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Journal of Biotechnology

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https://www.readbyqxmd.com/read/28438580/first-complete-genome-sequence-of-bacillus-glycinifermentans-b-27
#1
Kai Bernd Stadermann, Jochen Blom, Claudia Borgmeier, Natalie Sciberras, Sandra Herbold, Maike Kipker, Guido Meurer, Stella Molck, Daniel Petri, Stefan Pelzer, Jessica Schneider
The first complete genome sequence of Bacillus glycinifermentans B-27 was determined by SMRT sequencing generating a genome sequence with a total length of 4,607,442 bases. Based on this sequence 4,738 protein-coding sequences were predicted and used to identify gene clusters that are related to the production of secondary metabolites such as Lichenysin, Bacillibactin and Bacitracin. This genomic potential combined with the ability of B. glycinifermentans B-27 to grown in bile containing media might contribute to a future application of this strain as probiotic in productive livestock potentially inhibiting competing and pathogenic organisms...
April 21, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28438579/the-brenda-enzyme-information-system-from-a-database-to-an-expert-system
#2
I Schomburg, L Jeske, M Ulbrich, S Placzek, A Chang, D Schomburg
Enzymes, representing the largest and by far most complex group of proteins, play an essential role in all processes of life, including metabolism, gene expression, cell division, the immune system, and others. Their function, also connected to most diseases or stress control makes them interesting targets for research and applications in biotechnology, medical treatments, or diagnosis. Their functional parameters and other properties are collected, integrated, and made available to the scientific community in the BRaunschweig ENzyme DAtabase (BRENDA)...
April 21, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28435098/kinetics-of-chitin-deacetylase-activation-by-the-ionic-liquid-bmim-br
#3
Izabela Aspras, Malgorzata M Jaworska, Andrzej Górak
Chitin deacetylase is the only known enzyme that can deacetylate the N-acetyl-D-glucosamine units in chitin and chitosan to D-glucosamine. Unfortunately, this enzyme, originally obtained from fungi, usually has low activity. Here, we present that it is possible to enhance the activity of chitin deacetylase using the ionic liquid [Bmim][Br]. An increase in activity of up to 160% from the basal chitin deacetylase activity was observed. Kinetic investigations suggest that [Bmim][Br] is a non-essential activator...
April 20, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433724/whole-genome-de-novo-sequencing-of-wood-rot-fungus-fomitopsis-palustris-atcc62978-with-both-a-cellulolytic-and-ligninolytic-enzyme-system
#4
Chang-Young Hong, Su-Yeon Lee, Sun-Hwa Ryu, Myungkil Kim
Fomitopsis palustris is a model brown rot fungus causing destructive wood decay based on the cellulase system. Endoglucanase secreted by F. palustris hydrolyzes cellulose in both the crystalline and amorphous form. In this study, whole-genome sequencing was conducted to identify genes related to F. palustris cellulose degradation and their functions. We determined the 43-Mb complete draft genome of F. palustris (ATCC 62978), comprising 14,592 predicted gene models. Gene annotation provided crucial information about the location and function of protein-encoding genes...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433723/elimination-of-the-cryptic-plasmid-in-leuconostoc-citreum-by-crispr-cas9-system
#5
Ye-Ji Jang, Seung-Oh Seo, Seul-Ah Kim, Ling Li, Tae-Jip Kim, Sun Chang Kim, Yong-Su Jin, Nam Soo Han
Leuconostoc spp. are important lactic acid bacteria for the fermentation of foods. In particular, L. citreum strains isolated from various foods have been used as host strains for genetic and metabolic engineering studies. In order to develop a food-grade genetic engineering system, L. citreum CB2567 was isolated from Kimchi. However, the isolated bacterium contained a cryptic plasmid which was difficult to eliminate. As the existence of the plasmid might hinder strain engineering, we eliminated the plasmid using an RNA-guided DNA endonuclease CRISPR/Cas9 system...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433722/high-precision-genome-sequencing-of-engineered-g-oxydans-621h-by-combining-long-nanopore-and-short-accurate-illumina-reads
#6
Angela Kranz, Alexander Vogel, Ursula Degner, Ines Kiefler, Michael Bott, Björn Usadel, Tino Polen
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433721/optimizing-the-restored-chemotactic-behavior-of-anticancer-agent-salmonella-enterica-serovar-typhimurium-vnp20009
#7
Katherine M Broadway, Seungbeum Suh, Bahareh Behkam, Birgit E Scharf
Bacteria, including strains of Salmonella, have been researched and applied as therapeutic cancer agents for centuries. Salmonella are particularly of interest due to their facultative anaerobic nature, facilitating colonization of differentially oxygenated tumor regions. Additionally, Salmonella can be manipulated with relative ease, resulting in the ability to attenuate the pathogen or engineer vectors for drug delivery. It was recently discovered that the anti-cancer Salmonella enterica serovar Typhimurium strain VNP20009 is lacking in chemotactic ability, due to a non-synonymous single nucleotide polymorphism in cheY...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28427921/enhancement-of-ethyl-s-4-chloro-3-hydroxybutanoate-production-at-high-substrate-concentration-by-in-situ-resin-adsorption
#8
Li-Feng Chen, Hai-Yang Fan, Yi-Ping Zhang, Wei Wei, Jin-Ping Lin, Dong-Zhi Wei, Hua-Lei Wang
Asymmetric reduction of ethyl 4-chloro-3-oxobutyrate (COBE) by carbonyl reductases presents an efficient way to produce Ethyl (S)-4-chloro-3-hydroxybutanoate ((S)-CHBE), an important chiral intermediate for the synthesis of hydroxymethylglutaryl-CoA reductase inhibitors such as Lipitor(®). In this study, an NADPH-dependent carbonyl reductase (SrCR) from Synechocystis sp. was characterized to demonstrate a broad substrate spectrum, and the highest activity (53.1U/mg protein) with COBE. To regenerate the cofactor NADPH, Bacillus subtilis glucose dehydrogenase was successfully coexpressed with SrCR...
April 17, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28427920/genome-improvement-of-the-acarbose-producer-actinoplanes-sp-se50-110-and-annotation-refinement-based-on-rna-seq-analysis
#9
Timo Wolf, Susanne Schneiker-Bekel, Armin Neshat, Vera Ortseifen, Daniel Wibberg, Till Zemke, Alfred Pühler, Jörn Kalinowski
Actinoplanes sp. SE50/110 is the natural producer of acarbose, which is used in the treatment of diabetes mellitus type II. However, until now the transcriptional organization and regulation of the acarbose biosynthesis is only understood rudimentarily. The genome sequence of Actinoplanes sp. SE50/110 was known before, but was resequenced in this study to remove assembly artifacts and incorrect base callings. The annotation of the genome was refined in a multi-step approach, including modern bioinformatic pipelines, transcriptome and proteome data...
April 17, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28414068/modulation-of-anthraquinones-and-phloroglucinols-biosynthesis-in-hypericum-spp-by-cryogenic-treatment
#10
Katarína Bruňáková, Eva Čellárová
Beside the high post-cryogenic recovery rate, a reinstated scale of secondary metabolites in recovered plant tissues represents another inevitable aspect of an effective cryopreservation protocol for medicinal plants. The current study was aimed at evaluation of the elicitation potential of cryogenic treatment on secondary metabolism of some Hypericum species. In agreement with our assumption, the cold stimuli applied during the pre-cryogenic phase increased the tolerance to low temperatures (-196°C) in H...
April 13, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28412516/switching-between-nitrogen-and-glucose-limitation-unraveling-transcriptional-dynamics-in-escherichia-coli
#11
Michael Löffler, Joana Danica Simen, Jan Müller, Günter Jäger, Salaheddine Laghrami, Karin Schäferhoff, Andreas Freund, Ralf Takors, Ralf Takors
Transcriptional control under nitrogen and carbon-limitation conditions have been well analyzed for Escherichia coli. However, the transcriptional dynamics that underlie the shift in regulatory programs from nitrogen to carbon limitation is not well studied. In the present study, cells were cultivated at steady state under nitrogen (ammonia)-limited conditions then shifted to carbon (glucose) limitation to monitor changes in transcriptional dynamics. Nitrogen limitation was found to be dominated by sigma 54 (RpoN) and sigma 38 (RpoS), whereas the "housekeeping" sigma factor 70 (RpoD) and sigma 38 regulate cellular status under glucose limitation...
April 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28412515/genome-wide-determination-of-transcription-start-sites-reveals-new-insights-into-promoter-structures-in-the-actinomycete-corynebacterium-glutamicum
#12
Andreas Albersmeier, Katharina Pfeifer-Sancar, Christian Rückert, Jörn Kalinowski
The genome-wide identification of transcription start sites, enabled by high-throughput sequencing of a cDNA library enriched for native 5' transcript ends, is ideally suited for the analysis of promoters. Here, the transcriptome of Corynebacterium glutamicum, a non-pathogenic soil bacterium from the actinomycetes branch that is used in industry for the production of amino acids, was analysed by transcriptome sequencing of the 5'-ends of native transcripts. Total RNA samples were harvested from the exponential phase of growth, therefore the study mainly addressed promoters recognized by the main house-keeping sigma factor σ(A)...
April 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28412514/insights-from-the-genome-of-a-high-alkaline-cellulase-producing-aspergillus-fumigatus-strain-obtained-from-peruvian-amazon-rainforest
#13
Sujay Paul, Angel Zhang, Yvette Ludeña, Gretty K Villena, Fengan Yu, David H Sherman, Marcel Gutiérrez-Correa
Here, we report the complete genome sequence of a high alkaline cellulase producing Aspergillus fumigatus strain LMB-35Aa isolated from soil of Peruvian Amazon rainforest. The genome is ∼27.5mb in size, comprises of 228 scaffolds with an average GC content of 50%, and is predicted to contain a total of 8660 protein-coding genes. Of which, 6156 are with known function; it codes for 607 putative CAZymes families potentially involved in carbohydrate metabolism. Several important cellulose degrading genes, such as endoglucanase A, endoglucanase B, endoglucanase D and beta-glucosidase, are also identified...
April 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28400137/tools-for-the-determination-of-population-heterogeneity-caused-by-inhomogeneous-cultivation-conditions
#14
REVIEW
Anja Lemoine, Frank Delvigne, Anika Bockisch, Peter Neubauer, Stefan Junne
Population heterogeneity among a microbial culture can occur in various stages of a bioprocess. When a nutrient-limited fed-batch process is applied in the large scale, gradient formation (e.g. at the substrate concentration or the pH-value) can have a tremendous impact on the process performance. It might also have an impact on population heterogeneity, as the cells are opposed to stressful conditions that is an oscillating environment, when they pass the different zones evolved in the liquid phase. Nevertheless, the question whether these conditions support heterogeneity of a culture has not been clearly answered so far...
April 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28400136/reservoir-souring-latest-developments-for-application-and-mitigation
#15
Richard J Johnson, Benjamin D Folwell, Alexander Wirekoh, Max Frenzel, Torben Lund Skovhus
Sulphate-reducing prokaryotes (SRP) have been identified in oil field fluids since the 1920s. SRP reduce sulphate to sulphide, a toxic and corrosive species that impacts on operational safety, metallurgy and both capital and operational cost. Differences in water cut, temperature, pressure and fluid chemistry can impact on the observed H2S concentration, meaning that an increase in H2S concentration does not always correlate with activity of SRP. However it wasn't until the 1990s that SRP activity was accepted as the leading cause of reservoir souring (i...
April 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28396267/microbial-genomics-and-metagenomics-in-human-health-and-disease
#16
EDITORIAL
A Puehler, J Kalinowski
No abstract text is available yet for this article.
April 7, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28392422/the-effect-of-varying-the-peptide-linker-length-in-a-single-chain-variable-fragment-antibody-against-wogonin-glucuronide
#17
Madan Kumar Paudel, Seiichi Sakamoto, Le Van Huy, Hiroyuki Tanaka, Tomofumi Miyamoto, Satoshi Morimoto
Peptide linkers of three different lengths were constructed to join the variable regions of the heavy chain (VH) and the light chain (VL) in a single-chain variable fragment antibody (scFv) specific for wogonin glucuronide (Wgn) that has the structure VH-(GGGGS)n-VL (n=3, 5, or 7). The scFv antibodies, which were expressed in Escherichia coli, were derived from an anti-Wgn monoclonal antibody (315A). An indirect competitive enzyme-linked immunosorbent assay (icELISA) was used to evaluate their reactivity and sensitivity, which is also used for quantitative analysis of Wgn...
April 7, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28392421/phenylalanine-ammonia-lyase-from-arabidopsis-thaliana-atpal2-a-potent-enzyme-for-the-synthesis-of-non-canonical-aromatic-alpha-amino-acids-part-i-comparative-characterization-to-the-enzymes-from-petroselinum-crispum-pcpal1-and-rhodosporidium-toruloides-rtpal
#18
Alana Dreßen, Thomas Hilberath, Ursula Mackfeld, Arne Billmeier, Jens Rudat, Martina Pohl
Phenylalanine ammonia lyase (PAL) from Arabidopsis thaliana (AtPAL2) was comparatively characterized to the well-studied enzyme from parsley (PcPAL1) and Rhodosporidium toruloides (RtPAL) with respect to kinetic parameters for the deamination and the amination reaction, pH- and temperature optima and the substrate range of the amination reaction. Whereas both plant enzymes are specific for phenylalanine, the bifunctional enzyme from Rhodosporidium toruloides shows KM-values for L-Phe and L-Tyr in the same order of magnitude and, compared to both plant enzymes, a 10-15-fold higher activity...
April 6, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28385593/a-genome-scale-model-of-geobacillus-thermoglucosidasius-c56-ys93-reveals-its-biotechnological-potential-on-rice-straw-hydrolysate
#19
Ahmad Ahmad, Hassan B Hartman, S Krishnakumar, David A Fell, Mark G Poolman, Shireesh Srivastava
Rice straw is a major crop residue which is burnt in many countries, creating significant air pollution. Thus, alternative routes for disposal of rice straw are needed. Biotechnological treatment of rice straw hydrolysate has potential to convert this agriculture waste into valuable biofuel(s) and platform chemicals. Geobacillus thermoglucosidasius is a thermophile with properties specially suited for use as a biocatalyst in lignocellulosic bioprocesses, such as high optimal temperature and tolerance to high levels of ethanol...
April 4, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28385592/genome-scale-metabolic-modelling-common-cofactors-metabolism-in-microorganisms
#20
Nan Xu, Chao Ye, Xiulai Chen, Jia Liu, Liming Liu
The common cofactors ATP/ADP, NAD(P)(H), and acetyl-CoA/CoA are indispensable participants in biochemical reactions in industrial microbes. To systematically explore the effects of these cofactors on cell growth and metabolic phenotypes, the first genome-scale cofactor metabolic model, icmNX6434, including 6434 genes, 1782 metabolites, and 6877 reactions, was constructed from 14 genome-scale metabolic models of 14 industrial strains. The origin, consumption, and interactions of these common cofactors in microbial cells were elucidated by the icmNX6434 model, and they played important roles in cell growth...
April 4, 2017: Journal of Biotechnology
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