Springer protocols feed by Biotechnology 
This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.
This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Genome-Scale Model Management and Comparison
Spurred by recent innovations in genome sequencing, the reconstruction of genome-scale models has increased in recent years. Genome-scale models are now available for a wide range of organisms, and models have been successfully applied to a number of research topics including metabolic engineering, genome annotation, biofuel production, and interpretation of omics data sets. The challenge is how to manage the large amount of data in genome-scale models and perform comparative analysis to gain new biological insights. In this chapter, important standards for genome-scale modeling are outlined. Furthermore, management strate...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Computational Tools for Guided Discovery and Engineering of Metabolic Pathways
With a high demand for increasingly diverse chemicals, as well as sustainable synthesis for many existing chemicals, the chemical industry is increasingly looking to biosynthesis. The majority of biosynthesis examples of useful chemicals are either native metabolites made by an organism or the heterologous expression of known metabolic pathways into a more amenable host. For chemicals that no known biosynthetic route exists, engineers are increasingly relying on automated computational algorithms, as described here, to identify potential metabolic pathways. In this chapter, we review a broad range of approaches to predict ...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Kinetic Modeling of Metabolic Pathways: Application to Serine Biosynthesis
In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway using kinetic data from both experimental measurements and literature review. Our methodology is presented by using the example of serine biosynthesis in E. coli. (Source: Springer protocols feed by Biotechnology)
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering
Introduction of a heterologous metabolic pathway into a platform microorganism for applications in metabolic engineering and synthetic biology is often technically straightforward. However, the major challenge is to balance the flux in the pathway to obtain high yield and productivity in a target microorganism. To address this limitation, we recently developed a simple, efficient, and programmable approach named “customized optimization of metabolic pathways by combinatorial transcriptional engineering” (COMPACTER) for balancing the flux in a pathway under distinct metabolic backgrounds. Here we use two example...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Adaptive Laboratory Evolution for Strain Engineering
Complex phenotypes, such as tolerance to growth inhibitors, are difficult to rationally engineer into industrial model organisms due our poor understanding of their underlying molecular mechanisms. Adaptive evolution circumvents this issue by exploiting the linkage between growth rate and inhibitor resistance to select for mutants with enhanced tolerance. In order to aid experimentalists in the design and execution of adaptive laboratory evolution, we present detailed protocols for batch, continuous, and visualizing evolution in real-time (VERT) approaches to this technique. (Source: Springer protocols feed by Biotechnology)
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism)
The integration of transcriptional regulatory and metabolic networks is a crucial step in the process of predicting metabolic behaviors that emerge from either genetic or environmental changes. Here, we present a guide to PROM (probabilistic regulation of metabolism), an automated method for the construction and simulation of integrated metabolic and transcriptional regulatory networks that enables large-scale phenotypic predictions for a wide range of model organisms. (Source: Springer protocols feed by Biotechnology)
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Trackable Multiplex Recombineering for Gene-Trait Mapping in E. coli
Recent advances in homologous recombination in Escherichia coli have enabled improved genome engineering by multiplex recombineering. In this chapter, we present trackable multiplex recombineering (TRMR), a method for gene-trait mapping which creates simulated knockdown and overexpression mutants for virtually all genes in the E. coli genome. The method combines oligonucleotide synthesis with multiplex recombineering to create two libraries comprising of over 8,000 E. coli strains in total that can be selected for traits of interest via high-throughput screening or selection. DNA barcodes included in the recombineering cas...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Discovery of Posttranscriptional Regulatory RNAs Using Next Generation Sequencing Technologies
Next generation sequencing (NGS) has revolutionized the way by which we engineer metabolism by radically altering the path to genome-wide inquiries. This is due to the fact that NGS approaches offer several powerful advantages over traditional methods that include the ability to fully sequence hundreds to thousands of genes in a single experiment and simultaneously detect homozygous and heterozygous deletions, alterations in gene copy number, insertions, translocations, and exome-wide substitutions that include “hot-spot mutations.” This chapter describes the use of these technologies as a sequencing technique ...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Identification of Mutations in Evolved Bacterial Genomes
Directed laboratory evolution is a common technique to obtain an evolved bacteria strain with a desired phenotype. This technique is especially useful as a supplement to rational engineering for complex phenotypes such as increased biocatalyst tolerance to toxic compounds. However, reverse engineering efforts are required in order to identify the mutations that occurred, including single nucleotide polymorphisms (SNPs), insertions/deletions (indels), duplications, and rearrangements. In this protocol, we describe the steps to (1) obtain and sequence the genomic DNA, (2) process and analyze the genomic DNA sequence data, an...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
