Molecular Networking

The book builds on the analogy between social groups and assemblies of molecules to introduce the concepts of statistical mechanics, machine learning and data science. Applying a data analytics approach to molecular systems, we show how individual (molecular) features and interactions between molecules, or "communication" processes, allow for the prediction of properties and collective behavior of molecular systems - just as polling and social networking shed light on the behavior of social groups. Applications to systems at the cutting-edge of research for biological, environmental, and energy applications are also presented. Key features: Draws on a data analytics approach of molecular systems. Covers hot topics such as artificial intelligence and machine learning of molecular trends. Contains applications to systems at the cutting-edge of research for biological, environmental and energy applications. Discusses molecular simulation and links with other important, emerging techniques and trends in computational sciences and society. Authors have a well-established track record and reputation in the field.

This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.

A highly useful resource for professionals and students alike, this cutting-edge, first-of-its-kind book provides a thorough introduction to nanoscale communication networks. Written in a clear tutorial style, this volume covers a wide range of the most important topics in the area, from molecular communication and carbon nanotube nano-networks, to nanoscale quantum networking and the future direction of nano networks. Moreover, the book features numerous exercise problems at the end of each chapter to ensure a solid understanding of the material.

This book provides a complete analysis of molecular communications systems from the paradigm of TCP/IP network stack, and it exploits network theories (e.g. independent functions of a layer into a stack, addressing, flow control, error control, and traffic control) and applies them to biological systems. The authors show how these models can be applied in different areas such as industry, medicine, engineering, biochemistry, biotechnology, computer sciences, and other disciplines. The authors then explain how it is possible to obtain enormous benefits from these practices when applied in medicine, such as enhancing current treatment of diseases and reducing the side effects of drugs and improving the quality of treatment for patients. The authors show how molecular communications systems, in contrast to existing telecommunication paradigms, use molecules as information carriers. They show how sender biological nanomachines (bio-nano machines) encode data on molecules (signal molecules) and release the molecules into the environment. They go on to explain how the molecules then travel through the environment to reach the receiver bio-nano machines, where they biochemically react with the molecules to decipher information. This book is relevant to those studying telecommunications and biomedical students, engineers, masters, PhDs, and researchers.

Antimicrobial Peptides, Volume 663 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on Unifying the classification of antimicrobial peptides in the Antimicrobial Peptide Database, Optimizing peptide library creation for PepSAVI-MS (RP libraries, etc.), Discovery of novel Antimicrobial peptides using BioProspecting, Screening for cysteine-stabilized scaffolds for developing protelytic-resistant AMPs, Exploring synergy and its role in antimicrobial peptide biology, Colorimetric assays for the rapid and high-throughput screening of antimicrobial peptide activity against diverse bacterial pathogens, and much more. Other chapters cover Liquid chromatography-mass spectrometry-based analysis of naturally occurring neuropeptide diastereomers, Multiplexed Quantitative Neuropeptidomics via DiLeu Isobaric Tagging, In vitro evaluation of antibiotic resistance via proteomics, Molecular networking-based strategies in mass spectrometry, Development of Macrocyclic antimicrobial peptides and peptoids, and a host of other timely topics. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in Methods in Enzymology serials Updated release includes the latest information on Antimicrobial Peptides

Plant polyphenols are specialized metabolites that constitute one of the most common and widespread groups of natural products. They are essential plant components for adaptation to the environment and possess a large and diverse range of biological functions that provide many benefits to both plants and humans. Polyphenols, from their structurally simplest forms to their oligo/polymeric versions (i.e. tannins and lignins), are phytoestrogens, plant pigments, antioxidants, and structural components of the plant cell wall. The interactions between tannins and proteins are involved in plant defense against predation, cause astringency in foods and beverages, and affect the nutritional and health properties of human and animal food plants. This eighth volume of the highly regarded Recent Advances in Polyphenol Research series is edited by Juha-Pekka Salminen, Kristiina Wähälä, Victor de Freitas, and Stéphane Quideau, and brings together chapters written by some of the leading experts working in the polyphenol sciences today. Topics covered include: Structure, reactivity and synthesis Bioactivity and bioavailability Metabolomics, targeted analysis and big data Quality control & standardization Biogenesis and functions in plants and ecosystems Biomaterials & applied sciences Distilling the most recent and illuminating data available, this new volume is an invaluable resource for chemists, biochemists, plant scientists, pharmacognosists and pharmacologists, biologists, ecologists, food scientists and nutritionists.

This volume provides conceptual strategies and methodological know-how over a wide range of stress situations that can be used as stepping stones to unravel the intricacies of abiotic stress signaling networks in plants. Chapters guide readers through achievements and challenges in the field and through up-to-date protocols covering identification of novel processes, validation of hypothetical mechanisms, and further characterization of currently-known pathways. Written in the format of the highly successful Methods in Molecular Biology series, wet-lab chapters include an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Plant Abiotic Stress Signaling aims to be a comprehensive and innovative guide for students and researchers seeking to understand plant molecular mechanisms at the interface with environmental constraints and climate change.

We are now entering the third decade of the 21st Century, and, especially in the last years, the achievements made by scientists have been exceptional, leading to major advancements in the fast-growing field of Metabolomics. Frontiers has organized a series of Research Topics to highlight the latest advancements in science in order to be at the forefront of science in different fields of research. This editorial initiative of particular relevance, led by Dr Wolfram Weckwerth, Specialty Chief Editor of the Metabolomics section, is focused on new insights, novel developments, current challenges, latest discoveries, recent advances and future perspectives in the field of Metabolomics.