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https://www.readbyqxmd.com/read/28433722/high-precision-genome-sequencing-of-engineered-g-oxydans-621h-by-combining-long-nanopore-and-short-accurate-illumina-reads
#1
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/28429327/large-scale-cultivation-of-euglena
#2
Kengo Suzuki
From the middle of the twentieth century, microalgae have been exploited as a candidate biomass source of food and other products. One such candidate source is the fast-proliferating microalga Euglena gracilis. The commercial cultivation of E. gracilis began in 2007, after the success of its outdoor mass cultivation and improvement of the harvesting and drying methods suitable for Euglena cells. The commercialization of Euglena production is based on the strategy of "5Fs of Biomass," which refers to the development and production of commercial products including food, fiber, feed, fertilizer, and fuel from biomass...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28414239/a-novel-sample-preparation-for-shotgun-proteomics-characterization-of-hcps-in-antibodies
#3
Lihua Huang, Ning Wang, Charles E Mitchell, Tammy J Brownlee, Steven R Maple, Michael R De Felippis
Residual host cell proteins (HCPs) in biopharmaceuticals derived from recombinant DNA technology can present potential safety risks to patients or compromise product stability. Thus, the downstream purification process is designed to demonstrate robust removal of these impurities. ELISA using polyclonal anti-HCP antibodies as reagents for capture, detection and quantitation purposes is most commonly used to monitor HCP removal during process development but this technique has limitations. More recently, LC-MS for residual HCP characterization has emerged as a powerful tool to support purification process development...
April 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28394093/genome-editing-technologies-to-improve-research-reproduction-and-production-in-pigs
#4
REVIEW
Kevin D Wells, Randall S Prather
The ability to directly manipulate the pig genome through genetic engineering has been available to the research community for over three decades. This technology has progressed from the random insertion of foreign DNA, via a variety of techniques (pronuclear microinjection, sperm mediated gene transfer, and integration of mobile genetic elements), to manipulation of endogenous genes, via homologous recombination in somatic cells followed by somatic cell nuclear transfer. Over the last few years, designer nucleases facilitated the development of techniques that provide efficient ways to introduce foreign DNA or to modify endogenous genes in eggs, zygotes, or somatic cells...
April 10, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28390488/functional-fusion-proteins-and-prevention-of-electrode-fouling-for-a-sensitive-electrochemical-immunosensor
#5
A-Ram Kim, Tae Jung Park, Minseok S Kim, In-Ho Kim, Ki-Suk Kim, Kwang Hoe Chung, Sungho Ko
A highly sensitive electrochemical immunosensor was developed by preventing electrode fouling and using a novel fusion protein of silica binding polypeptides (SBP)-protein G (ProG) created by recombinant DNA technology as a functional crosslinker for rapid and self-oriented immobilization of antibodies onto silica nanoparticles (SiNPs). Antibody immobilization onto the SiNPs by the SBP-ProG could rapidly be achieved without any chemical treatment. The immunosensor was fabricated through bonding of a partially gold-deposited cyclic olefin copolymer (COC) (top substrate) and gold patterned interdigitated array COC electrode (bottom substrate)...
May 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28387174/institutional-oversight-of-occupational-health-and-safety-for-research-programs-involving-biohazards
#6
Melissa C Dyson, Calvin B Carpenter, Lesley A Colby
Research with hazardous biologic materials (biohazards) is essential to the progress of medicine and science. The fieldof microbiology has rapidly advanced over the years, partially due to the development of new scientific methods such as recombinant DNA technology, synthetic biology, viral vectors, and the use of genetically modified animals. This research poses a potential risk to personnel as well as the public and the environment. Institutions must have appropriate oversight and take appropriate steps to mitigate the risks of working with these biologic hazards...
April 6, 2017: Comparative Medicine
https://www.readbyqxmd.com/read/28369428/novel-approaches-to-neisseria-meningitidis-vaccine-design
#7
Myron Christodoulides, John Heckels
A range of vaccines is available for preventing life-threatening diseases caused by infection with Neisseria meningitidis (meningococcus, Men). Capsule polysaccharide (CPS)-conjugate vaccines are successful prophylactics for serogroup MenA, MenC, MenW and MenY infections and outer membrane vesicle (OMV) vaccines have been used successfully for controlling clonal serogroup MenB infections. MenB vaccines based on recombinant proteins identified by reverse vaccinology (Bexsero®) and proteomics (Trumenba®) approaches have recently been licensed and Bexsero® has been introduced into the UK infant immunization program...
March 22, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28361829/genetic-characterization-of-human-herpesvirus-type-1-full-length-genome-sequence-of-strain-obtained-from-an-encephalitis-case-from-india
#8
Vijay P Bondre, Vasudha Sankararaman, Vijaysinh Andhare, Manisha Tupekar, Gajanan N Sapkal
BACKGROUND & OBJECTIVES: Human herpes simplex virus 1 (HSV-1) is the most common cause of sporadic encephalitis in humans that contributes to >10 per cent of the encephalitis cases occurring worldwide. Availability of limited full genome sequences from a small number of isolates resulted in poor understanding of host and viral factors responsible for variable clinical outcome. In this study genetic relationship, extent and source of recombination using full-length genome sequence derived from a newly isolated HSV-1 isolate was studied in comparison with those sampled from patients with varied clinical outcome...
November 2016: Indian Journal of Medical Research
https://www.readbyqxmd.com/read/28360231/combination-of-short-read-long-read-and-optical-mapping-assemblies-reveals-large-scale-tandem-repeat-arrays-with-population-genetic-implications
#9
Matthias H Weissensteiner, Andy W C Pang, Ignas Bunikis, Ida Höijer, Olga Vinnere-Petterson, Alexander Suh, Jochen B W Wolf
Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow...
March 30, 2017: Genome Research
https://www.readbyqxmd.com/read/28325290/rna-guided-crispr-cas9-system-mediated-engineering-of-acute-myeloid-leukemia-mutations
#10
Oliver Brabetz, Vijay Alla, Linus Angenendt, Christoph Schliemann, Wolfgang E Berdel, Maria-Francisca Arteaga, Jan-Henrik Mikesch
Current acute myeloid leukemia (AML) disease models face severe limitations because most of them induce un-physiological gene expressions that do not represent conditions in AML patients and/or depend on external promoters for regulation of gene expression/repression. Furthermore, many AML models are based on reciprocal chromosomal translocations that only reflect the minority of AML patients, whereas more than 50% of patients have a normal karyotype. The majority of AML, however, is driven by somatic mutations...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28323062/new-strategies-and-approaches-for-engineering-biosynthetic-gene-clusters-of-microbial-natural-products
#11
REVIEW
Lei Li, Weihong Jiang, Yinhua Lu
With the rapidly growing number of sequenced microbial (meta)genomes, enormous cryptic natural product (NP) biosynthetic gene clusters (BGCs) have been identified, which are regarded as a rich reservoir for novel drug discovery. A series of powerful tools for engineering BGCs has accelerated the discovery and development of pharmaceutically active NPs. Here, we describe recent advances in the strategies for BGCs manipulation, which are driven by emerging technologies, including efficient DNA recombination systems, versatile CRISPR/Cas9 genome editing tools and diverse DNA assembly methods...
March 16, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28317025/marker-recycling-in-candida-albicans-through-crispr-cas9-induced-marker-excision
#12
Manning Y Huang, Aaron P Mitchell
We describe here a new approach to marker recycling, a controlled sequence of steps in which a genetic marker is selected and then lost. Marker recycling is important for genetic manipulation, because it allows a single selection marker to be used repeatedly. Our approach relies upon the ability of the CRISPR-Cas9 system to make a targeted double-strand break in DNA and the expectation that a double-strand break within a selection marker may promote recombination between directly repeated sequences that flank the marker...
March 2017: MSphere
https://www.readbyqxmd.com/read/28316014/rescue-of-recombinant-newcastle-disease-virus-a-short-history-of-how-it-all-started
#13
REVIEW
Aidin Molouki, Ben Peeters
Reverse genetics of viruses has come a long way, and many recombinant viruses have been generated since the first successful "rescues" were reported in the late 1970s. Recombinant Newcastle disease virus (rNDV), a non-segmented negative-sense RNA virus (NSNSV), was first rescued in 1999 using a reverse genetics approach similar to that reported for other recombinant viruses of the order Mononegavirales a few years before. The route from an original NDV isolate to the generation of its recombinant counterpart requires many steps that have to be sequentially and carefully completed...
March 18, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28303365/immunoglobulin-like-domain-4-mediated-ligand-independent-dimerization-triggers-vegfr-2-activation-in-huvecs-and-vegfr2-positive-breast-cancer-cells
#14
Sheng Zhang, Xiaoping Gao, Wei Fu, Shengwei Li, Limin Yue
PURPOSE: The extracellular region (EC) of the vascular endothelial growth factor (VEGF) receptor-2 (VEGFR-2) contains seven immunoglobulin-like (Ig-like) domains that are required for specific ligand binding and receptor dimerization. Studies of domain 4-7 deletions and substitutions provided insights into the interaction between receptors in the absence of VEGF. In this study, we investigated the effect of domain 4 in ligand-independent VEGFR-2 dimerization and activation in human vascular endothelial cells and human breast cancer cells...
March 16, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28283933/designing-of-a-recombinant-agip-bacmid-construct-with-infectious-properties-against-black-cutworm-agrotis-ipsilon-larvae
#15
Naglaa A Abdallah, Wael El-Menofy, Abdelhadi Abdallah Abdelhadi
In this study, Agrotis ipsilon nucleopolyhedrovirus bacmid has been constructed as an infectious bacmid in an attempt to allow genome recombination and generation of virus mutants. Since the FseI, a unique restriction site, is located in a viral coding region (ORF_119), PCR was performed to partially amplify the ORF_119 fragment containing the FseI site to facilitate the bacmid construction in a proper way without interrupting the ORF expression. Construction with repeated fragments at the end of the cloned viral was carried out in an attempt to facilitate circulation during infection in insect cells...
March 10, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28282262/new-insights-for-therapeutic-recombinant-human-mirnas-heterologous-production-rhodovolum-sulfidophilum-vs-escherichia-coli
#16
Patrícia Pereira, Augusto Q Pedro, João A Queiroz, Ana R Figueiras, Fani Sousa
RNA interference-based technologies have emerged as an attractive and effective therapeutic option with potential application in diverse human diseases. These tools rely on the development of efficient strategies to obtain homogeneous non-coding RNA samples with adequate integrity and purity, thus avoiding non-targeted gene-silencing and related side-effects that impair their application onto pre-clinical practice. These RNAs have been preferentially obtained by in vitro transcription using DNA templates or via chemical synthesis...
March 10, 2017: Bioengineered
https://www.readbyqxmd.com/read/28261237/progress-in-genome-editing-technology-and-its-application-in-plants
#17
REVIEW
Kai Zhang, Nadia Raboanatahiry, Bin Zhu, Maoteng Li
Genome editing technology (GET) is a versatile approach that has progressed rapidly as a mechanism to alter the genotype and phenotype of organisms. However, conventional genome modification using GET cannot satisfy current demand for high-efficiency and site-directed mutagenesis, retrofitting of artificial nucleases has developed into a new avenue within this field. Based on mechanisms to recognize target genes, newly-developed GETs can generally be subdivided into three cleavage systems, protein-dependent DNA cleavage systems (i...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28247205/the-mechanism-of-jurkat-cells-apoptosis-induced-by-aggregatibacter-actinomycetemcomitans-cytolethal-distending-toxin
#18
Hui-Ping Chen, Lu Li, Xu Chen, Mi-Fang Yang, Yu Ye, Xiao-Qian Wang, Yan Xu
Cytolethal distending toxin (CDT) which is produced by Aggregatibacter actinomycetemcomitans causes apoptosis in lymphocytes. But the specific mechanism is not clear. The aim of our research was to investigate the effect and mechanism during this process. The wild-type CdtA, CdtB, CdtC (CdtA(W), CdtB(W), CdtC(W)) and mutant CdtB (CdtB(M)) were expressed and purified respectively and the purity of each subunit was examined by BandScan software. And the type I deoxyribonuclease and PI-3,4,5-triphosphate (PI-3,4,5-P3, PIP3) phosphatase activity were detected by DNA agarose gel electrophoresis and enzyme-linked immunosorbent assay respectively...
June 2017: Apoptosis: An International Journal on Programmed Cell Death
https://www.readbyqxmd.com/read/28242597/advances-in-site-specific-integration-of-transgene-in-animal-genome
#19
Li Guoling, Zhong Cuili, Mo Jianxin, Quan Rong, Wu Zhenfang, Li Zicong, Yang Huaqiang, Zhang Xianwei
The traditional transgenic technologies, such as embryo microinjection, transposon-mediated integration, or lentiviral transfection, usually result in random insertions of the foreign DNA into the host genome, which could have various disadvantages in the establishment of transgenic animals. Therefore, a strategy for site-specific integration of a transgene is needed to generate genetically modified animals with accurate and identical genotypes. However, the efficiency for site-specific integration of transgene is very low, which is mainly caused by two issues...
February 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28240182/integration-of-novel-materials-and-advanced-omics-technologies-into-new-vaccine-design
#20
Wenzhen Liao, Tian-Tian Zhang, Liqian Gao, Su Seong Lee, Jie Xu, Han Zhang, Zhaogang Yang, Zhaoyu Liu, Wen Li
Designing new vaccines is one of the most challenging tasks for public health to prevent both infectious and chronic diseases. Even though many research scientists have spent great efforts in improving the specificity, sensitivity and safety of current available vaccines, there are still much space on how to effectively combine different biomaterials and technologies to design universal or personalized vaccines. Traditionally, vaccines were made based on empirical approaches designed to mimic immunity induced by natural infection...
February 24, 2017: Current Topics in Medicinal Chemistry
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