Glycobiophysics

Advances in Experimental Medicine and Biology

Book 1
Springer
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This book presents state of the art biophysical approaches to issues in glycobiology that have cutting-edge applications. Despite the importance of glycosylation, the complexity, heterogeneity, and flexibility of the glycans have inhibited their study. Each chapter in this book explains very recent significant advances in biophysical approaches through the use of techniques such as NMR spectroscopy, mass spectrometry, single-molecule imaging, X-ray crystallography, high-speed atomic force microscopy, and computational simulation and their integrative application. Concrete examples are provided of the value of these techniques in addressing key problems in the field. In addition, significant functional glycobiological issues are considered. For example, glycolipids can form dynamic clusters on cell membranes and provide platforms for molecules involved in cell recognition and subsequent signal transduction. The detailed delineation of these molecular systems is discussed, revealing their structural complexity and ability to assemble transiently. This timely book will be of value for graduate students and postdocs interested in frontier topics in glycoscience and also for senior bio-researchers in academic and industrial fields.
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About the author

Yoshiki Yamaguchi, PhD

Synthetic Cellular Chemistry Laboratory

RIKEN Cluster for Pioneering Research


Koichi Kato, PhD
Exploratory Research Center on Life and Living Systems
National Institutes of Natural Sciences


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Additional Information

Publisher
Springer
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Published on
Nov 27, 2018
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Pages
277
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ISBN
9789811321580
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Language
English
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Genres
Science / Life Sciences / Biochemistry
Science / Life Sciences / Biophysics
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Content Protection
This content is DRM protected.
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This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application.

The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies.

Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future.


The circulatory system is usually considered to be composed of tubes of various diameters, characterized by collateral and terminal branches. There is also a tendency to treat blood vessels merely as conducting tubes in which the various structures of the wall act as mechanical pumps wlrich modify their diameter. This is, of course, not so. In fact, we know that blood vessels, and in particular arteries, are organs with personalities of their own and a particular susceptibility to several diseases. In addition, blood vessels differ in structure, according to their localization, and age at differing rates. The experimental work car ried out so far clearly confirms the data that have come from spontaneous human pathology; experimentally induced arterial lesions have a definite tendency to appear in certain arteries and not in others, depending on the experimental procedures used, and in each specific artery the lesions appear to have a specific location. We now know that the arterial wall is a metabo licallyactive structure, in which a number of enzyme activities have been clearly demonstrated. It possesses a sensitive vasa vasorum apparatus and a specific reactivity to various lesion-inducing stimuli. We must also remember that the arterial wall is in continuous contact with the blood circulating through the endothelial cells lining the vascular bed. It is obvious, therefore, that any variation in the circulating blood mass can modify the morphology as well as the function of the vessel wall.
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