Showing papers in "Journal of Biotechnology in 2017"

TL;DR: SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences, where no validly described cultivated representatives are available.

TL;DR: Applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans.

TL;DR: A model that favors the design of donor DNAs with the change as close to the cleavage site as possible is proposed, which achieves up to 56% targeted integration efficiency with up to a six-nucleotide insertion in HEK293 cells.

TL;DR: The advance of "omics" technologies has recently given rise to new possibilities in improving these expression platforms and will significantly help developing new strategies, in particular for CHO (Chinese Hamster Ovary) cells.

TL;DR: This review summarizes recent metaproteomics software and addresses the introduced issues within the bioinformatic evaluation impede its success.

TL;DR: Investigation of the relationship between the bioactives and the antioxidant capacities in fucoxanthin-producing algae showed that both carotenoids and phenolic acids were significantly correlated with the antioxidant activities, indicating the influence of theseBioactives on the algal antioxidant capacities.

TL;DR: The data contents, the process of data acquisition, data integration and control, the ways to access the data, and visualizations provided by the website are described and discussed.

TL;DR: This review covers a range of strategies employed to use the feed rate as a manipulated variable in a control strategy, as it is seen that this variable may be used towards many different objectives depending on the process of interest, the characteristics of the strain, or the product being produced, which leads to different drivers for process optimisation.

TL;DR: This review paper presents selected extensions from the life sciences that simplify data exploration, analysis, and visualization and are interoperable due to KNIME's unified data model.

TL;DR: In this article, a review of PNAs' hybridization properties along with potential applications in diagnostics and pharmaceuticals are elaborated, and several methods based on PNs have been developed for designing various anticancer and antigene drugs.

TL;DR: In view of an industrial production of HMOs, the whole cell biotransformation is at this stage the most promising option to provide human milk oligosaccharides as food additive.

TL;DR: The biologically oriented process for the green synthesis of copper oxide nanoparticles (CuO NPs) by using Morus alba leaf extract as reducing agent highlights the spatial organization of oxidant biochemistry occurring in response to metal stress.

TL;DR: Several techniques used for the analysis of high-throughput bisulfite sequencing are reviewed, including specialized short-read alignment techniques as well as pre/post-alignment quality check methods to ensure data quality.

TL;DR: The paper reviews four existing models for MIC Threat Assessment and describes a new model that links the threat of MIC in the oil processing system located on an offshore platform with a Risk Based Inspection (RBI) approach.

TL;DR: Recent strategies for the biotechnological production of aromatic and related compounds from renewable biomass by Escherichia coli, Pseudomonas putida, C. glutamicum and Saccharomyces cerevisiae are summarized and metabolic engineering of the extended shikimate pathway is focused on.

TL;DR: The SeqAn library of efficient data types and algorithms has matured considerably since its first publication 9 years ago and its status as an established resource for programmers in the field of sequence analysis is reviewed.

TL;DR: OpenMS, a versatile open-source framework aimed at enabling reproducible analyses of high-throughput mass spectrometry data, provides implementations of frequently occurring processing operations on MS data through a clean application programming interface in C++ and Python.

TL;DR: Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy, and make them promising but challenging antimicrobials.

TL;DR: Replacing the peristaltic pump with a low shear centrifugal pump brought cell growth, cell lysis, particle concentration, and product sieving in a TFF perfusion system to levels comparable with that of an ATF, providing a correlation where poor product sieved can be partially explained by high shear in cell retention systems.

TL;DR: This review begins with a short introduction describing the general approaches and techniques used in computational modeling in the biosciences, before looking at typical applications of COPASI in biotechnology.

TL;DR: Environmental controlled stirred-tank bioreactors operating in perfusion are used as a powerful tool for bioprocess intensification of hiPSC production and demonstrate the importance of controlling the dissolved oxygen concentration at low levels and perfusion at 1.3day-1 dilution rate to improveHiPSC growth as aggregates in a xeno-free medium.

TL;DR: The results clearly showed that these models can be employed in the development of ethanol production processes using SSJ under both NG and HG conditions, and were also shown to be applicable to other ethanol fermentation systems employing pure and mixed sugars as carbon sources.

TL;DR: A short overview of RNA folding algorithms, recent additions and variations and address methods to align, compare, and cluster RNA structures are provided, followed by a tabular summary of the most important software suites in the fields.

TL;DR: It is shown for the first time that the bacterial prenyltransferase and the final enzyme of the cannabinoid pathway tetrahydrocannabinolic acid synthase can both be actively expressed in the yeasts Saccharomyces cerevisiae and Komagataella phaffii simultaneously.

TL;DR: Key functionalities of CellNetAnalyzer are presented and constraint-based modeling techniques such as metabolic fluxAnalysis, flux balance analysis, flux variability analysis, metabolic pathway analysis (elementary flux modes) and methods for computational strain design are reviewed.

TL;DR: The overproduction of L-malate is achieved by rewiring the reductive tricarboxylic acid (rTCA) pathway and L- Malate transport pathway of A. oryzae NRRL 3488 and the 6-phosphofructokinase encoded by the pfk gene was identified as a potential limiting step for L- malate synthesis.

TL;DR: This review has the objective of discussing CPPs and elucidating the prospective use of CPP-mediated transduction technology, particularly in genome modification and transgenesis.

TL;DR: It is demonstrated that biosynthesized Ag NPs can inhibit the proliferation of human breast cancer cell line MCF-7 in the IC50 at a dose of 12.85μg/mL and inhibit the proliferative effect of AgNPs against anti-growth arresting MCf-7 cell line.

TL;DR: Five nominally freshwater microalgae (Chlorella vulgaris, Choricystis minor, Neochloris sp., Pseudococcomyxa simplex, Scenedesmus sp.) with a known ability to produce high-levels of lipids for possible use as fuel oils were evaluated for their ability to thrive and produce lipids in seawater and brackish water.

TL;DR: The results suggest the aglycon promiscuity of Bs-YjiC and demonstrate its significant application prospect in biosynthesis of valuable natural products.