实验基础

Lignocellulosic biomass is a potential feedstock for bioethanol production. Biomass hydrolysates, prepared with a procedure including pretreatment and hydrolysis, are considered to be used as fermentation media for microorganisms, such as yeast. During the hydrolysate pre ...

While large amount of strains can be quickly generated via metabolic engineering, the speed/efficiency of evaluating each strain becomes the bottleneck in the process from strain development to final production. In this chapter, a method is introduced to rapidly evaluate strain perfo ...

Industrial biotechnology employs microorganisms (strains) for manufacture of certain food or industrial products to meet the increasing need of the world. To develop a bioproduction process, the first step is to screen out a production strain from isolated, mutated, or genetically en ...

Metabolic engineers modify biological systems through the use of modern molecular biology tools in order to obtain desired phenotypes. However, due to the extreme complexity and interconnectedness of metabolism in all organisms, it is often difficult to a priori predict which changes ...

Many proteins and peptides have been used in therapeutic or industrial applications. They are often produced as recombinant forms by microbial fermentation. Targeted metabolic engineering of the production strains has usually been the approach taken to increase protein product ...

A program of mutation and screening, with stepwise reverse engineering or “decoding” of the improved strain, is a way to better understand the genetics and physiology of the strain improvement process. As more is learned about the genetics of strain improvement, it is hoped that more fundament ...

The production of biofuels from renewable sources by microbial engineering has gained increased attention due to energy and environmental concerns. Butanol is one of the important gasoline-substitute fuels and can be produced by native microorganism Clostridium acetobutyli ...

Discrete mathematical formalisms are well adapted to model large biological networks, for which detailed kinetic data are scarce. This chapter introduces the reader to a well-established qualitative (logical) framework for the modelling of regulatory networks. Relying on GINs ...

Graph theory analysis of biological networks, such as protein–protein interactions (PPIs), gene regulatory, metabolic, etc., has identified a strong relationship between topology of these networks and the underlying cellular function and biological processes (Sharan et al. Mol ...

MCL is a general purpose cluster algorithm for both weighted and unweighted networks. The algorithm utilises network topology as well as edge weights, is highly scalable and has been applied in a wide variety of bioinformatic methods. In this chapter, we give protocols and case studies for clust ...

Data from high-throughput experimental methods are currently being used to construct complex biological networks. These include regulatory gene networks, regulatory protein–DNA networks, protein–protein interaction networks, or metabolic networks. Independent of i ...

The degree distribution has been viewed as an important characteristic of network data. Many biological networks have been labelled scale-free as their degree distribution can be approximately described by a power-law probability distribution. This chapter presents a formal sta ...

The ability to analyze large biological networks proves to be a computationally expensive task, but the information one can gain is worth the cost and effort. In cancer research for example, one is able to derive knowledge about putative drug targets by revealing the strengths and weaknesses in ...

Phylogenetic profiling involves the comparison of phylogenetic data across gene families. It is possible to construct phylogenetic trees, or related data structures, for specific gene families using a wide variety of tools and approaches. Phylogenetic profiling involves the com ...

Public online microarray databases contain tremendous amounts of expression data. Mining these data sources can provide a wealth of information on the underlying transcriptional networks. In this chapter, we illustrate how the web services COLOMBOS and DISTILLER can be used to ident ...

Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more ...

Enzymatic reactions form a hypergraph structure and their translation into a graph structure accompanies an information loss. This chapter introduces well-known topological transformations from metabolic reactions to a graph, and discusses their advantages and disadvan ...

The tree of life is the classical representation of the evolutionary relationships between existent species. A tree is appropriate to display the divergence of species through mutation, i.e., by vertical descent. However, lateral gene transfer (LGT) is excluded from such representati ...

The importance of horizontal/lateral gene transfer (LGT) in shaping the genomes of prokaryotic organisms has been recognized in recent years as a result of analysis of the increasing number of available genome sequences. LGT is largely due to the transfer and recombination activities of m ...

Metagenomics is revolutionizing the field of microbial ecology through techniques that eliminate the prerequisite of culturing. Metagenomic studies of microbial populations in different environments reveal the incredible diversity and adaptive capabilities of these ...