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  • Book
    Asheesh Shanker, editor.
    Summary: This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.

    Contents:
    Intellectual Property Rights and Bioinformatics: An Introduction
    Next-Generation Sequencing: Technology, Advancements, and Applications
    Sequence Alignment
    Understanding Genomic Variations in the Context of Health and Disease: Annotation, Interpretation, and Challenges
    Metagenomics: Focusing on the Haystack
    Computational Epigenomics and its Application in Regulatory Genomics
    Data Mining to Detect Common, Unique, and Polymorphic Simple Sequence Repeats
    R-Programming for Genome-Wide Data Analysis
    Computational Approaches to Studying Molecular Phylogenetics
    Structural Bioinformatics: Life Through the 3D Glasses
    A Survey of the Structural Parameters Used for Computational Prediction of Protein Folding Process
    Quality Assessment of Protein Tertiary Structures: Past, Present, and Future
    Predicting Protein Function Using Homology-Based Methods
    Drug Discovery: An In Silico Approach
    Advanced In Silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Coronavirus
    Machine Learning: What, Why, and How?
    Command-Line Tools in Linux for Handling Large Data Files.
    Digital Access Springer 2018
  • Article
    van Alphen L, Verkleij A, Leunissen-Bijvelt J, Lugtenberg B.
    J Bacteriol. 1978 Jun;134(3):1089-98.
    In a previous paper (A. Verkleij, L. van Alphen, J. Bijvelt, and B. Lugtenberg, Biochim. Biophys. Acta 466:269-282, 1977) we have hypothesized that particles on the outer fracture face of the outer membrane ([Formula: see text]), with corresponding pits on the inner fracture face of the outer membrane ([Formula: see text]), consist of lipopolysaccharide (LPS) aggregates stabilized by divalent cations and that they might contain protein and/or phospholipid. In the present paper the roles of LPS, cations, and proteins in these [Formula: see text] particles are described more extensively, using a strain that lacks the major outer membrane proteins, b, c, and d (b(-) c(-) d(-)), and has a reduction in the number of [Formula: see text] particles of 75%. To study the role of divalent cations in the formation of [Formula: see text] particles, these b(-) c(-) d(-) cells were grown or incubated with Ca(2+), Mg(2+), or putrescine. The presence of Ca(2+) resulted in the appearance of many [Formula: see text] particles and [Formula: see text] pits. Mg(2+) and putrescine were less effective than Ca(2+). Introduction of these particles was not accompanied by alterations in the relative amounts of LPS and cell envelope proteins. Ca(2+) treatment of a heptoseless derivative of a b(-) c(-) d(-) strain did not result in morphological changes. Incubation of Ca(2+)-treated cells with ethylenediaminetetraacetate caused the disappearance of the introduced particles as well as the release of more than 60% of the cellular LPS. These results strongly support the hypothesis that LPS is involved in the formation of [Formula: see text] particles and [Formula: see text] pits. The roles of various outer membrane proteins in the formation of [Formula: see text] particles were studied by comparing the freeze-fracture morphology of b(-) c(-) d(-) cells with that of cells which contain one of the outer membrane proteins b, c, d, and e or the receptor protein for bacteriophage lambda. The results showed that the presence of any of these five proteins in a b(-) c(-) d(-) background resulted in a large increase in the number of [Formula: see text] particles and [Formula: see text] pits, indicating that these proteins are, independent of each other, involved in the formation of [Formula: see text] particles and [Formula: see text] pits. The simplest explanation for the results is that in wild-type cells each particle consists of LPS complexed with some molecules of a single protein species, stabilized by either divalent cations or polyamines. It is hypothesized that the outer membrane of the wild-type cell contains a heterogeneous population of particles, of which 75% consists of protein b-LPS, protein c-LPS, and protein d-LPS particles. A function of these particles as aqueous pores is proposed.
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