Chapter 2 Data mining for microbiologists
Publication date: 2012 Source:Methods in Microbiology, Volume 39 Author(s): J.S. Hallinan The enormous amounts of molecular microbiological data currently produced by high-throughput analytical techniques pose both huge opportunities and huge challenges for microbiologists. With over 1000 databases online, it is clearly not feasible for researchers to manually search each one for information about the genes and processes in which they are interested. Much of the data stored in these databases never makes it into the peer-reviewed literature, and so becomes essentially unavailable in its entirety. A powerful approach t...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 1 High-resolution temporal analysis of global promoter activity in Bacillus subtilis
We describe promoter fusion methodology in detail and show how strain manipulations can be easily multiplexed for high-throughput global analysis. We show how multiple expression profiles can be visualized in a heat map format that facilitates comparative analysis. Finally, we evaluate the important components (e.g. plasmids, promoter containing fragments) and steps of the methodology so that optimal strategies can be devised for novel applications and bacterial systems. (Source: Methods in Microbiology)
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Series Advisors
Publication date: 2012 Source:Methods in Microbiology, Volume 39 (Source: Methods in Microbiology)
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 7 Platforms for Genetic Design Automation
Publication date: 2013 Source:Methods in Microbiology, Volume 40 Author(s): Chris J. Myers Crucial to the success of synthetic biology is the development of platforms for genetic design automation (GDA). This chapter presents the current state-of-the-art in GDA tools. This chapter also briefly describes the standards used for data representation that enable these GDA tools to work together to complete a genetic design task and the emerging repositories that are available to archive and share these data. Finally, this chapter compares tool capabilities and discusses future requirements for a complete GDA workflow. (Sou...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 6 Noise and Stochasticity in Gene Expression A Pathogenic Fate Determinant
Publication date: 2013 Source:Methods in Microbiology, Volume 40 Author(s): Mikkel Girke Jørgensen , Renske van Raaphorst , Jan-Willem Veening Not all cells in a bacterial population exhibit exactly the same phenotype, even though they grow in the same environment and are genetically identical. This phenomenon is known as phenotypic variation. The major source of phenotypic variation is noise or stochasticity in gene expression networks, which can directly promote the formation of population heterogeneity. Bistability, or the existence of two stable subpopulations, is a direct outcome of gene expression noise. In t...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 5 Engineering Microbial Biosensors
Publication date: 2013 Source:Methods in Microbiology, Volume 40 Author(s): Lisa Goers , Nicolas Kylilis , Marios Tomazou , Ke Yan Wen , Paul Freemont , Karen Polizzi The use of biological entities as ‘sensors’ has long been of interest to engineers and biologists. With recent advances in our ability to engineer biology, potential biosensors can be identified, engineered and tested faster than ever before. In this chapter, we discuss different types of biosensors and their potential uses and the considerations and requirements associated with engineering and using them. We give a step-by-step guide of how to ...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 4 Bacillus subtilis Model Gram-Positive Synthetic Biology Chassis
Publication date: 2013 Source:Methods in Microbiology, Volume 40 Author(s): Colin R. Harwood , Susanne Pohl , Wendy Smith , Anil Wipat The accumulation, over more than half a century, of detailed knowledge of the biochemistry, genetics and physiology of Bacillus subtilis, enhanced in recent years by a number of systematic ‘omics’ studies, has resulted in the recognition of this bacterium as a highly amenable chassis for synthetic biology. This chapter describes the features of this bacterium that support this recognition. Although the genome of B. subtilis was first published more that 15 years ago, recent geno...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 3 Social Dimensions of Microbial Synthetic Biology
We describe these through a series of important shifts that have taken place over the past few decades of social science research. We suggest a move away from discussions centred around ethical ‘implications’, speculations about the future and concerns about risk, regulation and public acceptance, towards a conversation that talks in terms of social ‘dimensions’, anticipating the future, managing uncertainty, tools of governance and research for the public good. We argue that these seemingly subtle changes in vocabulary open up a new and productive space for thinking about the social dimensions of synthetic biology...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 2 Constraints in the Design of the Synthetic Bacterial Chassis
Publication date: 2013 Source:Methods in Microbiology, Volume 40 Author(s): Antoine Danchin , Agnieszka Sekowska Synthetic biology is commonly viewed as a research and engineering domain of biology where a human-designed genetic program is synthesised and transplanted into a relevant cell type from an extant organism. The host cell’s ability to reproduce and express the program is taken for granted. By contrast, we discuss here the hierarchy of engineering functions that need to rule the host cell, using the top-down methodology of designer functional analysis. With the view that the final synthetic construct behav...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 1 Computational Intelligence in the Design of Synthetic Microbial Genetic Systems
Publication date: 2013 Source:Methods in Microbiology, Volume 40 Author(s): Jennifer S. Hallinan The large-scale engineering of novel bacterial systems is a complex, challenging task. Although small circuits can be designed manually, using the domain knowledge of the designer, this approach is not feasible for designs involving multiple pathways or even complete genomes. In this chapter, we address the value of computational intelligence approaches to the design of synthetic genetic circuits. Computational intelligence algorithms were designed to operate in complex, poorly understood domains in which the quality of a ...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Series Page
Publication date: 2013 Source:Methods in Microbiology, Volume 40 (Source: Methods in Microbiology)
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 2 Identification of conserved indels that are useful for classification and evolutionary studies
Publication date: Available online 3 June 2014 Source:Methods in Microbiology Author(s): Radhey S. Gupta Phylogenetic treeing approaches for the classification of organisms have a number of important limitations. The most significant of these drawbacks is that different groups/taxa are distinguished from each other primarily on the basis of their branching in the trees and, in most cases, no unique property of any kind (viz. biochemical, molecular, structural or physiological) is known that is specifically shared by members of different taxa. Analyses of genome sequences are leading to discovery of multiple kinds of m...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 14 An introduction to phylogenetics and the tree of life
We present an introduction to experimental design and hypothesis testing in phylogenetics, guiding the reader through the series of steps that are generally involved in making phylogenetic trees. These include choosing a phylogenetic question, selecting the appropriate sequences to analyse, aligning sequences and assessing the quality of sequence alignments, choosing the appropriate phylogenetic methods and interpreting the results. We provide a brief introduction to the freely available, open source software and Web services that can be used to perform these tasks and discuss the difficulties most frequently encountered w...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 9 Multi-locus sequence typing and the gene-by-gene approach to bacterial classification and analysis of population variation
Publication date: Available online 17 July 2014 Source:Methods in Microbiology Author(s): Alison J. Cody , Julia S. Bennett , Martin C.J. Maiden For nearly 30 years, 16S rRNA gene sequencing has been a fundamental tool for identification and cataloguing of bacterial diversity, but the diversity at this locus lacks the resolution to distinguish closely related bacteria. Multi-locus sequence typing (MLST) established the utility of a portable, gene-by-gene approach to population analyses, using both allelic and nucleotide sequence data that catalogue variation at seven housekeeping loci; however, it did not provide su...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 11 MALDI-TOF mass spectrometry applied to classification and identification of bacteria
Publication date: Available online 17 July 2014 Source:Methods in Microbiology Author(s): Peter Schumann , Thomas Maier Since the introduction of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for classification and identification of prokaryotes approximately 20 years ago, this technique has found increasing application in medical diagnostics, pharmaceutical quality control and environmental research as well as in veterinary medicine and the food industry. MALDI-TOF MS has become a promising alternative to conventional identification techniques and is even beginning to out...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
