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Chapter

Cover Introduction to Genomics

Systems Biology  

This chapter focuses on systems biology as an integrative approach to all the 'omics disciplines. It notes the static and dynamic aspects of biological networks, expounding the structure, dynamics, and evolution of metabolic networks and regulatory networks. It mentions the stability, adaptability, and robustness of living systems as well. The chapter also explores different ways of experimentally determining protein–protein and protein–nucleic acid interactions. It explains the basic features of the lytic-lysogenic switch in bacteriophage λ and the regulatory network of Escherichia coli. Finally, it talks about how transcriptomics are being used to reveal the different time courses of expression of various genes during the yeast diauxic shift.

Chapter

Cover Communication Skills for the Biosciences

Networking  

This chapter looks at the benefits of networking and describes some of the ways in which a student can network. It argues that networking is an important part of the academic career as it involves developing and maintaining contact with people who work in the same field or in a related field. The chapter begins by explaining what networking is and why it is important to network. It then details the different ways in which a student can network, including face-to-face networking and the use of web-based technologies. Lastly, the chapter explores some web-based tools for collaborative authoring, and it investigates how to network effectively and ethically online.

Chapter

Cover Introduction to Bioinformatics

Control of organization and organization of control  

This chapter studies more general control mechanisms, including gene expression. Life is a dynamic process, requiring robust control mechanisms. The chapter then looks at the goals of transcriptomics and proteomics—the measurement of amounts and distributions of RNAs and proteins within a cell or organism. Two major techniques for exploring the transcriptome are microarrays and RNA sequencing (RNAseq). DNA microarrays, or DNA chips, are devices for checking a sample simultaneously for the presence of many sequences. The chapter also considers the importance of protein–protein interaction networks, the methods available for generating them, and some of the databases that collect and present them. It details the structures and some of the building blocks of regulatory networks.

Chapter

Cover Genetics

Networks of Gene Regulation  

This chapter cites operons in bacteria as an example of gene regulatory networks, and it discusses transcriptional regulatory networks in eukaryotic organisms using recent information from many genome annotation projects, such as ENCODE. It explains that every gene has its own transcription pattern and changes in that pattern can have significant effects on phenotypes and morphological variation. It also points out that individual patterns of gene transcription must be coordinated so that the organism is transcribing all of the correct genes at the correct times and places. The chapter moves beyond the regulation of the expression of an individual gene to the orchestrated regulation of many genes. It highlights the processes by which gene expression is coordinated that are different in bacteria and eukaryotes but have some similar principles.

Chapter

Cover Study and Communication Skills for the Chemical Sciences

Career skills  

This chapter focuses on recognizing and articulating transferable skills. It explains how broader skills and capabilities enable a student to secure employment or get the most out of their future, whatever that may be. It also notes the importance of having something that can give students an edge in a climate where there are many more graduates than graduate-level positions. The chapter outlines the specific aspects of securing employment and considers networking, looking for jobs, preparing CVs, surviving interviews and assessment centres, and sources of support. It begins with networking, which is becoming increasingly important in securing employment as many vacancies are filled by word of mouth and through networking rather than through formal channels.

Chapter

Cover Genetic Analysis

Epistasis and genetic pathways  

This chapter explains epistasis, whereby the phenotype of one gene masks the phenotype of a different gene, and describes how it can be exploited to construct the logical pathway of the gene interactions that underlie a biological process. It notes that every biological process is the outcome of genes or gene products working together in pathways and networks, which may be linear or branched, and may involve many genes or few genes. The chapter discusses how gene interactions in negative, positive, and parallel pathways are inferred by using double mutants.

Chapter

Cover Mammalian Synthetic Biology

Mammalian Synthetic Biology as a Research Tool  

This chapter outlines the virtuous cycle in which basic science informs the design of synthetic systems, and new synthetic systems can be used to discover more basic science. It cites the two broad ways in which synthetic biology is applied to basic science: as a discovery tool and as a means of testing theories. It also elaborates on how synthetic biological techniques can allow experimenters to use light to activate specific neurons in an animal brain, defining RASSLs and demonstrating how they can be used to dissect complex signal pathways. The chapter examines the strengths and weaknesses of the methods of hypothesis testing, covering gene knockout, computer modelling, and modelling by synthetic biology. It discusses the concept of a functional motif and cites an example of a synthetic biological realization of a gene network motif.

Chapter

Cover Introduction to Bioinformatics

Introduction to systems biology  

This chapter describes systems biology. The key idea of systems biology is integration. Indeed, an initial goal of systems biology is to identify the active networks in cells, organisms, and ecosystems, and to understand the properties of their components and the interactions among them. The integrated activities of components of cells depend on networks of interactions. The chapter then looks at the general features of graphs, and the representation of networks by graphs. It considers which kinds of biological interaction patterns can profitably be thought of as networks. The chapter also identifies the distinction between static and dynamic properties of networks, before assessing the concepts of entropy and complexity and how to apply them to biological data. Finally, it outlines the properties of the Burrows-Wheeler transform and its applications.

Chapter

Cover An Introduction to Molecular Evolution and Phylogenetics

Phylogeny  

Tree of life

This chapter studies phylogeny. As populations divide and diverge, their DNA sequences become increasingly different from each other. DNA sequences sampled at the end point of this process carry the historical signal of population divergence. We can use alignments of DNA sequences to draw evolutionary trees that display the similarities between related lineages and the paths of descent of species. Sometimes the patterns in the sequences reveal a hierarchical history of populations dividing again and again. Because of this, we can use patterns of differences between DNA sequences from contemporary populations to reconstruct their evolutionary history. But sometimes the patterns are more complicated, if the historical signal has been erased, or when previously distinct lineages join back together through hybridization or gene transfer. One can represent many different histories in a network diagram.

Chapter

Cover Infection and Immunity

How pathogens escape innate immunity  

This chapter narrates how a pathogen escapes the powerful defence mechanisms of innate immunity. It follows the principal ways in which pathogens achieve this, then details how they are classified according to the immune component they are designed to avoid. The chapter also investigates how pathogens can circumvent the initial recognition of microbial surfaces in several ways, and how capsules can prevent activation of the alternative complement pathway. The chapter then shifts the focus to the phagocytic cell, noting it is the deadliest enemy for bacteria, fungi, and protozoa, particularly when it is assisted by complement and/or antibody. Next, the chapter explains the three main categories of pathogen survival strategies. It then considers the vital role of dendritic cell in T-cell activation, the interference of pathogens with the cytokine network, and the role of vectors.

Book

Cover Communication Skills for the Biosciences
Communication Skills for the Biosciences looks first at essential communication skills useful for the sciences. It examines recording and managing information and ethics in communication. It provides an introduction to the scientific literature available, how to conduct effective literature searches, and reviewing the literature. The text shows the reader how to write a literature review, a research proposal, a research paper, and an abstract. It also explains in detail how to prepare tables and figures, as this is one of the essential skills required for writing about biosciences. The text looks at beyond degree level and gives some tips on how to develop a Masters dissertation or a PhD thesis, and how to deliver an effective presentation or introduce a research poster. The last chapter of the book talks about networking.

Chapter

Cover Introduction to Genomics

Metabolomics  

This chapter expounds on metabolomics, which is focused on metabolites, that is, molecules undergoing a transformation in a biological system. The chapter notes that the metabolic networks of any organism correspond to graphs with metabolites as nodes and linking reactions as edges. It highlights the defining principles of the Enzyme Commission and the Gene Ontology Consortium classifications of the functions of biological molecules. It mentions the significance of accurate enzyme function annotations in databases of metabolic networks. The chapter also considers the ways in which metabolic pathways differ between species. It points out the physicochemical basis of enzymatic catalysis and the quantities needed to characterize enzyme kinetics—information needed to consider modelling flows through metabolic networks. It also talks about the difficulties in modelling the metabolic networks' traffic patterns.

Chapter

Cover Applications of Artificial Intelligence in Chemistry

Artificial neural networks  

This chapter covers artificial neural networks, which are an example of a connectionist model with many logical units that are connected in a network. It reviews the way in which the brain is believed to function, as the design of the artificial neural networks is inspired by the structure of that organ. It also explains that the neuron is the fundamental processing unit in a typical human brain. The chapter talks about the behaviour of the neuron as a threshold device that has a step-like shape known as a step function or Heaviside function. The chapter points out the crucial feature of the behaviour of the brain, which is that it does not need to be taught how to learn. It observes that artificial neural network programs are multi-purpose as they can solve problems by using spectral interpretation, propositional logic, image analysis, or fingerprint interpretation.

Chapter

Cover Genetic Analysis

Pathways, networks, and phenotypes  

This chapter looks into genetic interaction networks. It highlights the importance of understanding phenotype and genotype predictions despite the difficulty of categorizing and analysing genetic interactions. It notes that attempts are being made to map each network of physical interactions. It explores how interaction networks are also being integrated into systems-level descriptions. These include physical and genetic interactions. The chapter references a study which looked into a near complete genetic interaction network for cells. This then served as a template for general genetic and physical interactions. However, it clarifies that most complete networks of gene interactions do not record all of the cells and organisms' dynamic features. The chapter explains that direct interactions have been studied on a genome-wide scale, while indirect interactions are studied with mutants. It looks at some interaction maps that deliver some of the assembly instructions for constructing how parts interact to produce a phenotype.

Book

Cover Applications of Artificial Intelligence in Chemistry
Applications of Artificial Intelligence in Chemistry details the various applications of artificial intelligence in the chemical science fields. Artificial intelligence is not just about making machines think; it is also a powerful problem-solving tool. Many scientific problems can be solved only with difficulty using conventional methods, yet these same problems may be ideally suited to attack using artificial intelligence. The chapters cover artificial intelligence, artificial neural networks, expert systems, and genetic algorithms.

Chapter

Cover Neuroscience

Attention  

Edited by George J. Augustine, Jennifer Groh, Scott Huettel, Anthony-Samuel LaMantia, Leonard E. White, and Dale Purves,

This chapter focuses on the phenomenology of attention, its effects on sensory systems, and the neural systems that support its deployment. Endogenous attention refers to the ability to voluntarily direct attention based on one's goals, expectations, or knowledge. Meanwhile, exogenous attention refers to involuntary shifts of attention triggered by salient stimuli in the environment. Both lead to enhanced processing of the information to which attention has been directed. Recent research has identified a frontal-parietal network whose activity is associated with the engagement of attentional processes, as when a stimulus indicates the need to shift attention from one location in space to another. Ultimately, damage to cortical and subcortical regions can lead to deficits in attentional processing that have important clinical consequences.

Chapter

Cover Behavioral Neurobiology

Neuromodulation: The accommodation of motivational changes in behavior  

This chapter discusses neural mechanisms that mediate motivational changes in the behavior of animals. It tackles the two major neural mechanisms that mediate motivational changes in behavior: structural reorganization of neural networks and biochemical switching of neural networks. The chapter considers some well-studied model systems to illustrate underlying principles. It explains dendritic plasticity by examining the seasonal changes in chirping behavior of weakly electric knifefish. It also discusses the seasonal variation in dendritic morphology of motoneurons in white-footed mice. Furthermore, it explains axonal or synaptic plasticity as a mechanism for accommodating variability in reproductive behavior during the estrous cycle of female cats. Then it reviews the modulation of the stomatogastric ganglion and the modulation of crayfish aggressive behavior to explain biochemical switching.

Chapter

Cover Computational Chemistry

Introduction  

This introductory chapter provides an overview of computational chemistry, which is one of the fastest growing areas of chemistry. Although there are specialists in the field, increasingly the techniques are applied by experimental chemists using the ever-growing power of ever-cheaper computers. Ultimately, computational chemistry involves taking known theory and developing the computer software to solve chemical problems. The chapter then looks at the computer hardware and software that many computational chemists use. The main classes of problems which can be resolved by computer include single molecule calculations, assemblies of molecules, and reactions of molecules. Every time a significant advance has been made in computing technology or in application, computational chemists have seized the opportunity and incorporated it into their own field. The chapter considers two examples to illustrate this: computer graphics and neural networks.

Chapter

Cover Introduction to Bioinformatics

Metabolic pathways  

This chapter explores metabolic pathways, which are the road maps defining the possible transformations of metabolites. They form a network, representable as a graph, usually with the metabolites as nodes, and reactions connecting them as edges. The enzyme that catalyses each reaction labels the edge. The chapter then looks at the defining principles of the Enzyme Commission and the Gene Ontology ConsortiumTM classifications of the functions of biological molecules. It considers the importance of accurate annotation of enzyme function in databases, before outlining the databases of metabolic networks. The chapter also discusses the physicochemical basis of enzymatic catalysis, and the quantities needed to characterize their kinetics. Finally, it examines how the algorithms for comparison of nucleic acid and amino acid sequences can be generalized to compare and align metabolic pathways.

Book

Cover Polymers

David J. Walton and J. Phillip Lorimer

Polymers gives a thorough introduction to polymer chemistry, ranging from a historical perspective, through the development of high-tonnage materials earlier in the twentieth century, to modern high-performance materials that have a range of useful additional properties. Polymers are the archetypal modern materials, used in every aspect of everyday life. Chapters cover polymers, polymer properties and characterisation, chain polymerisation, step-growth polymers, three-dimensional networks, and functional polymers. The text also includes discussion of practical industrial aspects in the technology of these materials.