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Advances in Biochemical Engineering/biotechnology

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https://www.readbyqxmd.com/read/28070596/chip-seq-data-analysis-to-define-transcriptional-regulatory-networks
#1
Giulio Pavesi
The first step in the definition of transcriptional regulatory networks is to establish correct relationships between transcription factors (TFs) and their target genes, together with the effect of their regulatory activity (activator or repressor). Fundamental advances in this direction have been made possible by the introduction of experimental techniques such as Chromatin Immunoprecipitation, which, coupled with next-generation sequencing technologies (ChIP-Seq), permit the genome-wide identification of TF binding sites...
January 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28070595/photosynthetic-microbial-fuel-cells
#2
Joseph A Laureanti, Anne K Jones
This chapter presents the current state of research on bioelectrochemical systems that include phototrophic organisms. First, we describe what is known of how phototrophs transfer electrons from internal metabolism to external substrates. This includes efforts to understand both the source of electrons and transfer pathways within cells. Second, we consider technological progress toward producing bio-photovoltaic devices with phototrophs. Efforts to improve these devices by changing the species included, the electrode surfaces, and chemical mediators are described...
January 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28070594/network-metamodeling-effect-of-correlation-metric-choice-on-phylogenomic-and-transcriptomic-network-topology
#3
Deborah A Weighill, Daniel Jacobson
We explore the use of a network meta-modeling approach to compare the effects of similarity metrics used to construct biological networks on the topology of the resulting networks. This work reviews various similarity metrics for the construction of networks and various topology measures for the characterization of resulting network topology, demonstrating the use of these metrics in the construction and comparison of phylogenomic and transcriptomic networks.
January 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28058453/early-history-of-the-breeding-of-amino-acid-producing-strains
#4
Shigeru Nakamori
Amino acid production started in Japan in 1908 with the extraction of monosodium glutamate (MSG) from acid hydrolysates of proteins. In addition to extraction, other methods of amino acid production include chemical synthesis, fermentation, and enzymatic synthesis both for glutamic acid and other amino acids. In this chapter, we review the historical transition of these production methods; currently, fermentation is the chief production method of amino acids. All wild-type microorganisms possess a negative feedback control system (feedback inhibition and repression) on the enzymes within the amino acid biosynthetic pathways...
January 6, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27928579/protein-protein-interface-and-disease-perspective-from-biomolecular-networks
#5
Guang Hu, Fei Xiao, Yuqian Li, Yuan Li, Wanwipa Vongsangnak
Protein-protein interactions are involved in many important biological processes and molecular mechanisms of disease association. Structural studies of interfacial residues in protein complexes provide information on protein-protein interactions. Characterizing protein-protein interfaces, including binding sites and allosteric changes, thus pose an imminent challenge. With special focus on protein complexes, approaches based on network theory are proposed to meet this challenge. In this review we pay attention to protein-protein interfaces from the perspective of biomolecular networks and their roles in disease...
December 8, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27928578/reporter-gene-assays-in-ecotoxicology
#6
Tal Elad, Shimshon Belkin
The need for simple and rapid means for evaluating the potential toxic effects of environmental samples has prompted the development of reporter gene assays, based on tester cells (bioreporters) genetically engineered to report on sample toxicity by producing a readily quantifiable signal. Bacteria are especially suitable to serve as bioreporters owing to their fast responses, low cost, convenient preservation, ease of handling, and amenability to genetic manipulations. Various bacterial bioreporters have been introduced for general toxicity and genotoxicity assessment, and the monitoring of endocrine disrupting and dioxin-like compounds has been mostly covered by similarly engineered eukaryotic cells...
December 8, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27913830/genome-scale-modeling-of-thermophilic-microorganisms
#7
Sanjeev Dahal, Suresh Poudel, R Adam Thompson
Thermophilic microorganisms are of increasing interest for many industries as their enzymes and metabolisms are highly efficient at elevated temperatures. However, their metabolic processes are often largely different from their mesophilic counterparts. These differences can lead to metabolic engineering strategies that are doomed to fail. Genome-scale metabolic modeling is an effective and highly utilized way to investigate cellular phenotypes and to test metabolic engineering strategies. In this review we chronicle a number of thermophilic organisms that have recently been studied with genome-scale models...
December 3, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27913829/glutamate-fermentation-2-mechanism-of-l-glutamate-overproduction-in-corynebacterium-glutamicum
#8
Takashi Hirasawa, Masaaki Wachi
The nonpathogenic coryneform bacterium, Corynebacterium glutamicum, was isolated as an L-glutamate-overproducing microorganism by Japanese researchers and is currently utilized in various amino acid fermentation processes. L-Glutamate production by C. glutamicum is induced by limitation of biotin and addition of fatty acid ester surfactants and β-lactam antibiotics. These treatments affect the cell surface structures of C. glutamicum. After the discovery of C. glutamicum, many researchers have investigated the underlying mechanism of L-glutamate overproduction with respect to the cell surface structures of this organism...
December 3, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27913828/engineering-and-evolution-of-saccharomyces-cerevisiae-to-produce-biofuels-and-chemicals
#9
Timothy L Turner, Heejin Kim, In Iok Kong, Jing-Jing Liu, Guo-Chang Zhang, Yong-Su Jin
To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology...
December 3, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27909736/discovery-and-history-of-amino-acid-fermentation
#10
Shin-Ichi Hashimoto
There has been a strong demand in Japan and East Asia for L-glutamic acid as a seasoning since monosodium glutamate was found to present umami taste in 1907. The discovery of glutamate fermentation by Corynebacterium glutamicum in 1956 enabled abundant and low-cost production of the amino acid, creating a large market. The discovery also prompted researchers to develop fermentative production processes for other L-amino acids, such as lysine. Currently, the amino acid fermentation industry is so huge that more than 5 million metric tons of amino acids are manufactured annually all over the world, and this number continues to grow...
December 2, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872968/new-functions-and-potential-applications-of-amino-acids
#11
Hisayuki Uneyama, Hisamine Kobayashi, Naoto Tonouchi
Currently, several types of amino acids are being produced and used worldwide. Nevertheless, several new functions of amino acids have been recently discovered that could result in other applications. For example, oral stimulation by glutamate triggers the cephalic phase response to prepare for food digestion. Further, the stomach and intestines have specific glutamate-recognizing systems in their epithelial mucosa. Regarding clinical applications, addition of monosodium glutamate to the medicinal diet has been shown to markedly enhance gastric secretion in a vagus-dependent manner...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872967/l-methionine-production
#12
Jihyun Shim, Yonguk Shin, Imsang Lee, So Young Kim
L-Methionine has been used in various industrial applications such as the production of feed and food additives and has been used as a raw material for medical supplies and drugs. It functions not only as an essential amino acid but also as a physiological effector, for example, by inhibiting fat accumulation and enhancing immune response. Producing methionine from fermentation is beneficial in that microorganisms can produce L-methionine selectively using eco-sustainable processes. Nevertheless, the fermentative method has not been used on an industrial scale because it is not competitive economically compared with chemical synthesis methods...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872966/general-template-for-the-fmea-applications-in-primary-food-processing
#13
Sibel Özilgen, Mustafa Özilgen
Data on the hazards involved in the primary steps of processing cereals, fruit and vegetables, milk and milk products, meat and meat products, and fats and oils are compiled with a wide-ranging literature survey. After determining the common factors from these data, a general FMEA template is offered, and its use is explained with a case study on pasteurized milk production.
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872965/novel-technologies-for-optimal-strain-breeding
#14
Michael Bott, Lothar Eggeling
The implementation of a knowledge-based bioeconomy requires the rapid development of highly efficient microbial production strains that are able to convert renewable carbon sources to value-added products, such as bulk and fine chemicals, pharmaceuticals, or proteins at industrial scale. Starting from classical strain breeding by random mutagenesis and screening in the 1950s via rational design by metabolic engineering initiated in the 1970s, a range of powerful new technologies have been developed in the past two decades that can revolutionize future strain engineering...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872964/toward-sustainable-amino-acid-production
#15
Yoshihiro Usuda, Yoshihiko Hara, Hiroyuki Kojima
Because the global amino acid production industry has been growing steadily and is expected to grow even more in the future, efficient production by fermentation is of great importance from economic and sustainability viewpoints. Many systems biology technologies, such as genome breeding, omics analysis, metabolic flux analysis, and metabolic simulation, have been employed for the improvement of amino acid-producing strains of bacteria. Synthetic biological approaches have recently been applied to strain development...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872963/microbial-production-of-amino-acid-related-compounds
#16
Volker F Wendisch
Corynebacterium glutamicum is the workhorse of the production of proteinogenic amino acids used in food and feed biotechnology. After more than 50 years of safe amino acid production, C. glutamicum has recently also been engineered for the production of amino acid-derived compounds, which find various applications, e.g., as synthons for the chemical industry in several markets including the polymer market. The amino acid-derived compounds such as non-proteinogenic ω-amino acids, α,ω-diamines, and cyclic or hydroxylated amino acids have similar carbon backbones and functional groups as their amino acid precursors...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872962/l-cysteine-metabolism-and-fermentation-in-microorganisms
#17
Hiroshi Takagi, Iwao Ohtsu
L-Cysteine is an important amino acid both biologically and commercially. Although most amino acids are industrially produced by microbial fermentation, L-cysteine has been mainly produced by protein hydrolysis. Due to environmental and safety problems, synthetic or biotechnological products have been preferred in the market. Here, we reviewed L-cysteine metabolism, including biosynthesis, degradation, and transport, and biotechnological production (including both enzymatic and fermentation processes) of L-cysteine...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872961/boosting-anaplerotic-reactions-by-pyruvate-kinase-gene-deletion-and-phosphoenolpyruvate-carboxylase-desensitization-for-glutamic-acid-and-lysine-production-in-corynebacterium-glutamicum
#18
Atsushi Yokota, Kazunori Sawada, Masaru Wada
In the 1980s, Shiio and coworkers demonstrated using random mutagenesis that the following three phenotypes were effective for boosting lysine production by Corynebacterium glutamicum: (1) low-activity-level citrate synthase (CS(L)), (2) phosphoenolpyruvate carboxylase (PEPC) resistant to feedback inhibition by aspartic acid (PEPC(R)), and (3) pyruvate kinase (PYK) deficiency. Here, we reevaluated these phenotypes and their interrelationship in lysine production using recombinant DNA techniques.The pyk deletion and PEPC(R) (D299N in ppc) independently showed marginal effects on lysine production, but both phenotypes synergistically increased lysine yield, demonstrating the importance of PEPC as an anaplerotic enzyme in lysine production...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872960/branched-chain-amino-acids
#19
Keisuke Yamamoto, Atsunari Tsuchisaka, Hideaki Yukawa
Branched-chain amino acids (BCAAs), viz., L-isoleucine, L-leucine, and L-valine, are essential amino acids that cannot be synthesized in higher organisms and are important nutrition for humans as well as livestock. They are also valued as synthetic intermediates for pharmaceuticals. Therefore, the demand for BCAAs in the feed and pharmaceutical industries is increasing continuously. Traditional industrial fermentative production of BCAAs was performed using microorganisms isolated by random mutagenesis. A collection of these classical strains was also scientifically useful to clarify the details of the BCAA biosynthetic pathways, which are tightly regulated by feedback inhibition and transcriptional attenuation...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27872959/corynebacterium-glutamicum-for-sustainable-bioproduction-from-metabolic-physiology-to-systems-metabolic-engineering
#20
Judith Becker, Gideon Gießelmann, Sarah Lisa Hoffmann, Christoph Wittmann
Since its discovery 60 years ago, Corynebacterium glutamicum has evolved into a workhorse for industrial biotechnology. Traditionally well known for its remarkable capacity to produce amino acids, this Gram-positive soil bacterium, has become a flexible, efficient production platform for various bulk and fine chemicals, materials, and biofuels. The central turnstile of all these achievements is our excellent understanding of its metabolism and physiology. This knowledge base, together with innovative systems metabolic engineering concepts, which integrate systems and synthetic biology into strain engineering, has upgraded C...
November 22, 2016: Advances in Biochemical Engineering/biotechnology
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