This chapter considers the development of new technologies and their impact on
understanding the molecular biology of cells. It describes complete genome sequences of a
wide variety of organisms that provide a wealth of information that forms a new framework
for studies of cell and molecular biology and opens new possibilities in medical practice.
It also shows how the sequences of complete genomes are obtained and undertake large-scale
analyses of all RNAs and proteins expressed in individual cells. The chapter reviews global
experimental approaches that form the basis of the new field of systems biology, which seeks
a quantitative understanding of the integrated behavior of complex biological systems. It
outlines the basic approaches used in next-generation sequencing and global methods used to
study gene expression.
Chapter
Genomics, Proteomics, and Systems Biology
Chapter
Introduction To Cell Signalling
This chapter explains why the study of cell signalling is important and instrumental to modern biology and traces the history of cell signalling. It outlines the principles behind the workings of cell signalling, which can be applied to all living systems, and discusses a selection of diseases caused by cell signalling dysfunction. It also describes cell signalling as a regulatory system that enables cells to control their inner workings and perceive their environment and respond when changes are required. The chapter highlights the need of cells of multicellular organisms to respond to the messages created by other cells and to conditions on their outsides. It demonstrates how cells communicate between each other and influence each other's activities through the release and reception of hormones.
Chapter
Polar Marine Biology
This chapter explores polar marine biology. Polar ecosystems are influenced by strong seasonality, especially of ice cover. Also, a diverse phytoplankton assemblage fuels the polar food webs. Carnivores exert top-down effects, so overfishing of carnivores has had strong effects on polar food webs. The chapter considers the impact of climate change and ocean warming on the organization of polar ecosystems. It examines the food webs and the impact of climate change within Arctic marine systems and Antarctic marine systems. Global climate change is decreasing summer ice cover in the Arctic, so major changes are occurring in sea temperature and the organization of benthic communities.
Book
Jamie A. Davies
Mammalian Synthetic Biology starts by introducing the biology of mammals and providing a broad overview of how synthetic biology is applied to mammals. It then presents some special features of mammalian systems that distinguish mammals from other organisms before introducing methods used in mammalian synthetic biology. After that, the text moves on to look at mammalian synthetic biology as a research tool. It also examines teaching mammalian cells to make new, useful things, i.e. their role in bioproduction. Towards the end of the text there is an examination of synthetic biology, stem cells, and regenerative medicine. Finally, the text ends by looking at ethical concerns and responsibilities related to synthetic biology.
Chapter
An Introduction to Mammalian Synthetic Biology
This chapter describes various features of mammals that set them apart from other animals and looks at five features of mammalian synthetic biology. It covers the structure, function, behaviour, development, and evolution of mammals. The chapter also provides an overview of the two broad classes into which work in mammalian synthetic biology can be divided: in vitro and in vivo. It also elaborates on the difficulties that mammalian systems pose for synthetic biology projects. The chapter reviews recent developments that have seen the genetic alteration of mammals in terms of moving from making destructive interventions to test theories to constructive projects that confer an ability it did not have before on a mammal.
Chapter
Technologies for Mammalian Synthetic Biology
Leonard J. Nelson and Alistair Elfick
This chapter discusses methods by which DNA can be edited, written, and constructed, including the challenges faced in authoring DNA. It shows how the function of DNA instructions can be lost over time and how practitioners are seeking to protect DNA from corruption. It also analyses the aspiration of synthetic biology to create or improve function in biological systems by considering them as a type of material from which to design. The chapter talks about the engineering approach to synthetic biology which centres around the Design–Build–Test cycle as its key notion and aims for the optimization of each step towards a degree of predictability which allows a single orbit of that cycle to deliver a best design. The chapter also explains that the key underpinning technological tool that enables synthetic biology is the ability to produce genetic devices by modifying or creating DNA code.
Chapter
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
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
Patterns in the Marine Environment
This chapter examines major patterns in marine organisms and their biology. Doing so gives a strong insight into the processes that determine success and evolution of life on Earth. The chapter shows how the wide expanse of the oceanscape changes dramatically, from undersea mountain ranges to sediment plains and coral reefs to forests of kelp. Patterns of organisms, so obvious at the shore, are also evident from the poles to the tropics, from coasts to ocean centres, from the shallows to the deep abyss, and from millions of years ago to the present day. Patterns occur in species richness, abundance, ancientness, or size, all of which are indicators of powerful changes on the planet surface over time and space. Oceans have widened or been compressed, risen and fallen, heated and cooled, and remain dynamic as a habitat for life.
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Pathways are the key to signalling
This chapter highlights how signalling components are grouped together in pathways. It looks at the barriers to be crossed and distances to be travelled in situations where signalling is required. The chapter contends that the relay of the message in biological signalling usually involves many components and many mechanisms, which is illustrated by some simple examples. Clearly, there are many other examples that could have been used, but these well-characterized examples have been chosen because they illustrate pertinent points that can be used to understand more complicated pathways. Finally, the chapter considers computer modelling and a systems biology approach in terms of the complexity of pathways in the future.
Chapter
Computational biology
Introduction
Computational biology is the application of computational methods to all levels of exploration; molecules to ecosystems. This is huge area of research that can be subdivided in various ways. The computer is, of course, also an indispensible tool in every branch of biophysics discussed...
Book
Arthur M. Lesk
Introduction to Protein Science firstly outlines the topics ahead. The first main topic is protein structure and protein structure determination. The next subject the text considers is bioinformatics of protein sequence and structure. Proteins as catalysts is examined after that. This discussion particularly looks at enzyme structure, kinetics, and mechanisms. The text then moves on to describe proteins with partners, the evolution of protein structure and function, and protein folding and design. Finally, it looks at proteomics and systems biology.
Chapter
Synapsids and the Origin of Mammals
This chapter considers the sequential acquisition of the most important mammalian characters within the synapsid lineage. It explores the evolutionary history of synapsids in relation to their feeding, hearing, locomotion and breathing. The three clades of Mammalia range between Prototheria (monotremes and extinct relatives), Allotheria (multituberculates and related taxa), and Theria. Mammals have more complex social systems than most other vertebrates, and these complexities correlate with many features of their biology. The chapter cites that the classic features defining mammals are hair and mammary glands. It mentions how studying fossilized skeletons helps with the understanding of the origins of mammals.
Chapter
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.
Book
Arthur M. Lesk
Introduction to Genomics provides insight into many topics in the field of genomics, including the similarities and differences between organisms, how different organisms evolved, and how our understanding of genomics may inform human health and well-being in the future. After a general introduction, the book looks at the human genome project before turning its attention to mapping, sequencing, annotation, and databases. It also looks at evolution and genomic change. The text examines the following topics in more detail: the genomes of prokaryotes and viruses, the genomes of eukaryotes, and comparative genomics. It looks at the impact of genomics on human health and disease and the relationship between genomics and anthropology. Finally transcriptomics, proteomics, metabolomics, and systems biology are considered.
Chapter
Proteomics and systems biology
This chapter studies systems biology and proteomics. Systems biology tries to synthesize proteomic, genomic, and other data into an integrated picture of the structure, dynamics, logistics, and, ultimately, the logic of living things. The chapter begins by looking at the methods for separation and analysis of proteins, including several techniques based on polyacrylamide gel electrophoresis (PAGE). It then considers the experimental techniques and results of measurements of protein expression patterns, including mass spectrometry and microarrays, and RNA sequencing (RNAseq). The chapter also explores the developments in metagenomics and metaproteomics: the applications of methods from the laboratory to natural ecosystems. Finally, it examines protein complexes, gene regulation, and the adaptability of the yeast regulatory network.
