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recombinant DNA technology

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https://www.readbyqxmd.com/read/28092459/toward-high-throughput-and-multiplexed-imaging-of-genome-organization
#1
Eric F Joyce
Dr. Eric Joyce from the Department of Genetics at the University of Pennsylvania was awarded The President's Innovation award at the annual Society of Biomolecular Imaging and Informatics meeting held in Boston, September 2016. Chromosome interactions are a fundamental aspect of nuclear organization that can activate and silence genes or even direct chromosome rearrangements. However, the molecular mechanisms underlying how chromosomal segments find each other and form stable interactions within cells remain unknown...
January 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28067217/characterization-of-the-interplay-between-dna-repair-and-crispr-cas9-induced-dna-lesions-at-an-endogenous-locus
#2
Anne Bothmer, Tanushree Phadke, Luis A Barrera, Carrie M Margulies, Christina S Lee, Frank Buquicchio, Sean Moss, Hayat S Abdulkerim, William Selleck, Hariharan Jayaram, Vic E Myer, Cecilia Cotta-Ramusino
The CRISPR-Cas9 system provides a versatile toolkit for genome engineering that can introduce various DNA lesions at specific genomic locations. However, a better understanding of the nature of these lesions and the repair pathways engaged is critical to realizing the full potential of this technology. Here we characterize the different lesions arising from each Cas9 variant and the resulting repair pathway engagement. We demonstrate that the presence and polarity of the overhang structure is a critical determinant of double-strand break repair pathway choice...
January 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28060945/examining-sources-of-error-in-pcr-by-single-molecule-sequencing
#3
Vladimir Potapov, Jennifer L Ong
Next-generation sequencing technology has enabled the detection of rare genetic or somatic mutations and contributed to our understanding of disease progression and evolution. However, many next-generation sequencing technologies first rely on DNA amplification, via the Polymerase Chain Reaction (PCR), as part of sample preparation workflows. Mistakes made during PCR appear in sequencing data and contribute to false mutations that can ultimately confound genetic analysis. In this report, a single-molecule sequencing assay was used to comprehensively catalog the different types of errors introduced during PCR, including polymerase misincorporation, structure-induced template-switching, PCR-mediated recombination and DNA damage...
2017: PloS One
https://www.readbyqxmd.com/read/28045956/recombinase-polymerase-amplification-assay-a-simple-fast-and-cost-effective-alternative-to-real-time-pcr-for-specific-detection-of-feline-herpesvirus-1
#4
Jianchang Wang, Libing Liu, Jinfeng Wang, Xiaoxia Sun, Wanzhe Yuan
Feline herpesvirus 1 (FHV-1), an enveloped dsDNA virus, is one of the major pathogens of feline upper respiratory tract disease (URTD) and ocular disease. Currently, polymerase chain reaction (PCR) remains the gold standard diagnostic tool for FHV-1 infection but is relatively expensive, requires well-equipped laboratories and is not suitable for field tests. Recombinase polymerase amplification (RPA), an isothermal gene amplification technology, has been explored for the molecular diagnosis of infectious diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28042089/paf53-is-essential-in-mammalian-cells-crispr-cas9-fails-to-eliminate-paf53-expression
#5
Lawrence I Rothblum, Katrina Rothblum, Eugenie Chang
When mammalian cells are nutrient and/or growth factor deprived, exposed to inhibitors of protein synthesis, stressed by heat shock or grown to confluence, rDNA transcription is essentially shut off. Various mechanisms are available to accomplish this downshift in ribosome biogenesis. Muramatsu's laboratory (Hanada et al., 1996) first demonstrated that mammalian PAF53 was essential for specific rDNA transcription and that PAF53 levels were regulated in response to growth factors. While S. cerevisae A49, the homologue of vertebrate PAF53, is not essential for viability (Liljelund et al...
December 29, 2016: Gene
https://www.readbyqxmd.com/read/28038868/marek-s-disease-vaccines-current-status-and-strategies-for-improvement-and-development-of-vector-vaccines
#6
Sanjay M Reddy, Yoshihiro Izumiya, Blanca Lupiani
Marek's disease (MD) is a lymphoproliferative viral disease of chickens, which has been controlled through vaccination since 1969. MD vaccines protect against tumors but do not provide sterilizing immunity, and thus it is generally believed that their use has contributed to increase virulence of field strains with the ability to cause MD in vaccinated chickens. Traditional methods of developing vaccines, like cell culture attenuation, have proved unsuccessful for the development of improved vaccines to protect against highly virulent MD virus (MDV) field strains...
November 24, 2016: Veterinary Microbiology
https://www.readbyqxmd.com/read/28027431/from-classical-mutagenesis-to-nuclease-based-breeding-directing-natural-dna-repair-for-a-natural-end-product
#7
Michael Pacher, Holger Puchta
The production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damages in an error-prone way. In case of radiation, multiple double strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site directed nucleases (SDNs), also referred to as sequence specific nucleases (SSNs), like the CRISPR/Cas system, enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at predefined sites in plant genomes...
December 27, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28025504/reverse-genetics-approaches-for-the-development-of-influenza-vaccines
#8
REVIEW
Aitor Nogales, Luis Martínez-Sobrido
Influenza viruses cause annual seasonal epidemics and occasional pandemics of human respiratory disease. Influenza virus infections represent a serious public health and economic problem, which are most effectively prevented through vaccination. However, influenza viruses undergo continual antigenic variation, which requires either the annual reformulation of seasonal influenza vaccines or the rapid generation of vaccines against potential pandemic virus strains. The segmented nature of influenza virus allows for the reassortment between two or more viruses within a co-infected cell, and this characteristic has also been harnessed in the laboratory to generate reassortant viruses for their use as either inactivated or live-attenuated influenza vaccines...
December 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28017152/rdna-mediated-bioconjugates-fusion-proteins-and-their-intended-use-in-medicine
#9
Ayşe Göksu Kaya-Özsan, Ayşe Filiz Öner
Protein bioconjugates can be synthesized by using chemical reactions, enzymatic reactions or genetic engineering technologies. Naturally occurred protein fusion event is used on purpose in the development of better biopharmaceuticals by applying genetic engineering methodologies. This review will mainly focus on the types of fusion proteins produced with the use of recombinant DNA technology, by combining genes or parts of genes from the same or different organisms, in order to be used in pharmaceutical applications for several purposes...
December 22, 2016: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/27976757/efficient-and-versatile-crispr-engineering-of-human-neurons-in-culture-to-model-neurological-disorders
#10
Ruth R Shah, Justyna Cholewa-Waclaw, Faith C J Davies, Katie M Paton, Ronan Chaligne, Edith Heard, Catherine M Abbott, Adrian P Bird
The recent identification of multiple new genetic causes of neurological disorders highlights the need for model systems that give experimental access to the underlying biology. In particular, the ability to couple disease-causing mutations with human neuronal differentiation systems would be beneficial. Gene targeting is a well-known approach for dissecting gene function, but low rates of homologous recombination in somatic cells (including neuronal cells) have traditionally impeded the development of robust cellular models of neurological disorders...
November 15, 2016: Wellcome Open Res
https://www.readbyqxmd.com/read/27957856/high-throughput-identification-of-dna-encoded-igg-ligands-that-distinguish-active-and-latent-mycobacterium-tuberculosis-infections
#11
Kimberly R Mendes, Marie Lynne Malone, John Maina Ndungu, Irena Suponitsky-Kroyter, Valerie J Cavett, Patrick J McEnaney, Andrew B MacConnell, Todd M Doran, Katharina Ronacher, Kim Stanley, Ofelia Utset, Gerhard Walzl, Brian M Paegel, Thomas Kodadek
The circulating antibody repertoire encodes a patient's health status and pathogen exposure history, but identifying antibodies with diagnostic potential usually requires knowledge of the antigen(s). We previously circumvented this problem by screening libraries of bead-displayed small molecules against case and control serum samples to discover "epitope surrogates" (ligands of IgGs enriched in the case sample). Here, we describe an improved version of this technology that employs DNA-encoded libraries and high-throughput FACS-based screening to discover epitope surrogates that differentiate noninfectious/latent (LTB) patients from infectious/active TB (ATB) patients, which is imperative for proper treatment selection and antibiotic stewardship...
December 13, 2016: ACS Chemical Biology
https://www.readbyqxmd.com/read/27933101/study-of-holtermanniella-wattica-leucosporidium-creatinivorum-naganishia-adeliensis-solicoccozyma-aeria-and-solicoccozyma-terricola-for-their-lipogenic-aptitude-from-different-carbon-sources
#12
Sara Filippucci, Giorgia Tasselli, Alessandro Scardua, Simone Di Mauro, Maria Rita Cramarossa, Davide Perini, Benedetta Turchetti, Andrea Onofri, Luca Forti, Pietro Buzzini
BACKGROUND: The ability of some microorganisms to accumulate lipids is well known; however, only recently the number of studies on microbial lipid biosynthesis for obtaining oleochemical products, namely biofuels and some building blocks for chemistry, is rapidly and spectacularly increased. Since 1990s, some oleaginous yeasts were studied for their ability to accumulate lipids up to 60-70% of their dry weight. Due to the vast array of engineering techniques currently available, the recombinant DNA technology was the main approach followed so far for obtaining lipid-overproducing yeasts, mainly belonging to the Yarrowia lipolytica...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27914076/reconstructing-the-ancestral-relationships-between-bacterial-pathogen-genomes
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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