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Journal of Biotechnology

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https://www.readbyqxmd.com/read/28822795/strategies-for-analyzing-bisulfite-sequencing-data
#1
Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, Yassen Assenov, Altuna Akalin
DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it has been shown to play a role in cell-type specific regulation of gene expression, and therefore cell-type identity. Bisulfite sequencing is the gold-standard for measuring methylation over the genomes of interest. Here, we review several techniques used for the analysis of high-throughput bisulfite sequencing. We introduce specialized short-read alignment techniques as well as pre/post-alignment quality check methods to ensure data quality...
August 16, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28822794/lipidomics-informatics-for-life-science
#2
D Schwudke, A Shevchenko, N Hoffmann, R Ahrends
Lipidomics encompasses analytical approaches that aim to identify and quantify the complete set of lipids, defined as lipidome in a given cell, tissue or organism as well as their interactions with other molecules. The majority of lipidomics workflows is based on mass spectrometry and has been proven as a powerful tool in system biology in concert with other Omics disciplines. Unfortunately, bioinformatics infrastructures for this relatively young discipline are limited only to some specialists. Search engines, quantification algorithms, visualization tools and databases developed by the 'Lipidomics Informatics for Life-Science' (LIFS) partners will be restructured and standardized to provide broad access to these specialized bioinformatics pipelines...
August 16, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28818601/complete-genome-sequence-of-pseudomonas-antarctica-pamc-27494-a-bacteriocin-producing-psychrophile-isolated-from-antarctica
#3
Jaejin Lee, Yong-Joon Cho, Jae Young Yang, You-Jung Jung, Soon Gyu Hong, Ok-Sun Kim
Antimicrobial-producing, cold-adapted microorganisms have great potential for biotechnological applications in food, pharmaceutical, and cosmetic industries. Pseudomonas antarctica PAMC 27494, a psychrophile exhibiting antimicrobial activity, was isolated from an Antarctic freshwater sample. Here we report the complete genome of P. antarctica PAMC 27494. The strain contains a gene cluster encoding microcin B which inhibits DNA regulations by targeting the DNA gyrase. PAMC 27494 may produce R-type pyocins and also contains a complete set of proteins for the biosynthesis of adenosylcobalamin and possibly induces plant growth by supplying pyrroloquinoline quionone molecules...
August 14, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28811216/complete-genome-sequence-of-maribacter-sp-t28-a-polysaccharide-degrading-marine-flavobacteria
#4
Peiwen Zhan, Kai Tang, Xiaofeng Chen, Limei Yu
The degradation of plant polysaccharides by enzymes is an industry of increasing importance. Here we present the complete genome sequence of a marine flavobacteria, Maribacter sp. T28 (=CGMCC 1.15788). The genome comprises 4,271,158bp in a circular chromosome with a G+C content of 34.4% and contains genes encoding xylanolytic, alginolytic and pectinolytic enzymes. Genes encoding alginate lyases and a pectin degradation protein (kdgF) are located on a polysaccharide utilization locus. Maribacter sp. T28 has the ability to utilize xylan, alginate and pectin for growth...
August 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28811215/molecular-mechanisms-underlying-protection-against-h9n2-influenza-virus-challenge-in-mice-by-recombinant-lactobacillus-plantarum-with-surface-displayed-ha2-ltb
#5
Yanlong Jiang, Guilian Yang, Qi Wang, Zhannan Wang, Wentao Yang, Wei Gu, Chunwei Shi, Jianzhong Wang, Haibin Huang, Chunfeng Wang
It has been considered that the Avian influenza virus (AIV) causes severe threats to poultry industry. In this study, we constructed a series of recombinant Lactobacillus plantarum (L. plantarum) with surface displayed hemagglutinin subunit 2 (HA2) alone or together with heat-labile toxin B subunit (LTB) from enterotoxigenic Escherichia coli. Balb/c mice were used as model to evaluate the protective effects of recombinant L. plantarum strains against H9N2 subtype challenge. The results showed that the presence of LTB significantly increased the percentages of CD3(+)CD4(+)IL-4(+), CD3(+)CD4(+)IFN-γ(+) and CD3(+)CD4(+)IL-17(+) T cells, as well as CD3(+)CD8(+)IFN-γ(+) T cells in spleen and MLNs determined by Fluorescence-Activated Cell Sorting assay...
August 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28811214/semi-empirical-modeling-of-microalgae-photosynthesis-in-different-acclimation-states-application-to-n-gaditana
#6
Andrea Bernardi, Andreas Nikolaou, Andrea Meneghesso, Benoît Chachuat, Tomas Morosinotto, Fabrizio Bezzo
The development of mathematical models capable of accurate predictions of the photosynthetic productivity of microalgae under variable light conditions is paramount to the development of large-scale production systems. The process of photoacclimation is particularly important in outdoor cultivation systems, whereby seasonal variation of the light irradiance can greatly influence microalgae growth. This paper presents a dynamic model that captures the effect of photoacclimation on the photosynthetic production...
August 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28803971/otp-an-automatized-system-for-managing-and-processing-ngs-data
#7
Eva Reisinger, Lena Genthner, Jules Kerssemakers, Philip Kensche, Stefan Borufka, Alke Jugold, Andreas Kling, Manuel Prinz, Ingrid Scholz, Gideon Zipprich, Roland Eils, Christian Lawerenz, Jürgen Eils
The One Touch Pipeline (OTP) is an automation platform managing Next-Generation Sequencing (NGS) data and calling bioinformatic pipelines for processing these data. OTP handles the complete digital process from import of raw sequence data via alignment of sequencing reads to identify genomic events in an automated and scalable way. Three major goals are pursued: firstly, reduction of human resources required for data management by introducing automated processes. Secondly, reduction of time until the sequences can be analyzed by bioinformatic experts, by executing all operations more reliably and quickly...
August 10, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28801067/dna-methylation-in-cho-cells
#8
Anna Wippermann, Thomas Noll
Chinese hamster ovary (CHO) cells account for the production of the majority of biopharmaceutical molecules - however, the molecular basis for their versatile properties is not entirely understood yet and the underlying cellular processes need to be characterized in detail. One such process that is supposed to contribute significantly to CHO cell phenotype is methylation of DNA at cytosine residues. DNA methylation was shown to be involved in several central biological processes in humans and to contribute to diseases like cancer...
August 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28797630/enzymatic-in-situ-saccharification-of-sugarcane-bagasse-pretreated-with-low-loading-of-alkalic-salts-na2so3-na3po4-by-autoclaving
#9
Chun-Xia Jiang, Yu-Cai He, Gang-Gang Chong, Jun-Hua Di, Ya-Jie Tang, Cui-Luan Ma
Sugarcane bagasse (SCB) is an abundant, renewable and inexpensive agricultural byproduct for the production of biofuel and other biobased products. To effectively saccharify SCB with cellulases, combination with dilute alkali salts Na2SO3/Na3PO4 (0.4% Na3PO4, 0.03% Na2SO3) at 7.5% sulfidity and hot water (DASHW) in "one-pot" pretreatment media by autoclaving at 110°C for 40min was attempted to pretreat SCB in this study. Furthermore, FT-IR, XRD and SEM were employed to characterize the changes in the cellulose structural characteristics (porosity, morphology, and crystallinity) of the pretreated Na2SO3/Na3PO4-SCB solid residue, which indicated that combination pretreatment could effectively remove lignin and hemicellulose for enhancing enzymatic saccharification...
August 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28793235/-r-r-butane-2-3-diol-dehydrogenase-from-bacillus-clausii-dsm-8716-t-cloning-and-expression-of-the-bdha-gene-and-initial-characterization-of-enzyme
#10
Lukas Muschallik, Denise Molinnus, Johannes Bongaerts, Martina Pohl, Torsten Wagner, Michael J Schöning, Petra Siegert, Thorsten Selmer
The gene encoding a putative (R,R)-butane-2,3-diol dehydrogenase (bdhA) from Bacillus clausii DSM 8716(T) was isolated, sequenced and expressed in Escherichia coli. The amino acid sequence of the encoded protein is only distantly related to previously studied enzymes (identity 33-43%) and exhibited some uncharted peculiarities. An N-terminally StrepII-tagged enzyme variant was purified and initially characterized. The isolated enzyme catalyzed the (R)-specific oxidation of (R,R)- and meso-butane-2,3-diol to (R)- and (S)-acetoin with specific activities of 12U/mg and 23U/mg, respectively...
August 6, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28780163/online-monitoring-of-cell-concentration-in-high-cell-density-escherichia-coli-cultivations-using-in-situ-microscopy
#11
D Marquard, C Schneider-Barthold, S Düsterloh, T Scheper, P Lindner
In situ Microscopy (ISM) is an optical non-invasive technique to monitor cells in bioprocesses in real-time. Escherichia coli is the most studied and used organism in biotechnology. In this article the cell density in Escherichia coli cultivations was monitored by applying ISM in these cultivations. The acquired images were analyzed with an image processing algorithm to determine the turbidity of the cultivation medium. In three cultivations the cell density was monitored with the algorithm and offline samples were taken to determine the dry cell mass (DCM)...
August 2, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28780162/in-vitro-production-of-spodoptera-exigua-multiple-nucleopolyhedrovirus-with-enhanced-insecticidal-activity-using-a-genotypically-defined-virus-inoculum
#12
Khin Nyein Chan, Saengchai Akepratumchai, Phenjun Mekvichitsaeng, Kanokwan Poomputsa
Defective virus accumulations during baculovirus passages in insect cell culture are impediments to large scale baculovirus production. A genotypically defined virus inoculum comprises of stable genotypes was proposed for production of a Thailand isolated SeMNPV in Se-UCR1 insect cells. Targeted genotypes were from wild-type SeMNPV containing naturally mixed genotypes. Plaque assays, PCR screening and XbaI restriction analysis were employed for genotype purification, genotype selection and genome analysis, respectively...
August 2, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28778693/placenta-specific-gene-manipulation-in-rabbits
#13
Gabriella Skoda, Orsolya Ivett Hoffmann, Elen Gócza, Lilla Bodrogi, Andrea Kerekes, Zsuzsanna Bösze, Laszlo Hiripi
Lentiviral gene constructs can be efficiently and specifically delivered to trophoblast cell lineages in rodents. In vivo genetic manipulation of trophoblast cell lines enables functional and developmental studies in the placenta. In this report we show that genetic modification can be produced in the extraembryonic tissues of rabbits by lentiviral gene constructs. When 8-16 cell stage embryos were injected with lentiviral particles, strong reporter gene expression resulted in the rabbit placenta. The expression pattern displayed some mosaicism...
August 1, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28774672/structure-based-protein-engineering-for-thermostable-and-alkaliphilic-enhancement-of-endo-%C3%AE-1-4-xylanase-for-applications-in-pulp-bleaching
#14
Katewadee Boonyapakron, Aritsara Jaruwat, Benjamas Liwnaree, Thidarat Nimchua, Verawat Champreda, Penchit Chitnumsub
In the pulp bleaching industry, enzymes with robust activity at high pH and temperatures are desirable for facilitating the pre-bleaching process with simplified processing and minimal use of chlorinated compounds. To engineer an enzyme for this purpose, we determined the crystal structure of the Xyn12.2 xylanase, a xylan-hydrolyzing enzyme derived from the termite gut symbiont metagenome, as the basis for structure-based protein engineering to improve Xyn12.2 stability in high heat and alkaline conditions...
July 31, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28774671/complete-genome-sequence-of-ruminococcaceae-bacterium-cpb6-a-newly-isolated-culture-for-efficient-n-caproic-acid-production-from-lactate
#15
Yong Tao, Xiaoyu Zhu, Han Wang, Yi Wang, Xiangzhen Li, Hong Jin, Junpeng Rui
n-caproic acid (CA) is a valuable chemical feedstock for various industrial applications. Biological production of CA from renewable carbon sources has attracted a lot of attentions recently. We lately reported the new culture Ruminococcaceae bacterium CPB6, which was isolated from a microbiome for efficient CA production from lactate. To further elucidate its metabolism, we sequenced the whole genome of the strain. The size of the complete genome is 2,069,994bp with 50.58% GC content; no plasmid was identified...
July 31, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28764970/urinary-exosomal-mir-2909-a-novel-pathognomonic-trait-of-prostate-cancer-severity
#16
S Wani, D Kaul, R S Mavuduru, N Kakkar, A Bhatia
The global occurrence of prostate cancer with a range of patient outcome has prompted various investigators to explore novel molecular biomarkers that can precisely detect and track this type of cancer severity. Several studies suggest that micro-RNAs have emerged to act as a new largely unexplored class of biomarkers because of their inherent stability, resilience and recruitment into exosomes present in various human body fluids. With this study, we aim to reveal the nature of urinary-exosomal miR-2909 & miR-615-3p recruitment in patients suffering from either prostate cancer (n=90) or bladder cancer (n=60) as compared to that in either prostate disease-control subjects having benign prostate hyperplasia (n=10) or healthy subjects (n=50)...
July 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28764969/peptide-nucleic-acids-advanced-tools-for-biomedical-applications
#17
REVIEW
Anjali Gupta, Anuradha Mishra, Nidhi Puri
Peptide Nucleic Acids (PNAs) are the DNA/RNA analogues in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. PNA contains neutral backbone hence due to the absence of electrostatic repulsion, its hybridization shows remarkable stability towards complementary oligonucleotides. PNAs are highly resistant to cleavage by chemicals and enzymes due to the substrate specific nature of enzymes and therefore not degraded inside the cells. PNAs are emerging as new tools in the market due to their applications in antisense and antigene therapies by inhibiting translation and transcription respectively...
July 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28764968/production-of-human-milk-oligosaccharides-by-enzymatic-and-whole-cell-microbial-biotransformations
#18
Georg A Sprenger, Florian Baumgärtner, Christoph Albermann
Human milk oligosaccharides (HMO) are almost unique constituents of breast milk and are not found in appreciable amounts in cow milk. Due to several positive aspects of HMO for the development, health, and wellbeing of infants, production of HMO would be desirable. As a result, scientist from different disciplines have developed methods for the preparation of single HMO compounds. Here, we review approaches to HMO preparation by (chemo-)enzymatic syntheses or by whole-cell biotransformation with recombinant bacterial cells...
July 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28760444/cloning-expression-and-characterization-of-a-%C3%AE-carrageenase-from-marine-bacterium-wenyingzhuangia-fucanilytica-a-biocatalyst-for-producing-%C3%AE-carrageenan-oligosaccharides
#19
Jingjing Shen, Yaoguang Chang, Shujun Dong, Feng Chen
ι-Carrageenan is an algal polysaccharide widely applied in the food industry. Specific glycoside hydrolases are valuable tools for modifying polysaccharides and producing oligosaccharides. In this study, the gene of a novel GH82 family ι-carrageenase was cloned from the genome of marine bacterium Wenyingzhuangia fucanilytica. The ι-carrageenase designated as Cgi82A was expressed in Escherichia coli, and its biochemical properties, kinetic constants and hydrolysis pattern were characterized. The enzyme could reach its highest activity at 25°C, which is lower than all hitherto reported GH82 ι-carrageenases...
July 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28760443/self-cycling-fermentation-for-1-3-propanediol-production-comparative-evaluation-of-metabolite-flux-in-cell-recycling-simple-batch-and-continuous-processes-using-lactobacillus-brevis-n1e9-3-3-strain
#20
Narisetty Vivek, T V Aswathi, Petit Riff Sven, Ashok Pandey, Parameswaran Binod
The microbial conversion of biodiesel derived crude glycerol to 1,3-propanediol (1,3-PDO) has attained high industrial value due to the broad range of applications as a monomer (1,3-PDO) in textile, cosmetic and polymer industries. This fine chemical through biological production addressed several limitations of the chemical process like high temperatures, pressure and expensive catalysts. In this study 1,3-propanediol production was achieved from a non-pathogenic lactic acid bacterial strain Lactobacillus brevis N1E9...
July 29, 2017: Journal of Biotechnology
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