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Homologous recombination

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https://www.readbyqxmd.com/read/28448436/role-of-archaeal-hera-protein-in-the-biology-of-the-bacterium-thermus-thermophilus
#1
Alba Blesa, Nieves G Quintans, Ignacio Baquedano, Carlos P Mata, José R Castón, José Berenguer
Intense gene flux between prokaryotes result in high percentage of archaeal genes in the genome of the thermophilic bacteria Thermus spp. Among these archaeal genes a homolog to the Sulfolobus spp. HerA protein appears in all of the Thermus spp. strains so far sequenced (HepA). The role of HepA in Thermus thermophilus HB27 has been analyzed using deletion mutants, and its structure resolved at low resolution by electron microscopy. Recombinant HepA shows DNA-dependent ATPase activity and its structure revealed a double ring, conically-shaped hexamer with an upper diameter of 150 Å and a bottom module of 95 Å...
April 27, 2017: Genes
https://www.readbyqxmd.com/read/28447610/parp3-is-a-promoter-of-chromosomal-rearrangements-and-limits-g4-dna
#2
Tovah A Day, Jacob V Layer, J Patrick Cleary, Srijoy Guha, Kristen E Stevenson, Trevor Tivey, Sunhee Kim, Anna C Schinzel, Francesca Izzo, John Doench, David E Root, William C Hahn, Brendan D Price, David M Weinstock
Chromosomal rearrangements are essential events in the pathogenesis of both malignant and nonmalignant disorders, yet the factors affecting their formation are incompletely understood. Here we develop a zinc-finger nuclease translocation reporter and screen for factors that modulate rearrangements in human cells. We identify UBC9 and RAD50 as suppressors and 53BP1, DDB1 and poly(ADP)ribose polymerase 3 (PARP3) as promoters of chromosomal rearrangements across human cell types. We focus on PARP3 as it is dispensable for murine viability and has druggable catalytic activity...
April 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28445939/epigenetic-therapy-with-inhibitors-of-histone-methylation-suppresses-dna-damage-signaling-and-increases-glioma-cell-radiosensitivity
#3
Ozge Gursoy-Yuzugullu, Chelsea Carman, Rodolfo Bortolozo Serafim, Marios Myronakis, Valeria Valente, Brendan D Price
Radiation therapy is widely used to treat human malignancies, but many tumor types, including gliomas, exhibit significant radioresistance. Radiation therapy creates DNA double-strand breaks (DSBs), and DSB repair is linked to rapid changes in epigenetic modifications, including increased histone methylation. This increased histone methylation recruits DNA repair proteins which can then alter the local chromatin structure and promote repair. Consequently, combining inhibitors of specific histone methyltransferases with radiation therapy may increase tumor radiosensitivity, particularly in tumors with significant therapeutic resistance...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28444231/whole-genome-sequencing-of-7-strains-of-staphylococcus-lugdunensis-allows-identification-of-mobile-genetic-elements
#4
Xavier Argemi, Véronique Martin, Valentin Loux, Sandrine Dahyot, Jérémie Lebeurre, Aurélien Guffroy, Mickael Martin, Aurélie Velay, Daniel Keller, Philippe Riegel, Yves Hansmann, Nicodème Paul, Gilles Prévost
Coagulase negative staphylococci are normal inhabitant of the human skin flora that account for an increasing number of infections, particularly hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most virulent species causing various infections with clinical characteristics close to what clinicians usually observe with Staphylococcus aureus and both bacteria share more than 70% of their genome. Virulence of S. aureus relies on a large repertoire of virulence factors, many of which are encoded on mobile genetic elements...
April 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28443118/the-absence-of-the-arabidopsis-chaperone-complex-caf-1-produces-mitotic-chromosome-abnormalities-and-changes-in-the-expression-profiles-of-genes-involved-in-dna-repair
#5
Javier Varas, Juan L Santos, Mónica Pradillo
Chromatin Assembly Factor 1 (CAF-1) is an evolutionary conserved heterotrimeric chaperone complex that facilitates the incorporation of histones H3 and H4 onto newly synthesized DNA. We demonstrate here that the mutant deficient for the large subunit of the complex, fas1-4, and in minor extent, the mutant deficient for the middle subunit, fas2-1, display chromosome abnormalities throughout Arabidopsis mitosis. Among them, we observed multicentromeric chromosomes at metaphase, and chromatid bridges and acentric fragments at anaphase-telophase...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442542/missense-mutations-in-the-wd40-domain-of-ahi1-cause-non-syndromic-retinitis-pigmentosa
#6
Thanh-Minh T Nguyen, Sarah Hull, Ronald Roepman, L Ingeborgh van den Born, Machteld M Oud, Erik de Vrieze, Lisette Hetterschijt, Stef J F Letteboer, Sylvia E C van Beersum, Ellen A Blokland, Helger G Yntema, Frans P M Cremers, Paul A van der Zwaag, Gavin Arno, Erwin van Wijk, Andrew R Webster, Lonneke Haer-Wigman
BACKGROUND: Recent findings suggesting that Abelson helper integration site 1 (AHI1) is involved in non-syndromic retinal disease have been debated, as the functional significance of identified missense variants was uncertain. We assessed whether AHI1 variants cause non-syndromic retinitis pigmentosa (RP). METHODS: Exome sequencing was performed in three probands with RP. The effects of the identified missense variants in AHI1 were predicted by three-dimensional structure homology modelling...
April 25, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28442498/identification-and-characterization-of-a-novel-ppar%C3%AE-regulated-and-7%C3%AE-hydroxyl-bile-acid-preferring-cytosolic-sulfotransferase-ml-stl-sult2a8
#7
Lu Feng, Yee-Lok Yuen, Jian Xu, Xing Liu, Martin Yan-Chun Chan, Kai Wang, Wing-Ping Fong, Wing-Tai Cheung, Susanna Sau-Tuen Lee
PPARα has been known to play a pivotal role in orchestrating lipid, glucose, and amino acid metabolism via transcriptional regulation of its target genes expression during energy deprivation. Recent evidence also suggesting PPARα is involved in bile acid metabolism, but how PPARα modulates the homeostasis of bile acids during fasting is still not clear. In a mechanistic study aiming to dissect the spectrum of PPARα target genes involved in metabolic response to fasting, we identified a novel mouse gene (herein named mL-STL) which shared extensive homology to Sult2a subfamily of a superfamily of cytosolic sulfotransferases, implying its potential function in sulfonation...
April 25, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28442426/identification-of-a-wza-like-gene-involved-in-capsule-biosynthesis-pathogenicity-and-biofilm-formation-in-riemerella-anatipestifer
#8
Haibo Yi, Biao Yuan, Jibin Liu, Dekang Zhu, Ying Wu, Mingshu Wang, Renyong Jia, Kunfeng Sun, Qiao Yang, Shun Chen, Mafeng Liu, Xiaoyue Chen, Anchun Cheng
Duck infectious serositis is the most serious bacterial disease of ducks. It is caused by Riemerella anatipestifer (RA) infection. The capsule plays an important role in virulence of many pathogenic bacteria. In addition, the capsule has some key biological features. However, few studies have explored the characteristics of the RA capsule. In this study, we mainly constructed a capsular mutants of RA by inactivating the wza gene using homologous recombination. We found that the mutant was failed to produce a capsule layer...
April 22, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28440490/microrna-15a-inhibition-protects-against-hypoxia-reoxygenation-induced-apoptosis-of-cardiomyocytes-by-targeting-mothers-against-decapentaplegic-homolog-7
#9
Yang Yang, Shiao Ding, Gaojun Xu, Fei Chen, Fangbao Ding
Myocardial ischemia/reperfusion (I/R) injury is a major pathological process in coronary heart disease and cardiac surgery, and is associated with aberrant microRNA (miR) expression. Previous studies have demonstrated that inhibition of miR-15a expression may ameliorate I/R‑induced myocardial injury. In the present study, the potential role and underlying mechanism of miR‑15a in hypoxia/reoxygenation‑induced apoptosis of cardiomyocytes was investigated. Myocardial I/R was simulated in cultured H9c2 cells by 24 h hypoxia followed by 24 h reoxygenation...
April 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28439991/melatonin-a-pleiotropic-molecule-that-modulates-dna-damage-response-and-repair-pathways
#10
REVIEW
Maryam Majidinia, Alireza Sadeghpour, Saeed Mehrzadi, Russel J Reiter, Nasrin Khatami, Bahman Yousefi
DNA repair is responsible for maintaining the integrity of the genome. Perturbations in the DNA repair pathways have been identified in several human cancers. Thus, compounds targeting DNA damage response (DDR) hold great promise in cancer therapy. A great deal of effort, in pursuit of new anticancer drugs, has been devoted to understanding the basic mechanisms and functions of the cellular DNA repair machinery. Melatonin, a widely-produced indoleamine in all organisms is associated with a reduced risk of cancer and has multiple regulatory roles on the different aspects of the DDR and DNA repair...
April 25, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/28439853/crispr-cas-mediated-in-planta-gene-targeting
#11
Simon Schiml, Friedrich Fauser, Holger Puchta
The recent emergence of the CRISPR/Cas system has boosted the possibilities for precise genome engineering approaches throughout all kingdoms of life. The most common application for plants is targeted mutagenesis, whereby a Cas9-mediated DNA double-strand break (DSB) is repaired by mutagenic nonhomologous end joining (NHEJ). However, the site-specific alteration of a genomic sequence or integration of a transgene relies on the precise repair by homologous recombination (HR) using a suitable donor sequence: this poses a particular challenge in plants, as NHEJ is the preferred repair mechanism for DSBs in somatic tissue...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28438837/an-unpredicted-aggregation-critical-region-of-the-actin-polymerizing-protein-triobp-1-tara-determined-by-elucidation-of-its-domain-structure
#12
Nicholas J Bradshaw, Antony S K Yerabham, Rita Marreiros, Tao Zhang, Luitgard Nagel-Steger, Carsten Korth
Protein aggregation resulting from disruptions in proteostasis in the brains of patients with chronic mental illness is an emerging theme particularly in the study of schizophrenia. For example, proteins such as Disrupted in Schizophrenia 1 (DISC1) and dysbindin-1B are present in insoluble aggregates, detectable within brain homogenates from such patients. Using an epitope discovery and proteomics approach to compare post-mortem brain samples from schizophrenia patients and controls, we recently identified TRIO-Binding Protein 1 (TRIOBP-1, also known as Tara) as another aggregation-associated protein...
April 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28438686/expression-purification-and-molecular-characterization-of-a-novel-endoglucanase-protein-from-bacillus-subtilis-sb13
#13
Xuefang Guan, Penglian Chen, Qingxian Xu, Lei Qian, Juqing Huang, Bin Lin
Bacillus subtilis strain SB13 which is isolated in our previous work was confirmed to produce endoglucanase. In this study, a novel endoglucanase gene (accession number: KX576676) was identified and cloned from SB13. Compared with other consensus sequence of reported endoglucanase genes in the GenBank database, this gene displays five differences (including T740C,A874G,A983G, T1210G and T1301C), which leading to five amino acid changes. Homology modeling has indicated that these five changes were located in the α-helix and random coil regions of the glycosyl hydrolase family 5 (GH5) domain, the random coil and β-sandwich of the type 3 carbohydrate-binding module (CBM3) domain, and the random coil domain...
April 21, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28438410/vaccination-with-recombinant-modified-vaccinia-ankara-mva-viruses-expressing-single-african-horse-sickness-virus-vp2-antigens-induced-cross-reactive-virus-neutralising-antibodies-vnab-in-horses-when-administered-in-combination
#14
Nicola Mary Manning, Katarzyna Bachanek-Bankowska, Peter Paul Clement Mertens, Javier Castillo-Olivares
African horse sickness is a lethal viral disease of equids transmitted by biting midges of the Genus Culicoides. The disease is endemic to sub-Saharan Africa but outbreaks of high mortality and economic impact have occurred in the past in non-endemic regions of Africa, Asia and Southern Europe. Vaccination is critical for the control of this disease but only live attenuated vaccines are currently available. However, there are bio-safety concerns over the use of this type of vaccines, especially in non-endemic countries, and live attenuated vaccines do not have DIVA (Differentiation of Infected from Vaccinated Animals) capacity...
April 21, 2017: Vaccine
https://www.readbyqxmd.com/read/28438207/large-scale-validation-of-an-efficient-crispr-cas-based-multi-gene-editing-protocol-in-escherichia-coli
#15
Francesca Zerbini, Ilaria Zanella, Davide Fraccascia, Enrico König, Carmela Irene, Luca F Frattini, Michele Tomasi, Laura Fantappiè, Luisa Ganfini, Elena Caproni, Matteo Parri, Alberto Grandi, Guido Grandi
BACKGROUND: The exploitation of the CRISPR/Cas9 machinery coupled to lambda (λ) recombinase-mediated homologous recombination (recombineering) is becoming the method of choice for genome editing in E. coli. First proposed by Jiang and co-workers, the strategy has been subsequently fine-tuned by several authors who demonstrated, by using few selected loci, that the efficiency of mutagenesis (number of mutant colonies over total number of colonies analyzed) can be extremely high (up to 100%)...
April 24, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28437612/combinatorial-library-based-on-restriction-enzyme-mediated-modular-assembly
#16
Cuiping Ma, Chao Liang, Yifan Wang, Mei Pan, Qianqian Jiang, Chao Shi
Combinatorial approaches in directed evolution were proven to be more efficient for exploring sequence space and innovating the function of protein. We presented modular assembly of secondary structures (MASS) for constructing a combinatorial library. In this approach, secondary structure elements were extracted from natural existing proteins, the common linkers were flanking secondary structure elements, then digested by Hinf I restriction endonuclease that was used in the construction of combinatorial library for the first time...
April 24, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28436588/reduced-erg-dosage-impairs-survival-of-hematopoietic-stem-and-progenitor-cells
#17
Ying Xie, Mia Lee Koch, Xin Zhang, Melanie J Hamblen, Frank J Godinho, Yuko Fujiwara, Huafeng Xie, Jan-Henning Klusmann, Stuart H Orkin, Zhe Li
ERG, an ETS family transcription factor frequently overexpressed in human leukemia, has been implicated as a key regulator of hematopoietic stem cells. However, how ERG controls normal hematopoiesis, particularly at the stem and progenitor cell level, and how it contributes to leukemogenesis remain incompletely understood. Using homologous recombination, we generated an Erg knockdown allele (Erg(kd) ) in which Erg expression can be conditionally restored by Cre recombinase. Erg(kd/kd) animals die at E10.5-E11...
April 24, 2017: Stem Cells
https://www.readbyqxmd.com/read/28436337/molecular-cloning-expression-and-characterization-of-e2f-transcription-factor-4-from-antheraea-pernyi
#18
M N Abbas, S Kausar, Y-X Sun, Y Sun, L Wang, C Qian, G-Q Wei, B-J Zhu, C-L Liu
The E2F transcription factor family is distributed widely in eukaryotes and has been well studied among mammals. In the present study, the E2F transcription factor 4 (E2F4) gene was isolated from fat bodies of Antheraea pernyi and sequenced. E2F4 comprised a 795 bp open reading frame encoding a deduced amino acid sequence of 264 amino acid residues. The recombinant protein was expressed in Escherichia coli (Transetta DE3), and anti-E2F4 antibodies were prepared. The deduced amino acid sequence displayed significant homology to an E2F4-like protein from Bombyx mori L...
April 24, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28436335/localization-of-the-werner-protein-together-with-h2ax-in-%C3%AE-irradiation-induced-neoplastic-transformed-human-mesenchymal-stem-cells
#19
Nedime Serakinci, Tufan Cankaya, Steen Kølvraa
The H2A histone family, member X (H2AX), and Werner (WRN) are important proteins for genome and telomere maintenance. WRN has a major role in genome stability, particularly during DNA replication, transcription, recombination, and repair of DNA double-stranded breaks (DSBs) via base excision repair, homologous recombination, or nonhomologous end joining. H2AX plays a part in the rapid, sensitive, cellular response to the ionizing radiation or DNA-damaging chemotherapeutic agents that cause DSBs. This occurs when radiation-induced DSBs trigger the activation of H2AX and begin the damage-repair process...
2017: Critical Reviews in Eukaryotic Gene Expression
https://www.readbyqxmd.com/read/28435908/development-of-a-japanese-encephalitis-virus-like-particle-vaccine-in-silkworms-using-codon-optimised-prm-and-envelope-genes
#20
Sayaka Matsuda, Reiko Nerome, Kenichi Maegawa, Akira Kotaki, Shigeo Sugita, Kazunori Kawasaki, Kazumichi Kuroda, Ryoji Yamaguchi, Tomohiko Takasaki, Kuniaki Nerome
We have successfully prepared a Japanese encephalitis virus (JEV) - Nakayama virus like particle (NVLP) vaccine using synthetic codon-optimized prM and E genes. The expression of the recombinant JEV Nakayama-BmNPV (JEV-NNPV) virus was determined in infected silkworm Bm-N cells by fluorescence and Western blot analysis. The recombinant was inoculated into silkworm pupae and the yield of Nakayama VLP (NVLP) reached a peak in the homogenates after 3 days. Additionally, in the peptide analysis of infected pupae homogenate, it appeared approximately 300-500 μg E protein/pupa were produced...
April 2017: Heliyon
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