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Journal of Biotechnology

Dejan Gagoski, Zhenyu Shi, Lars Keld Nielsen, Claudia E Vickers, Stephen Mahler, Robert Speight, Wayne A Johnston, Kirill Alexandrov
The rapid expansion in the number of sequenced genomes and metagenomes provides an exceptional resource for mining of the enzymes with biotechnologically relevant properties. However, the majority of protein production and analysis methods are not sufficiently cost-efficient and scalable to experimentally verify the results of computational genomic mining. Here, we present a pipeline based on Leishmania tarentolae cell-free system that was used to characterise 30 putative thermostable endo-1,4-β-glucanases and xylanases identified in public genomic databases...
July 17, 2017: Journal of Biotechnology
Iva Anic, Arijit Nath, Pedro Franco, Rolf Wichmann
In this report, a method for a simultaneous production and separation of a microbially synthesized rhamnolipid biosurfactant is presented. During the aerobic cultivation of flagella-free Pseudomonas putida EM383 in a 3.1L stirred tank reactor on glucose as a sole carbon source, rhamnolipids are produced and excreted into the fermentation liquid. Here, a strategy for biosurfactant capture from rhamnolipid enriched fermentation foam using hydrophobic-hydrophobic interaction was investigated. Five adsorbents were tested independently for the application of this capture technique and the best performing adsorbent was tested in a fermentation process...
July 16, 2017: Journal of Biotechnology
Qing Jin, Qiuyue Jiang, Lei Zhao, Cuizhu Su, Songshuo Li, Fangyi Si, Shanshan Li, Chenhao Zhou, Yonglin Mu, Ming Xiao
Antagonistic soil microorganisms, which are non-toxic, harmless non-pollutants, can effectively reduce the density of pathogenic species by some ways. Bacillus velezensis strain S3-1 was isolated from the rhizosphere soil of cucumber, and was shown to inhibit plant pathogens, promote plant growth and efficiently colonize rhizosphere soils. The strain produced 13 kinds of lipopeptide antibiotics, belonging to the surfactin, iturin and fengycin families. Here, we presented the complete genome sequence of S3-1...
July 12, 2017: Journal of Biotechnology
J Yu, J Blom, S P Glaeser, S Jaenicke, T Juhre, O Rupp, O Schwengers, S Spänig, A Goesmann
The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics...
July 10, 2017: Journal of Biotechnology
Thomas Schmutzer, Marie E Bolger, Stephen Rudd, Jinbo Chen, Heidrun Gundlach, Daniel Arend, Markus Oppermann, Stephan Weise, Matthias Lange, Manuel Spannagl, Björn Usadel, Klaus F X Mayer, Uwe Scholz
Plant genetic resources are a substantial opportunity for plant breeding, preservation and maintenance of biological diversity. As part of the German Network for Bioinformatics Infrastructure (de.NBI) the German Crop BioGreenformatics Network (GCBN) focuses mainly on crop plants and provides both data and software infrastructure which are tailored to the needs of the plant research community. Our mission and key objectives include: (1) provision of transparent access to germplasm seeds, (2) the delivery of improved workflows for plant gene annotation, and (3) implementation of bioinformatics services that link genotypes and phenotypes...
July 8, 2017: Journal of Biotechnology
Julia Schulte, Meike Baumgart, Michael Bott
Cyclic adenosine monophosphate (cAMP) plays a regulatory role as second messenger in many species. In the industrial model organism Corynebacterium glutamicum, cAMP acts as effector of the global transcriptional regulator GlxR, a homolog of enterobacterial Crp. The cAMP-GlxR complex activates or represses the expression of about 200 target genes. CyaB, a membrane-bound class III adenylate cyclase, synthesizes cAMP from ATP, but another yet unknown cAMP-forming enzyme is likely present in C. glutamicum. Recently, we identified the cAMP phosphodiesterase CpdA, which catalyzes the conversion of cAMP to AMP...
July 8, 2017: Journal of Biotechnology
Mehdi Ariana, Javad Hamedi
Nisin is a safe, approved and commercial bacteriocin that is produced by Lactococcus lactis subsp. lactis. Since lactate accumulation in fermentation medium reduces L. lactis growth and nisin production, Yarrowia lipolytica, a lactate consuming yeast and L. lactis subsp. lactis, were simultaneously cultured in a molasses based medium. Y. lipolytica is not able to consume sucrose as carbon source, but rather consumes lactate and hence decrease lactic acid titer by 10% in the medium. Lactic acid consumption, 15% increased pH value and stimulated L...
July 8, 2017: Journal of Biotechnology
Bastian Zirpel, Friederike Degenhardt, Chantale Martin, Oliver Kayser, Felix Stehle
Δ(9)-tetrahydrocannabinolic acid (THCA) is a plant derived secondary natural product from the plant Cannabis sativa l. The discovery of the human endocannabinoid system in the late 1980s resulted in a growing number of known physiological functions of both synthetic and plant derived cannabinoids. Thus, manifold therapeutic indications of cannabinoids currently comprise a significant area of research. Here we reconstituted the final biosynthetic cannabinoid pathway in yeasts. The use of the soluble prenyltransferase NphB from Streptomyces sp...
July 7, 2017: Journal of Biotechnology
Huaxiang Deng, Ruijie Gao, Xiangru Liao, Yujie Cai
Shiraia bambusicola can produce a type of hypocrellin, which is applied in antibacterial, antitumoral, and antiviral areas. Studies on the hypocrellin pathway have not been confirmed due to the deficiency of suitable genetic methods We constructed a clustered regularly interspaced short palindromic repeat sequences (CRISPR)/Cas9 system in Shiraia sp. SUPER-H168 and targeted a polyketide synthase (SbaPKS). No hypocrellin production was detected in the ΔSbaPKS mutant. Relative expression levels of SbaPKS and its adjacent genes were extremely down-regulated in the ΔSbaPKS mutant compared to those in the wild strain...
July 6, 2017: Journal of Biotechnology
Jörg Fallmann, Sebastian Will, Jan Engelhardt, Björn Grüning, Rolf Backofen, Peter F Stadler
In the realm of nucleic acid structures, secondary structure forms a conceptually important intermediate level of description and explains the dominating part of the free energy of structure formation. Secondary structures are well conserved over evolutionary time-scales and for many classes of RNAs evolve slower than the underlying primary sequences. Given the close link between structure and function, secondary structure is routinely used as a basis to explain experimental findings. Recent technological advances, finally, have made it possible to assay secondary structure directly using high throughput methods...
July 6, 2017: Journal of Biotechnology
Sang Yoon Kim, Hajin Song, Mee Kyung Sang, Hang-Yeon Weon, Jaekyeong Song
The bacterial strain Bacillus velezensis GH1-13, isolated from rice paddy soil in Korea, has been shown to promote plant growth and have strong antagonistic activities against pathogens. Here, we report the complete genome sequence of GH1-13, revealing that it possesses a single 4,071,980-bp circular chromosome with 46.2% GC-content. The chromosome encodes 3,930 genes, and we have also identified a unique plasmid in the strain that encodes a further 104 genes (71,628bp and 31.7% GC-content). The genome was found to contain various enzyme-encoding operons, including indole-3-acetic acid (IAA) biosynthesis proteins, 2,3-butanediol dehydrogenase, various non-ribosomal peptide synthetases, and several polyketide synthases...
July 6, 2017: Journal of Biotechnology
Ha Taek Kwon, Eun Hyuk Jang, Seung Kyun Na, A Ram Shin, Augustine Yonghwi Kim, Young Min Chi, Hyun Park
Hydroxy fatty acids are used in various industries due to their availability, and in particular, Stenotrophomonas sp. has been regarded as a potential candidate for biotechnological applications, including biotransformation that hydrate unsaturated fatty acids into their derivatives. Here we complete the genome sequence of Stenotrophomonas sp. KCTC 12332 which has a size of 4,541,594bp (G+C content of 63.83%) with 3790 coding DNA sequences (CDSs), 67 tRNA and 3 rRNA operons. The genome contains gene encoding oleate hydratase that can convert oleic acid into 10-hydroxyoctadecanoic acid...
July 6, 2017: Journal of Biotechnology
Erika Hagrot, Hildur Æsa Oddsdóttir, Joan Gonzalez Hosta, Elling W Jacobsen, Véronique Chotteau
Mammalian cell lines are characterized by a complex and flexible metabolism. A single model that could describe the variations in metabolic behavior triggered by variations in the culture conditions would be a precious tool in bioprocess development. In this paper, we introduce an approach to generate a poly-pathway model and use it to simulate diverse metabolic states triggered in response to removal, reduction or doubling of amino acids in the culture medium of an antibody-producing CHO cell line. Macro-reactions were obtained from a metabolic network via elementary flux mode enumeration and the fluxes were modeled by kinetic equations with saturation and inhibition effects from external medium components...
July 5, 2017: Journal of Biotechnology
Maricruz Fernandez, Agustina Godino, Analía Príncipe, Gustavo M Morales, Sonia Fischer
Phage tail-like bacteriocins, called tailocins, represent a class of protein complexes produced by a multitude of bacteria. Pseudomonas fluorescens SF4c, a strain isolated from wheat rhizosphere, produces a bacteriocin similar to phage tail-like pyocins of Pseudomonas aeruginosa. This tailocin has antimicrobial activity against several phytopathogenic strains of the genus Xanthomonas and Pseudomonas. In this work, the effect of the SF4c tailocin on the phytopathogenic strain X. axonopodis pv vesicatoria Xcv Bv5-4a was analyzed through Atomic Force Microscopy (AFM)...
July 5, 2017: Journal of Biotechnology
Torben Lund Skovhus, Richard B Eckert, Edgar Rodrigues
Microbiologically influenced corrosion (MIC) is the terminology applied where the actions of microorganisms influence the corrosion process. In literature, terms such as microbial corrosion, biocorrosion, microbially influenced/induced corrosion, and biodegradation are often applied. MIC research in the oil and gas industry has seen a revolution over the past decade, with the introduction of molecular microbiological methods: (MMM) as well as new industry standards and procedures of sampling biofilm and corrosion products from the process system...
July 4, 2017: Journal of Biotechnology
Steffen Gruber, Helmut Schwab, Petra Heidinger
The biotechnologically important Gram-negative β-proteobacterium Ralstonia eutropha H16 is able to grow lithoautotrophically by utilizing CO2 and H2 as sole carbon and energy sources, respectively. CO2 is fixed by the CBB cycle, which is encoded in duplicate on the genome of R. eutropha H16. The transcription of both cbb operons is controlled by the transcription regulator CbbR dependent on intracellular PEP levels as a response to the carbon-state of the cell. As demonstrated in this study transcription control of both cbb operons appears to be more complex and additionally involves, next to CbbR, the transcription regulator RegA as part of the global transcription regulation system RegA/RegB...
July 4, 2017: Journal of Biotechnology
Ozan Ötes, Hendrik Flato, Johannes Winderl, Jürgen Hubbuch, Florian Capito
The protein A capture step is the main cost-driver in downstream processing, with high attrition costs especially when using protein A resin not until end of resin lifetime. Here we describe a feasibility study, transferring a batch downstream process to a hybrid process, aimed at replacing batch protein A capture chromatography with a continuous capture step, while leaving the polishing steps unchanged to minimize required process adaptations compared to a batch process. 35g of antibody were purified using the hybrid approach, resulting in comparable product quality and step yield compared to the batch process...
July 3, 2017: Journal of Biotechnology
Dominik Kopczynski, Albert Sickmann, Robert Ahrends
Computational proteomics is a constantly growing field to support end users with powerful and reliable tools for performing several computational steps within an analytics workflow for proteomics experiments. Typically, after capturing with a mass spectrometer, the proteins have to be identified and quantified. After certain follow-up analyses, an optional targeted approach is suitable for validating the results. The de.NBI (German network for bioinformatics infrastructure) service center in Dortmund provides several software applications and platforms as services to meet these demands...
July 1, 2017: Journal of Biotechnology
Steffen C Lott, Markus Wolfien, Konstantin Riege, Andrea Bagnacani, Olaf Wolkenhauer, Steve Hoffmann, Wolfgang R Hess
RNA-Sequencing (RNA-Seq) has become a widely used approach to study quantitative and qualitative aspects of transcriptome data. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. In this review, we aim to explain the impact of structured pre-selection, classification and integration of best-performing tools within modularized data analysis workflows and ready-to-use computing infrastructures towards experimental data analyses...
July 1, 2017: Journal of Biotechnology
Dorina Strieth, Julia Schwing, Stephan Kuhne, Michael Lakatos, Kai Muffler, Roland Ulber
Biodiversity forms the basis for a large pool of potential products and productive organisms offered by terrestrial cyanobacteria. They are stuck together by EPS (extracellular polymeric substances) that can obtain antiviral, antibacterial or anti-inflammatory substances. Most stress conditions, e.g. drought, induce the production of protective EPS or biotechnological-products for pharmaceutical application. However, the growth of a phototrophic biofilm is limited under submerged conditions. Therefore, a semi-continuous process to produce EPS by cyanobacteria was developed in an aerosol-based ePBR (emerse photobioreactor) that imitates the natural habitat of terrestrial cyanobacteria...
July 1, 2017: Journal of Biotechnology
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