Springer protocols feed by Biotechnology 
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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.Lipophilic-Formulated Gold Porphyrin Nanoparticles for Chemotherapy
Lipophilic formulation is an invaluable technique for the delivery of cancer drugs. Incorporation of poorly soluble and toxic compounds into a lipophilic carrier vehicle improves both the stability and compatibility in blood and body fluids. Currently, although a large proportion of novel cancer drugs are poorly water soluble, most existing drug carriers are only able to encapsulate hydrophilic drugs. As the ultimate goal of drug delivery (in particular cancer drug delivery) is to achieve high therapeutic effect with minimal toxicity, it would thus be beneficial to invest substantial efforts in the development of lipophili...
Source: Springer protocols feed by Biotechnology - April 11, 2013 Category: Biotechnology Source Type: news
Retrosynthetic Design of Heterologous Pathways
Tools from metabolic engineering and synthetic biology are synergistically used in order to develop high-performance cell factories. However, the number of successful applications has been limited due to the complexity of exploring efficiently the metabolic space for the discovery of candidate heterologous pathways. To address this challenge, retrosynthetic biology provides an integrated framework to formalize and rationalize the problem of importing biosynthetic pathways into a chassis organism using methods at the interface from bottom-up and top-down strategies. Here, we describe step by step the process of implementing...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
13C-Based Metabolic Flux Analysis: Fundamentals and Practice
Isotope-based metabolic flux analysis is one of the emerging technologies applied to system level metabolic phenotype characterization in metabolic engineering. Among the developed approaches, 13C-based metabolic flux analysis has been established as a standard tool and has been widely applied to quantitative pathway characterization of diverse biological systems. To implement 13C-based metabolic flux analysis in practice, comprehending the underlying mathematical and computational modeling fundamentals is of importance along with carefully conducted experiments and analytical measurements. Such knowledge is also crucial w...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Nuclear Magnetic Resonance Methods for Metabolic Fluxomics
Fluxomics, through its core methodology of metabolic flux analysis (MFA), enables quantification of carbon traffic through cellular biochemical pathways. Isotope labeling experiments aid MFA by providing information on intracellular fluxes, especially through parallel and cyclic pathways. Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are two complementary methods to measure abundances of isotopomers generated in these experiments. 2-D [13C, 1H] heteronuclear correlation NMR spectra can detect 13C isotopes coupled to protons and thus noninvasively separate molecules and atoms with a specific isotopic content f...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Using Multiple Tracers for 13C Metabolic Flux Analysis
13C-Metabolic flux analysis (13C-MFA) is a powerful technique for quantifying intracellular metabolic fluxes in living cells. These in vivo fluxes provide important information on the physiology of cells in culture, which can be used for metabolic engineering purposes and serve as inputs for systems biology modeling. The 13C-MFA technique consists of several steps: (1) selecting appropriate tracers for a given system of interest, (2) performing isotopic labeling experiments, (3) measuring isotopic labeling distributions in metabolic products, (4) estimating metabolic fluxes using least-squares regression, and (5) evaluatin...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Isotopically Nonstationary 13C Metabolic Flux Analysis
We describe protocols for performing the necessary isotope labeling experiments, for quenching and extraction of intracellular metabolites, for mass spectrometry (MS) analysis of metabolite labeling, and for computational flux estimation using INST-MFA. By combining several recently developed experimental and computational techniques, INST-MFA provides an important new platform for mapping carbon fluxes that is especially applicable to animal cell cultures, autotrophic organisms, industrial bioprocesses, high-throughput experiments, and other systems that are not amenable to steady-state 13C MFA experiments. (Source: Sprin...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs)
The non-synonymous SNPs, the so-called non-silent SNPs, which are single-nucleotide variations in the coding regions that give “birth” to amino acid mutations, are often involved in the modulation of protein function. Understanding the effect of individual amino acid mutations on a protein/enzyme function or stability is useful for altering its properties for a wide variety of engineering studies. Since measuring the effects of amino acid mutations experimentally is a laborious process, a variety of computational methods have been discussed here that aid to extract direct genotype to phenotype information. (Sou...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Sample Preparation and Biostatistics for Integrated Genomics Approaches
Genomics is based on the ability to determine the transcriptome, proteome, and metabolome of a cell. These technologies only have added value when they are integrated and based on robust and reproducible workflows. This chapter describes the experimental design, sampling, sample pretreatment, data evaluation, integration, and interpretation. The actual generation of the data is not covered in this chapter since it is highly depended on available equipment and infrastructure. (Source: Springer protocols feed by Biotechnology)
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Linking RNA Measurements and Proteomics with Genome-Scale Models
Genome-scale metabolic models (GMMs) have been recognized as being powerful tools for capturing system-wide metabolic phenomena and connecting those phenomena to underlying genetic and regulatory changes. By formalizing and codifying the relationship between the levels of gene expression, protein concentration, and reaction flux, metabolic models are able to translate changes in gene expression to their effects on the metabolic network. A number of methods are then available to interpret how those changes are manifest in the metabolic flux distribution. In addition to discussing how gene expression datasets can be interpre...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Comparative Transcriptome Analysis for Metabolic Engineering
Transcriptome profiling allows massively parallel analysis of the dynamic expression of all genes and captures the cell physiology and regulatory mechanism in a holistic manner. Compared to other “omic” techniques, transcriptome is more tractable and sensitive. Transcriptomics has profoundly promoted development and applications of metabolic engineering by analysis of cell metabolism at a system level. Our recent effort was performed on a comparative transcriptome profiling between a riboflavin-producing Bacillus subtilis strain RH33 and the wild-type strain B. subtilis 168 to rationally identify new targets fo...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation
By the combinations of high-throughput analytical technologies in the fields of transcriptomics, proteomics, and metabolomics, we are now able to gain comprehensive and quantitative snapshots of the intracellular processes. Dynamic intracellular activities and their regulations can be elucidated by systematic observation of these multi-omics data. On the other hand, careful statistical analysis is necessary for such integration, since each of the omics layers as well as the specific analytical methodologies harbor different levels of noise and variations. Moreover, interpretation of such multitude of data requires an intui...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Resolving Cell Composition Through Simple Measurements, Genome-Scale Modeling, and a Genetic Algorithm
The biochemical composition of a cell is very complex and dynamic. It varies greatly among different organisms and environmental conditions. Inclusion of proper cell composition data is critical for accurate genome-scale metabolic flux modeling using flux balance analysis (FBA). However, determining cell composition experimentally is currently time-consuming and resource intensive. In this chapter, a method for predicting cell composition using a genome-scale model and “easy to measure” culture data (e.g., glucose uptake rate, and specific growth rate) is presented. The method makes use of a genetic algorithm f...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Linking Genome-Scale Metabolic Modeling and Genome Annotation
Genome-scale metabolic network reconstructions, assembled from annotated genomes, serve as a platform for integrating data from heterogeneous sources and generating hypotheses for further experimental validation. Implementing constraint-based modeling techniques such as flux balance analysis (FBA) on network reconstructions allows for interrogating metabolism at a systems level, which aids in identifying and rectifying gaps in knowledge. With genome sequences for various organisms from prokaryotes to eukaryotes becoming increasingly available, a significant bottleneck lies in the structural and functional annotation of the...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Metabolic Model Refinement Using Phenotypic Microarray Data
Phenotypic microarray (PM) is a standardized, high-throughput technology for profiling phenotypes of microorganisms, which allows for characterization on around 2,000 different media conditions. The data generated using PM can be incorporated into genome-scale metabolic models to improve their predictive capability. In addition, a comparison of phenotypic profiles of wild-type and gene knockout mutants can give essential information about gene functions of unknown genes. In this chapter, we present a protocol to refine preconstructed metabolic models using the PM data. Both manual refinement and algorithmic approaches for ...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED
Over the past decade, genome-scale metabolic models have proven to be a crucial resource for predicting organism phenotypes from genotypes. These models provide a means of rapidly translating detailed knowledge of thousands of enzymatic processes into quantitative predictions of whole-cell behavior. Until recently, the pace of new metabolic model development was eclipsed by the pace at which new genomes were being sequenced. To address this problem, the RAST and the Model SEED framework were developed as a means of automatically producing annotations and draft genome-scale metabolic models. In this chapter, we describe the...
Source: Springer protocols feed by Biotechnology - February 19, 2013 Category: Biotechnology Source Type: news
