This volume explores recent techniques for the computational inference of gene regulatory networks (GRNs). The chapters in this book cover topics such as methods to infer GRNs from time-varying data; the extraction of causal information from biological data; GRN inference from multiple heterogeneous data sets; non-parametric and hybrid statistical methods; the joint inference of differential networks; and mechanistic models of gene regulation dynamics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, descriptions of recently developed methods for GRN inference, applications of these methods on real and/ or simulated biological data, and step-by-step tutorials on the usage of associated software tools. Cutting-edge and thorough, Gene Regulatory Networks: Methods and Protocols is an essential tool for evaluating the current research needed to further address the common challenges faced by specialists in this field.

Membrane processes today play a signifi cant role in the replacement therapy for acute and chronic organ failure diseases. Current extracorporeal blood purifi cation and oxygenation devices employ membranes acting as selective barriers for the removal of endogeneous and exogeneous toxins and for gas exchange, respectively. Additionally, membrane technology offers new interesting opportunities for the design of bioartificial livers, pancreas, kidneys, lungs etc. This book reviews the latest developments in membrane systems for bioartificial organs and regenerative medicine, investigates how membrane technology can improve the quality and efficiency of biomedical devices, and highlights the design procedures for membrane materials covering the preparation, characterization, and sterilization steps as well as transport phenomena. The different strategies pursued for the development of membrane bioartifi cial organs, including crucial issues related to blood/cell-membrane interactions are described with the aim of opening new and exciting frontiers in the coming decades. The book is a valuable tool for tissue engineers, clinicians, biomaterials scientists, membranologists as well as biologists and biotechnologists. It is also a source of reference for students, academic and industrial researchers in the topic of biotechnology, biomedical engineering, materials science and medicine.

This book focuses on the state-of-the-art of biosensor research and development for specialists and non-specialists. It introduces the fundamentals of the subject with relevant characteristics of transducer elements, as well as biochemical recognition molecules. This book is ideal for researchers of nanotechnology, materials science and biophysics.

Biology and Engineering of Stem Cell Niches covers a wide spectrum of research and current knowledge on embryonic and adult stem cell niches, focusing on the understanding of stem cell niche molecules and signaling mechanisms, including cell-cell/cell-matrix interactions. The book comprehensively reviews factors regulating stem cell behavior and the corresponding approaches for understanding the subsequent effect of providing the proper matrix molecules, mechanical cues, and/or chemical cues. It encompasses a variety of tools and techniques for developing biomaterials-based methods to model synthetic stem cell niches in vivo, or to enhance and direct stem cell fate in vitro. A final section of the book discusses stem cell niche bioengineering strategies and current advances in each tissue type.

Epigenetics and Systems Biology highlights the need for collaboration between experiments and theoretical modeling that is required for successful application of systems biology in epigenetics studies. This book breaks down the obstacles which exist between systems biology and epigenetics researchers due to information barriers and segmented research, giving real-life examples of successful combinations of systems biology and epigenetics experiments. Each section covers one type of modeling and one set of epigenetic questions on which said models have been successfully applied. In addition, the book highlights how modeling and systems biology relate to studies of RNA, DNA, and genome instability, mechanisms of DNA damage signaling and repair, and the effect of the environment on genome stability.

In order to grow replacement tissues, 3D scaffolds are widely used as a template for tissue engineering and regeneration. These scaffolds, which are typically 'seeded' with cells, support the growth of new tissues. However, in order to achieve successful tissue growth, the scaffold must meet specific requirements and are often 'functionalized' to accentuate particular properties. Functional 3D tissue engineering scaffolds: materials, technologies, and applications, is a comprehensive review of functional 3D scaffolds, providing information on the fundamentals, technologies, and applications. Part 1 focuses on the fundamentals of 3D tissue scaffolds, examining information on materials, properties, and trends. Part 2 discusses a wide range of conventional technologies for engineering functional 3D scaffolds, leading the way to a discussion on CAD and advanced technologies for functional 3D scaffold engineering. Chapters in part 3 study methods for functionalizing scaffolds to support a variety of in vivo functions whilst the final set of chapters provides an important review of the most significant applications of functional 3D scaffolds within tissue engineering. This book is a valuable resource for biomaterial scientists and biomedical engineers in academia and industry, with interests in tissue engineering and regenerative medicine.

Membrane Characterization provides a valuable source of information on how membranes are characterized, an extremely limited field that is confined to only brief descriptions in various technical papers available online. For the first time, readers will be able to understand the importance of membrane characterization, the techniques required, and the fundamental theory behind them. This book focuses on characterization techniques that are normally used for membranes prepared from polymeric, ceramic, and composite materials.

An in-depth look at the latest research, methods, and applications in the field of protein bioinformatics This book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems. Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics: * Highlights protein analysis applications such as protein-related drug activity comparison * Incorporates salient case studies illustrating how to apply the methods outlined in the book * Tackles the complex relationship between proteins from a systems biology point of view * Relates the topic to other emerging technologies such as data mining and visualization * Includes many tables and illustrations demonstrating concepts and performance figures Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.

Why a Second Edition?
The Second Edition provides practical answers to the general question, "How can I obtain useful sequence information from my protein or peptide?" rather than the more specific question asked in the first edition, "How can I obtain the N-terminal sequence?" Important new methods include ways of dealing with blocked N termini, computer analysis of protein sequences, and the recent revolution in mass spectrometry.
Key Features
Highlights of the Second Edition:
* Mass spectrophotometric characterization of proteins and peptides
* N-terminal sequencing of proteins with blocked N termini
* Internal amino acid sequence analysis after protease digestion in-gel and on-blot
* Improved microscale peptide purification methods
* Computer analysis of protein sequences
* New protocols tested and refined through everyday use in authors' laboratories
* Updated reference chapter covering all aspects of protein microsequencing

This Volume presents methods for analysing and quantifying petroleum, hydrocarbons and lipids, based on their chemical and physical properties as well as their biological effects. It features protocols for extracting hydrocarbons from solid matrices, water and air, and a dedicated chapter focusing on volatile organic compounds. Several approaches for separating and detecting diverse classes of hydrocarbons and lipids are described, including: (tandem) gas chromatography (GC) coupled with mass spectrometry (MS) or flame-ionisation detection, Fourier-transform induction-coupled-resonance MS, and fluorescence-based techniques. The book details high-performance liquid chromatography MS for microbial lipids, as well as a combination of techniques for naphthenic acids. Two chapters focus on quantifying bioavailable hydrocarbon fractions by using cyclodextrin sorbents and bacterial bioreporters, respectively, while a closing chapter explains how compound-specific stable-isotope analysis can be used to measure the fate of hydrocarbons in the environment. Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Proteomics, like other post-genomics tools, has been growing at a rapid pace and has important applications in numerous fields of science. While its use in animal and veterinary sciences is still limited, there have been considerable advances in this field in recent years, in areas as diverse as physiology, nutrition and food of animal origin processing. This is mainly as a consequence of a wider availability and better understanding of proteomics methodologies by animal and veterinary researchers. This book provides a comprehensive, state-of-the-art account of the status of farm-animal proteomics research, focusing on the principles behind proteomics methodologies and its specific applications and offering clear example.

Gellan Gum as a Biomedical Polymer details key topics and fundamental aspects of gellan gum and its biomedical applications in drug delivery, proteins and peptides delivery, cell delivery, tissue engineering, wound dressings and enzyme immobilizations in developing high quality products. Sections introduce gellan gum, its source, production and gelation mechanism, discuss biomedical materials, and provides ways it can be used for biomedical applications. The book also examines the used of gellan gum as pharmaceutical excipients for drug delivery. Future developments and challenges round out the book’s coverage. With contributions for an international group of experts, this book is a useful reference for scientists, researchers and those in industry engaged in biomedical product development using natural polysaccharides.

High Throughput Formulation Development of Biopharmaceuticals: Practical Guide to Methods and Applications provides the latest developments and information on the science of stable and safe drug product formulations, presenting a comprehensive review and detailed description of modern methodologies in the field of formulation development, a process starting with candidate and pre-formulation screening in its early development phase and then progressing to the refinement of robust formulations during commercialization in the later phases of development. The title covers topics such as experiment design, automation of sample preparation and measurements, high-throughput analytics, stress-inducing methods, statistical analysis of large amounts of formulation study data, emerging technologies, and the presentation of several case studies, along with a concluding summary.

This book covers both basic and applied sciences in a rather specified area of pulp and paper manufacture. The basic science of lignocellulose enzymology and plant genetics is covered also in many other contexts, whereas the application of biotechnology in process and product development is thoroughly reviewed. All the latest advances as well as new ideas of the research field are covered. This book will serve as an updated and compact information package of biotechnical aspects and the most recent advances of the pulp and paper industry sector.

What will our lives be like fifty years from now? What will we know about ourselves as humans, and how will that affect our lives? It's impossible to know the future for certain, but one thing we do know--perhaps nothing will alter our future more than the Genetics Revolution of the past thirty-five years. This book clarifies the history and examines the possible impact of five major areas of genetic research:

• The Human Genome Project and genetic engineering
• In vitro fertilization (IVF) and the technology of reproduction
• The Human Genome Diversity Project, which is studying the variation of the human genome
• Embryonic stem-cell research
• Cloning

Nature, by dint of its constitution, harbors many unassuming mysteries broadly manifested by its constituent cohorts. If physics is the pivot that holds nature and chemistry provides reasons for its existence, then the rest is just manifestation. Nanoscience and technology harbor the congruence of these two core subjects, whereby many phenomenon may be studied in the same perspective. That nature operates at nanoscale-obeying the principles of thermodynamics and supramolecular chemistry-is a well understood fact manifested in a variety of life processes: bones are restored after a fracture; clots potentially leading to cerebral strokes can be dissolved. The regeneration of new structures in our system follows a bottom-up approach. Be it a microbe (benign or pathogenic), plant (lower or higher), plant parts/organs, food beneficiaries, animal (lower), higher animal processing wastes, these all are found to deliver nanomaterials under amenable processing conditions. Identically, the molecules also seem to obey the thermodynamic principles once they get dissociated/ionized and the energy captured in the form of bonding helps in the synthesis of a myriad of nanomaterials. This edited volume explores the various green sources of nanomaterial synthesis and evaluates their industrial and biomedical applications with a scope of scaling up. It provides useful information to researchers involved in the green synthesis of nanomaterials in fields ranging from medicine to integrated agricultural management.

The paddy field is a unique agro-ecosystem and provides services such as food, nutrient recycling and diverse habitats. However, chemical contamination of paddy soils has degraded the quality of this important ecosystem. This book provides an overview of our current understanding of paddy soil pollution, addressing topics such as the major types of pollutants in contaminated paddy soil ecosystems; factors affecting the fate of pollutants in paddy soil; biomonitoring approaches to assess the contaminated paddy soil; the impact of chemicals on soil microbial diversity; and climate change. It also covers arsenic and heavy metal pollution of paddy soils and their impact on rice quality. Further, new emerging contaminants such as antibiotics and antibiotics resistance genes (ARGs) in paddy soil and their impact on environmental health are also discussed. The last chapters focus on the bioremediation approaches for the management of paddy soils.

Bioremediation refers to the clean-up of pollution in soil, groundwater, surface water, and air using typically microbiological processes. It uses naturally occurring bacteria and fungi or plants to degrade, transform or detoxify hazardous substances to human health or the environment. For bioremediation to be effective, microorganisms must enzymatically attack the pollutants and convert them to harmless products. As bioremediation can be effective only where environmental conditions permit microbial growth and action, its application often involves the management of ecological factors to allow microbial growth and degradation to continue at a faster rate. Like other technologies, bioremediation has its limitations. Some contaminants, such as chlorinated organic or high aromatic hydrocarbons, are resistant to microbial attack. They are degraded either gradually or not at all, hence, it is not easy to envisage the rates of clean-up for bioremediation implementation. Bioremediation represents a field of great expansion due to the important development of new technologies. Among them, several decades on metagenomics expansion has led to the detection of autochthonous microbiota that plays a key role during transformation. Transcriptomic guides us to know the expression of key genes and proteomics allow the characterization of proteins that conduct specific reactions. In this book we show specific technologies applied in bioremediation of main interest for research in the field, with special attention on fungi, which have been poorly studied microorganisms. Finally, new approaches in the field, such as CRISPR-CAS9, are also discussed. Lastly, it introduces management strategies, such as bioremediation application for managing affected environment and bioremediation approaches. Examples of successful bioremediation applications are illustrated in radionuclide entrapment and retardation, soil stabilization and remediation of polycyclic aromatic hydrocarbons, phenols, plastics or fluorinated compounds. Other emerging bioremediation methods include electro bioremediation, microbe-availed phytoremediation, genetic recombinant technologies in enhancing plants in accumulation of inorganic metals, and metalloids as well as degradation of organic pollutants, protein-metabolic engineering to increase bioremediation efficiency, including nanotechnology applications are also discussed.