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https://www.readbyqxmd.com/read/27914076/reconstructing-the-ancestral-relationships-between-bacterial-pathogen-genomes
#1
Caitlin Collins, Xavier Didelot
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27907066/b-cell-based-seamless-engineering-of-antibody-fc-domains
#2
Koji Hashimoto, Kohei Kurosawa, Akiho Murayama, Hidetaka Seo, Kunihiro Ohta
Engineering of monoclonal antibodies (mAbs) enables us to obtain mAbs with additional functions. In particular, modifications in antibody's Fc (fragment, crystallizable) region can provide multiple benefits such as added toxicity by drug conjugation, higher affinity to Fc receptors on immunocytes, or the addition of functional modules. However, the generation of recombinant antibodies requires multiple laborious bioengineering steps. We previously developed a technology that enables rapid in vitro screening and isolation of specific mAb-expressing cells from the libraries constructed with chicken B-cell line DT40 (referred to as the 'ADLib system')...
2016: PloS One
https://www.readbyqxmd.com/read/27905914/development-of-a-gene-synthesis-platform-for-the-efficient-large-scale-production-of-small-genes-encoding-animal-toxins
#3
Ana Filipa Sequeira, Joana L A Brás, Catarina I P D Guerreiro, Renaud Vincentelli, Carlos M G A Fontes
BACKGROUND: Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. In addition, when coupled with efficient gene design algorithms that optimize codon usage, it leads to high levels of recombinant protein expression. RESULTS: Here, we describe the development of an optimized gene synthesis platform that was applied to the large scale production of small genes encoding venom peptides...
December 1, 2016: BMC Biotechnology
https://www.readbyqxmd.com/read/27898094/crispr-cas9-aav-mediated-knock-in-at-nrl-locus-in-human-embryonic-stem-cells
#4
Xianglian Ge, Haitao Xi, Fayu Yang, Xiao Zhi, Yanghua Fu, Ding Chen, Ren-He Xu, Ge Lin, Jia Qu, Junzhao Zhao, Feng Gu
Clustered interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome engineering technologies are sparking a new revolution in biological research. This technology efficiently induces DNA double strand breaks at the targeted genomic sequence and results in indel mutations by the error-prone process of nonhomologous end joining DNA repair or homologous recombination with a DNA repair template. The efficiency of genome editing with CRISPR/Cas9 alone in human embryonic stem cells is still low...
November 29, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27878207/plasma-derived-versus-recombinant-factor-concentrates-in-pups-a-never-ending-debate
#5
Erik Berntorp
Inhibitor development in haemophilia is a serious complication to treatment with factor concentrates. Since the advent of more pure products, especially developed using recombinant DNA technology, some studies have shown an increased incidence of inhibitors in previously untreated patients (PUPs) receiving recombinant products whereas plasma-derived concentrates sometimes have been claimed to have a protective role, probably due to the content of von Willebrand factor (VWF). In fact, experiments indicate that the VWF may block uptake of factor VIII into macrophages for further processing to the immune system...
November 23, 2016: Hämostaseologie
https://www.readbyqxmd.com/read/27874287/impact-of-saccharomyces-cerevisiae-metabolites-produced-during-fermentation-on-bread-quality-parameters-a-review
#6
Mareile Heitmann, Emanuele Zannini, Elke Arendt
Although bread making with the use of Baker's yeast has a long tradition in human history, little attention has been paid to the connection between yeast addition and the final bread quality. Nowadays, bakers mainly use different flour additives such as enzymes (amylases, hemicellulases, and proteases) to change and improve dough properties and/or bread quality. Another strategy is the use of modified industrial Baker's yeast. To date, there is no yeast strain used in the baking industry, which is genetically modified, despite some studies demonstrating that the application of recombinant DNA technology is a possibility for improved strains suitable for baking...
November 22, 2016: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/27869438/immunology-update-biologics
#7
S Paul Starr
Biologics are substances made from a living organism or its products. These include genes, proteins (eg, antibodies, receptors, enzymes, inhibitors), recombinant proteins, and fusion proteins. Biologics often are produced using recombinant DNA technology. For example, monoclonal antibodies are produced by inserting human genes into immortalized cell cultures, which then produce the gene product (ie, an antibody) in large quantity. Another approach is to fuse genetic material from nonhuman sources (eg, mice) with human genetic material...
November 2016: FP Essentials
https://www.readbyqxmd.com/read/27846338/an-evolutionary-perspective-on-basal-insulin-in-diabetes-treatment-innovations-in-insulin-insulin-degludec-u-100-and-u-200
#8
Athena Philis-Tsimikas
Insulin degludec (IDeg) is a long-acting basal human insulin analog produced using recombinant DNA technology. The insulin structure is modified at the B30 position to allow a di-hexamer conformation in the presence of phenol and zinc.
October 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27845165/applications-of-genome-editing-by-programmable-nucleases-to-the-metabolic-engineering-of-secondary-metabolites
#9
REVIEW
Ana Lúcia Leitão, Marina C Costa, Francisco J Enguita
Genome engineering is a branch of modern biotechnology composed of a cohort of protocols designed to construct and modify a genotype with the main objective of giving rise to a desired phenotype. Conceptually, genome engineering is based on the so called genome editing technologies, a group of genetic techniques that allow either to delete or to insert genetic information in a particular genomic locus. Ten years ago, genome editing tools were limited to virus-driven integration and homologous DNA recombination...
November 11, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27837351/biomanufacturing-history-and-perspective
#10
REVIEW
Yi-Heng Percival Zhang, Jibin Sun, Yanhe Ma
Biomanufacturing is a type of manufacturing that utilizes biological systems (e.g., living microorganisms, resting cells, animal cells, plant cells, tissues, enzymes, or in vitro synthetic (enzymatic) systems) to produce commercially important biomolecules for use in the agricultural, food, material, energy, and pharmaceutical industries. History of biomanufacturing could be classified into the three revolutions in terms of respective product types (mainly), production platforms, and research technologies...
November 11, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27829353/a-magic-population-based-genome-wide-association-study-reveals-functional-association-of-ghrbb1_a07-gene-with-superior-fiber-quality-in-cotton
#11
Md Sariful Islam, Gregory N Thyssen, Johnie N Jenkins, Linghe Zeng, Christopher D Delhom, Jack C McCarty, Dewayne D Deng, Doug J Hinchliffe, Don C Jones, David D Fang
BACKGROUND: Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders' ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP)...
November 9, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27796547/rabies-vaccine-development-by-expression-of-recombinant-viral-glycoprotein
#12
REVIEW
Renato Mancini Astray, Soraia Attie Calil Jorge, Carlos Augusto Pereira
The rabies virus envelope glycoprotein (RVGP) is the main antigen of rabies virus and is the only viral component present in all new rabies vaccines being proposed. Many approaches have been taken since DNA recombinant technology became available to express an immunogenic recombinant rabies virus glycoprotein (rRVGP). These attempts are reviewed here, and the relevant results are discussed with respect to the general characteristics of the rRVGP, the expression system used, the expression levels achieved, the similarity of the rRVGP to the native glycoprotein, and the immunogenicity of the vaccine preparation...
October 31, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27793847/dna-repair-capacity-in-multiple-pathways-predicts-chemoresistance-in-glioblastoma-multiforme
#13
Zachary D Nagel, Gaspar J Kitange, Shiv K Gupta, Brian A Joughin, Isaac A Chaim, Patrizia Mazzucato, Douglas A Lauffenburger, Jann N Sarkaria, Leona D Samson
Cancer cells can resist the effects of DNA-damaging therapeutic agents via utilization of DNA repair pathways, suggesting that DNA repair capacity (DRC) measurements in cancer cells could be used to identify patients most likely to respond to treatment. However, the limitations of available technologies have so far precluded adoption of this approach in the clinic. We recently developed fluorescence-based multiplexed host cell reactivation (FM-HCR) assays to measure DRC in multiple pathways. Here we apply a mathematical model that uses DRC in multiple pathways to predict cellular resistance to killing by DNA-damaging agents...
October 28, 2016: Cancer Research
https://www.readbyqxmd.com/read/27790704/bromelain-from-production-to-commercialisation
#14
REVIEW
Aizi Nor Mazila Ramli, Tuan Norsyalieza Tuan Aznan, Rosli Md Illias
Bromelain is a mixture of proteolytic enzymes found in pineapple (Ananas comosus) plants. Bromelain can be found in several parts of the pineapple plant, including the stem, fruit, leaves and peels. High demand from bromelain has resulted in gradual increases in bromelain production. Such increases in production have led to the need for a bromelain production strategy that yields more purified bromelain at a lower cost and with fewer productions steps. Previously, bromelain was purified using conventional centrifugation, ultrafiltration and lyophilisation...
October 28, 2016: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/27774932/-construction-of-rev-erb%C3%AE-gene-knockout-hek293-cell-line-with-crispr-cas9-system
#15
Fang Chen, Weifeng Zhang, Junli Zhao, Peiyan Yang, Rui Ma, Haibin Xia
Objective To prepare Rev-erbβ knockout HEK293 cells using clustered regularly interspaced short palindromic repeats/Cas 9 nuclease (CRISPR/Cas9) gene editing technology. Methods The knock-in or knockout of Rev-erbβ gene could be realized by single-guide RNA (sgRNA)-mediated Cas9 cutting of target DNA, and followed by DNA homologous recombination or non-homologous end joining-mediated DNA repair. Firstly, four sgRNAs were designed for Rev-erbβ gene. The sgRNA1 and sgRNA2 with the higher activity were respectively used to construct pCMV-hCas9-U6-Rev-erbβ sgRNA1 and pCMV-hCas9-U6-Rev-erbβ sgRNA2...
November 2016: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/27769596/vaccine-development-from-concept-to-early-clinical-testing
#16
Anthony L Cunningham, Nathalie Garçon, Oberdan Leo, Leonard R Friedland, Richard Strugnell, Béatrice Laupèze, Mark Doherty, Peter Stern
In the 21st century, an array of microbiological and molecular allow antigens for new vaccines to be specifically identified, designed, produced and delivered with the aim of optimising the induction of a protective immune response against a well-defined immunogen. New knowledge about the functioning of the immune system and host pathogen interactions has stimulated the rational design of vaccines. The design toolbox includes vaccines made from whole pathogens, protein subunits, polysaccharides, pathogen-like particles, use of viral/bacterial vectors, plus adjuvants and conjugation technology to increase and broaden the immune response...
October 18, 2016: Vaccine
https://www.readbyqxmd.com/read/27768719/rlj-rgd3-a-novel-recombinant-toxin-protein-from-lampetra-japonica-protects-against-cerebral-reperfusion-injury-following-middle-cerebral-artery-occlusion-involving-the-integrin-pi3k-akt-pathway-in-rats
#17
Qian Lu, Jihong Wang, Junshu Jiang, Shengnan Wang, Qilan Jia, Yue Wang, Weiping Li, Qin Zhou, Li Lv, Qingwei Li
BACKGROUND: The RGD-toxin protein Lj-RGD3 is a naturally occurring 118 amino acid peptide that can be obtained from the salivary gland of the Lampetra japonica fish. This unique peptide contains 3 RGD (Arg-Gly-Asp) motifs in its primary structure. Lj-RGD3 is available in recombinant form (rLj-RGD3) and can be produced in large quantities using DNA recombination techniques. The pharmacology of the three RGD motif-containing peptides has not been studied. This study investigated the protective effects of rLj-RGD3, a novel polypeptide, against ischemia/reperfusion-induced damage to the brain caused by middle cerebral artery occlusion (MCAO) in a rat stroke model...
2016: PloS One
https://www.readbyqxmd.com/read/27747882/gene-regulation-and-genetics-in-neurochemistry-past-to-future
#18
Steven W Barger
Ask any neuroscientist to name the most profound discoveries in the field in the past 60 years, and at or near the top of the list will be a phenomenon or technique related to genes and their expression. Indeed, our understanding of genetics and gene regulation has ushered in whole new systems of knowledge and new empirical approaches, many of which could not have even been imagined prior to the molecular biology boon of recent decades. Neurochemistry, in the classic sense, intersects with these concepts in the manifestation of neuropeptides, obviously dependent upon the central dogma (the established rules by which DNA sequence is eventually converted into protein primary structure) not only for their conformation but also for their levels and locales of expression...
October 17, 2016: Journal of Neurochemistry
https://www.readbyqxmd.com/read/27729009/a-new-high-throughput-sequencing-method-for-determining-diversity-and-similarity-of-t-cell-receptor-tcr-%C3%AE-and-%C3%AE-repertoires-and-identifying-potential-new-invariant-tcr-%C3%AE-chains
#19
Kazutaka Kitaura, Tadasu Shini, Takaji Matsutani, Ryuji Suzuki
BACKGROUND: High-throughput sequencing of T cell receptor (TCR) genes is a powerful tool for analyses of antigen specificity, clonality and diversity of T lymphocytes. Here, we developed a new TCR repertoire analysis method using 454 DNA sequencing technology in combination with an adaptor-ligation mediated polymerase chain reaction (PCR). This method allows the amplification of all TCR genes without PCR bias. To compare gene usage, diversity and similarity of expressed TCR repertoires among individuals, we conducted next-generation sequencing (NGS) of TRA and TRB genes in peripheral blood mononuclear cells from 20 healthy human individuals...
October 11, 2016: BMC Immunology
https://www.readbyqxmd.com/read/27706659/molecular-cloning-overexpression-purification-and-sequence-analysis-of-the-giant-panda-ailuropoda-melanoleuca-ferritin-light-polypeptide
#20
L Fu, Y L Hou, X Ding, Y J Du, H Q Zhu, N Zhang, W R Hou
The complementary DNA (cDNA) of the giant panda (Ailuropoda melanoleuca) ferritin light polypeptide (FTL) gene was successfully cloned using reverse transcription-polymerase chain reaction technology. We constructed a recombinant expression vector containing FTL cDNA and overexpressed it in Escherichia coli using pET28a plasmids. The expressed protein was then purified by nickel chelate affinity chromatography. The cloned cDNA fragment was 580 bp long and contained an open reading frame of 525 bp. The deduced protein sequence was composed of 175 amino acids and had an estimated molecular weight of 19...
August 30, 2016: Genetics and Molecular Research: GMR
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