oligonucleotide displacement strategy to purify ribonucleoprotein complexes applied to human telomerase /Isabel Kurth, Gaël Cristofari, Joachim Lingner -- 3. RNA affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes / Scott C. Walker ... [et al.] -- 4. Assembly and glycerol gradient isolation of yeast spliceosomes containing transcribed or synthetic U6 SnRNA / Ken Dery, Shyue-Lee Yean, Ren-Jang Lin -- 5. Purification of ribonucleoproteins using peptide-elutable antibodies and other affinity techniques / Scott Stevens -- 6. CLIP: cross-linking and immunoprecipitation of in vivo RNA targets of RNA binding proteins / Kirk B Jensen, Robert B. Darnell -- 7. Quantitative analysis of protein-RNA interactions by gel mobility shift / Sean P. Ryder, Michael I. Recht, James R. Williamson -- 8. Monitoring assembly of ribonucleoprotein complexes by isothermal titration calorimetry / Michael I. Recht, Sean P. Ryder, James R. Williamson -- 9. Characterization of RNA-protein interactions by phosphorothioate footprinting and its applications to the ribosome / A. Ozlem Tastan Bishop, ... [et al.] -- 10. In vivo analysis of ribonucleoprotein complexes using nucleotide analog interference mapping / Lara Weinstein Szewczak -- 11. T7 RNA polymerase mediated incorporation of 8-N3AMP into RNA for studying protein-RNA interactions / Rajesh Gaur -- 12. A simple crosslinking method, CLAMP, to map the sites of RNA contacting domains within a protein / Hiren Banerjee, Ravinder Singh -- 13. Proteins specifically modified with a chemical nuclease as probes of RNA-protein interaction / Oliver A. Ken, Andrew M. MacMillan -- 14. RNA-protein crosslink mapping using TEV protease / Ian A. Turner, ... [et al.] -- 15 Structural analysis of protein-RNA interactions with mass spectrometry / Mamuka Kvaratskhelia, Stuart F.J. Le Grice -- 16. Analysing RNA-protein cross-linking sites in unlabeled ribonucleoprotein complexes by mass spectrometry / Henning Urlaub, Eva Kühn-Hölsken, Reinhard Lührmann -- 17. In vitro selection of random RNA fragments to identify protein binding sites within large RNAs / Ulrich Stelzl, Knud H. Nierhaus -- 18. Immunoprecipitation analysis to study RNA-protein interactions in xenopus oocytes / Naoto Mabuchi, Kaoru Masuyama, Mutsuhito Ohno -- 19. Mapping the regions of RNase P catalytic RNA that are potentially in close contact with its protein cofactor / Phong Trang, Fenyong Liu -- 20. Quantification of microRNAs, splicing isoforms, and homologous mRNAs with the invader assay / Peggy S. Eis, Mariano Garcia-Blanco -- 21. Analysis of RNA structure and RNA-protein interactions in mammalian cells by use of terminal transferase-dependent PCR / Hsiu-Hua Chen, Jeanne LeBon, Arthur D. Riggs -- 22. Duplex unwinding and RNP remodeling with RNA helicases / Eckhard Jankowsky, Margaret E. Fairman -- 23. Preparation of efficient splicing extracts from whole cells, nuclei, and cytoplasmic fractions / Naoyuki Kataoka, Gideon Dreyfuss -- 24. Designing and utilization of siRNAs targeting RNA-binding proteins / Dong-Ho Kim, Mark Behlke, John J. Rossi -- 25. The use of saccharomyces cerevisiae proteomic libraries to identify RNA-modifying proteins / Jane E. Jackman, Eric M. Phizicky.
  • RNAi design and application 2008
    Springer Protocols
  • RT-PCR protocols 2002
    Springer Protocols
  • Applications of pressure cycling technology (PCT) in proteomics / Feng Tao ... [et al.] -- Applications of ion-exchange (IEX) chromatography to reduce sample complexity prior to two-dimensional gel electrophoresis (2DE) / Malcolm G. Pluskal, Eva Golenko, and Mary F. Lopez -- Separations in proteomics: use of camelid antibody fragments in the depletion and enrichment of human plasma proteins for proteomics applications / Mark ten Haaft, Pim Hermans, and Bruce Dawson -- Novel plasma protein separation strategy using multiple avian IgY antibodies for proteomic analysis / Sun W. Tam ... [et al.] -- Immunoaffinity depletion of high-abundant proteins for proteomic sample preparation / Nina Zolotarjova ... [et al.] -- Isolation of plasma membrane proteins for proteomic analysis / Catherine Fenselau and Amir Rahbar -- New ultrafiltration and solid phase extraction techniques improve serum peptide detection / Elena Chernokalskaya ... [et al.] -- Tools for sample preparation and prefractionation in two-dimensional (2D) gel electrophoresis / Anton Posch, Aran Paulus, and Mary Grace Brubacher -- Optic nerve fractionation for proteomics / Sanjoy K. Bhattacharya ... [et al.] -- Fractionation of retina for proteomic analyses / Sanjoy K. Bhattacharya ... [et al.] -- Reducing protein sample complexity with free flow electrophoresis (FFE) / Askar Kuchumov, Gerhard Weber, Christoph Eckerskorn -- Destreaking strategies for two-dimensional electrophoresis / Fengju Bai, Sheng Liu, and Frank A. Witzmann -- Proteomic approaches to the study of rheumatoid arthritis / Mikaela Antonovici ... [et al.] -- Immunoglobulin patterns in health and disease / Ingrid Miller and Marcia Goldfarb -- Difference gel electrophoresis (DIGE) / Mustafa Unlu and Jonathan Minden -- Principles and challenges of basic protein separation by two-dimensional (2D) electrophoresis / Anton Posch, Aran Paulus, and Mary Grace Brubacher -- Multidimensional separation of membrane proteins / Susan Francis-McIntyre and Simon J. Gaskell -- Structural approaches to glycoproteomics / Heidi Geiser, Cristina Silvescu, and Vernon Reinhold -- Enrichment and analysis of glycoproteins in the proteome / Nicole L. Wilson, Niclas G. Karlsson, and Nicolle H. Packer -- Proteomic analyses using high-efficiency separations and accurate mass measurements / Jon M. Jacobs and Richard D. Smith -- Middle-out proteomics: incorporating multidimensional protein fractionation and intact protein mass analysis as elements of a proteomic workflow / Scott J. Berger ... [et al.] -- Polymeric monolithic capillary columns in proteomics / Alexander R. Ivanov -- Proteins staining in polyacrylamide gels / Gary B. Smejkal -- Multiplexed proteomics: fluorescent detection of proteins, glycoproteins, and phosphoproteins in two-dimensional (2D) gels / Birte Aggeler-Schulenberg -- Glyoxyl agarose and its composite gels: advantageous alternatives to polyacrylamide gel electrophoresis for very large and small proteins and peptides and all sizes in between / John R. Shainoff -- Nuclear magnetic resonance-driven chemical proteomics: the functional and mechanistic complement to proteomics / Phani Kumar Pullela and Daniel S. Sem -- Electrophoretic nuclear magnetic resonance in proteomics: toward high-throughput structural characterization of biological signaling processes / Qiuhong He and Xiangjin Song.
  • Single molecule biology 2009
    The "single molecule" paradigm / Alex E. Knight -- Single molecule studies of myosins / Rachel E. Farrow ... [et al.] -- Single molecule experiments and the kinesin motor protein superfamily : walking hand in hand / Lukas C. Kapitein and Erwin J.G. Peterman -- Force-generating mechanisms of dynein revealed through single molecule studies / Kazuhiro Oiwa and Hiroaki Kojima -- The bacterial flagellar motor / Yoshiyuki Sowa and Richard M. Berry -- Single molecule studies of chromatin structure and dynamics / Sanford H. Leuba and Laurence R. Brewer -- Single molecule studies of nucleic acid enzymes / Samir M. Hamdan and Antoine M. van Oijen -- Single molecule studies of prokaryotic translation / Colin Echeverría Aitken ... [et al.] -- Single ion channels / David Colquhoun, Remigijus Lape, and Lucia Sivilotti -- Single molecule fluorescence in membrane biology / Lydia M. Harriss and Mark I. Wallace -- Single molecule microarray analysis / Jan Hesse ... [et al.].
  • Star polymer surface passivation for single-molecule detection / Jürgen Groll and Martin Moeller -- Azide-specific labeling of biomolecules by Staudinger-Bertozzi ligation: phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy / Anirban Chakraborty ... [et al.] -- Preparation of fluorescent pre-mRNA substrates for an smFRET study of pre-mRNA splicing in yeast / John Abelson, Haralambos Hadjivassiliou and Christine Guthrie -- Nanovesicle trapping for studying weak protein interactions by single-molecule FRET / Jaime J. Benítez, Aaron M. Keller and Peng Chen -- Droplet confinement and fluorescence measurement of single molecules / Lori S. Goldner, Ana M. Jofre and Jianyong Tang -- Single-molecule fluorescence spectroscopy using phospholipid bilayer nanodiscs / Abhinav Nath ... [et al.] -- Single-molecule spectroscopy using microfluidic platforms / Samuel Kim and Richard N. Zare -- Detection of protein-protein interactions in the live cell plasma membrane by quantifying prey redistribution upon bait micropatterning / Julian Weghuber ... [et al.] -- Analysis of complex single-molecule FRET time trajectories / Mario Blanco and Nils G. Walter -- Single-molecule fluorescence studies of intrinsically disordered proteins / Allan Chris M. Ferreon ... [et al.] -- Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer / Max Greenfield and Daniel Herschlag -- A highly purified, fluorescently labeled in vitro translation system for single-molecule studies of protein synthesis / Jingyi Fei ... [et al.] -- Watching individual proteins acting on single molecules of DNA / Ichiro Amitani ... [et al.] -- DNA curtains for high-throughput single-molecule optical imaging / Eric C. Greene ... [et al.] -- Scanning FCS for the characterization of protein dynamics in live cells / Zdenĕk Petrás̆ek, Jonas Ries and Petra Schwille -- Observing protein interactions and their stoichiometry in living cells by brightness analysis of fluorescence fluctuation experiments / Yan Chen ... [et al.] -- Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes / Arjin Raj and Sanjay Tyagi -- Single mRNA tracking in live cells / Hye Yoon Park, Adina R. Buxbaum and Robert H. Singer -- Single-molecule sequencing: sequence methods to enable accurate quantitation / Christopher Hart ... [et al.] -- Real-time DNA sequencing from single polymerase molecules / Jonas Korlach ... [et al.].
  • The Expanding World of Small Molecule Microarrays / Mahesh Uttamchandani and Shao Q. Yao -- Construction of Photo-Cross-Linked Microarrays of Small Molecules / Naoki Kanoh -- Small Molecule Microarray : Functional-Group Specific Immobilization of Small Molecules / Hyang Yeon Lee and Seung Bum Park -- Detecting Protein-Small Molecule Interactions Using Fluorous Small Molecule Microarrays / Arturo J. Vegas and Angela N. Koehler -- A Method for Small Molecule Microarray-Based Screening for the Rapid Discovery of Affinity-Based Probes / Haibin Shi, Mahesh Uttamchandani, and Shao Q. Yao -- Nanodroplet Chemical Microarrays and Label-Free Assays / Dhaval Gosalia and Scott L. Diamond -- Nanodroplet Microarrays for High-Throughput Enzyme Screening / Kang L.D. Aw, Shao Q. Yao, and Mahesh Uttamchandani. The Application of the Chemical Array for Biological Study / Isao Miyazaki, Siro Simizu, and Hiroyuki Osada -- Peptide Arrays with a Chip / Alexander Nesterov, Edgar Dörsam, Yun-Chien Cheng, Christopher Schirwitz, Frieder Märkle, Felix Löffler, Kai König, Volker Stadler, Ralf Bischoff, and Frank Breitling -- In situ Chemical Modification of Peptide Microarrays : Characterization by Desorption/Ionization on Silicon Nanowires / Gaëlle Piret, Herv Drobecq, Carine Rouanet, Karim Chemlal, Anne-Sophie Debrie, Jean-Michel Hougardy, Françoise Mascart, Camille Locht, and Oleg Melnyk -- Peptide Microarrays on Coated Silicon Slides for Highly Sensitive Antibody Detection / Marina Cretich, Francesco Damin, Renato Longhi, Cecilia Gotti, Clelia Galati, Lucio Renna, and Marcella Chiari. Antibody Signatures Defined by High-Content Peptide Microarray Analysis / Antonia Masch, Johannes Zerweck, Ulf Reimer, Holger Wenschuh, and Mike Schutkowski -- High Density Peptide Microarrays for Proteome-Wide Fingerprinting of Kinase Activities in Cell Lysates / Alexandra Thiele, Matthias Weiwad, Johannes Zerweck, Gunter Fischer, and Mike Schutkowski -- A Peptide Microarray for Detecting Protein Kinase Activity in Cell Lysates / Xiaoming Han and Yoshiki Katayama -- Chemical Microarrays Constructed by Selective Attachment of Hydrazide-Conjugated Substances to Epoxide Surfaces and Their Applications / Sungjin Park, Myung-Ryul Lee, and Injae Shin -- A Microarray-Based Method to Perform Nucleic Acid Selections / Olga Aminova and Matthew D. Disney.
  • Hydrogen-bonded synthetic mimics of protein secondary structure as disruptors of protein-protein interactions / M.J. Adler, A.G. Jamieson and Andrew D. Hamilton -- Small-molecule inhibitors of IL-2/IL-2R : Lessons learned and applied / C.G. Wilson and M.R. Arkin -- Small molecule inhibitors of the human papillomavirus E1-E2 interaction / P.W. White, Anne-Marie Faucher and Nathalie Goudreau -- Design of small-molecule Smac mimetics as IAP antagonists / Shaomeng Wang -- Small-molecule inhibitors reveal a new function for Bcl-2 as a proangiogenic signaling molecule / Benjamin D. Zeitlin and Jacques E. Nör -- Small-molecule modulators of c-Myc/Max and Max/Max interactions / Thorsten Berg -- Small-molecule inhibitors of the p53-MDM2 interaction / Binh T. Vu and Lyubomir Vassilev.

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