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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
#1
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/27932754/-overexpression-of-lentivirus-rfx1-and-its-inhibitory-effect-on-proliferation-of-glioblastoma-cells
#2
Kai Cheng, Haojie Sun, Mingzhi Zhang, Li Shen
To construct overexpression lentivirus vector for human regulatory factor X1 (RFX1) gene, and to explore its effect on proliferation of F98 cell line.
 Methods: Huamn RFX1 gene was amplified by polymerase reaction. Gene amplification products were inserted into lentivirus vector pITA, and the lentivirus vector pITA-RFX1 was constructed. The constructed vector was verified by agarose gel electrophoresis and DNA sequencing. Lentivirus vector pITA-RFX1 and virus packaging plasmids were cotransfected into 293T cells, and then transfected into F98 cells...
November 28, 2016: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/27932493/prdm9-interactions-with-other-proteins-provide-a-link-between-recombination-hotspots-and-the-chromosomal-axis-in-meiosis
#3
Emil D Parvanov, Hui Tian, Timothy Billings, Ruth L Saxl, Catrina Spruce, Rakesh Aithal, Lumir Krejci, Kenneth Paigen, Petko M Petkov
In mammals, meiotic recombination occurs at 1-2 kb genomic regions termed hotspots, whose positions and activities are determined by PRDM9, a DNA-binding histone methyltransferase. We now show that the KRAB domain of PRDM9 forms complexes with additional proteins to allow hotspots to proceed into the next phase of recombination. By a combination of yeast-two hybrid assay, in vitro binding, and co-immunoprecipitation from mouse spermatocytes, we identified four proteins that directly interact with PRDM9's KRAB domain, namely CXXC1, EWSR1, EHMT2, and CDYL...
December 8, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27932447/unloading-of-homologous-recombination-factors-is-required-for-restoring-double-stranded-dna-at-damage-repair-loci
#4
Yulia Vasianovich, Veronika Altmannova, Oleksii Kotenko, Matthew D Newton, Lumir Krejci, Svetlana Makovets
Cells use homology-dependent DNA repair to mend chromosome breaks and restore broken replication forks, thereby ensuring genome stability and cell survival. DNA break repair via homology-based mechanisms involves nuclease-dependent DNA end resection, which generates long tracts of single-stranded DNA required for checkpoint activation and loading of homologous recombination proteins Rad52/51/55/57. While recruitment of the homologous recombination machinery is well characterized, it is not known how its presence at repair loci is coordinated with downstream re-synthesis of resected DNA We show that Rad51 inhibits recruitment of proliferating cell nuclear antigen (PCNA), the platform for assembly of the DNA replication machinery, and that unloading of Rad51 by Srs2 helicase is required for efficient PCNA loading and restoration of resected DNA As a result, srs2Δ mutants are deficient in DNA repair correlating with extensive DNA processing, but this defect in srs2Δ mutants can be suppressed by inactivation of the resection nuclease Exo1...
December 8, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27932446/topoisomerase-i-mediated-cleavage-at-unrepaired-ribonucleotides-generates-dna-double-strand-breaks
#5
Shar-Yin N Huang, Jessica S Williams, Mercedes E Arana, Thomas A Kunkel, Yves Pommier
Ribonuclease activity of topoisomerase I (Top1) causes DNA nicks bearing 2',3'-cyclic phosphates at ribonucleotide sites. Here, we provide genetic and biochemical evidence that DNA double-strand breaks (DSBs) can be directly generated by Top1 at sites of genomic ribonucleotides. We show that RNase H2-deficient yeast cells displayed elevated frequency of Rad52 foci, inactivation of RNase H2 and RAD52 led to synthetic lethality, and combined loss of RNase H2 and RAD51 induced slow growth and replication stress...
December 8, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27932420/the-plastid-genome-of-polytoma-uvella-is-the-largest-known-among-non-photosynthetic-algae-and-plants
#6
Francisco Figueroa Martinez, Aurora M Nedelcu, David Roy Smith, Adrian Reyes Prieto
The loss of photosynthesis is frequently associated with parasitic or pathogenic lifestyles, but it can also occur in free-living, plastid-bearing lineages. A common consequence of becoming non-photosynthetic is the reduction in size and gene content of the plastid genome. In exceptional circumstances, it can even result in the complete loss of the plastid DNA (ptDNA), as recently reported in several lineages, including the nonphotosynthetic green algal genus Polytomella. Closely related to Polytomella is the genus Polytoma, the members of which lost photosynthesis independently of Polytomella...
December 8, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27932392/digital-gene-expression-profiling-analysis-of-dna-repair-pathways-in-colon-cancer-stem-population-of-ht29-cells
#7
Wenxue Wang, Guoxiu Zhang, Jing Yang, Huan Gu, Lei Ding, Haijing Yu, Min Yu, Qinghua Cui, Xinglai Ji, Meizhang Li
Cancer stem cells (CSCs) contribute to the relapse and development of new neoplasm lesions. While most available clinical approaches, such as chemical and radiation therapies, will kill the majority of cancer cells, they do not kill them all. Some resisting cells, like CSCs, are able to survive due to their excellent self-maintaining capabilities, even in challenging environments. In the present study, we investigated the mRNA level of DNA repair genes of colon CSCs from the HT29 cell line in response to single-strand damage and double-strand breaks, as well as the evident upregulation of key genes in base excision repair, mismatch repair, non-homologous end-joining, and homologous recombination pathways in these cells...
December 7, 2016: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/27932085/development-of-a-sensitive-and-false-positive-free-pma-qpcr-viability-assay-to-quantify-vbnc-escherichia-coli-and-evaluate-disinfection-performance-in-wastewater-effluent
#8
Richard Kibbee, Banu Örmeci
The detection and quantification of viable Escherichia coli cells in wastewater treatment plant effluent is very important as it is the main disinfection efficacy parameter for assessing its public health risk and environmental impact. The aim of this study was to develop a sensitive and false-positive free propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assay to quantify the viable but non-culturable (VBNC) E. coli present in secondary wastewater effluent after chlorine disinfection. The qPCR target was the E...
December 5, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27930825/modulation-of-meiotic-homologous-recombination-by-dna-helicases
#9
Alexander Lorenz
DNA helicases are ATP-driven motor proteins which translocate along DNA capable of dismantling DNA-DNA interactions and/or removing proteins bound to DNA. These biochemical capabilities make DNA helicases main regulators of crucial DNA metabolic processes, including DNA replication, DNA repair, and genetic recombination. This budding topic will focus on reviewing the function of DNA helicases important for homologous recombination during meiosis, and discuss recent advances in how these modulators of meiotic recombination are themselves regulated...
December 8, 2016: Yeast
https://www.readbyqxmd.com/read/27927599/angiotensin-converting-enzyme-2-amplification-limited-to-the-circulation-does-not-protect-mice-from-development-of-diabetic-nephropathy
#10
Jan Wysocki, Minghao Ye, Ahmed M Khattab, Agnes Fogo, Aline Martin, Nicolae Valentin David, Yashpal Kanwar, Mark Osborn, Daniel Batlle
Blockers of the renin-angiotensin system are effective in the treatment of experimental and clinical diabetic nephropathy. An approach different from blocking the formation or action of angiotensin II (1-8) that could also be effective involves fostering its degradation. Angiotensin-converting enzyme 2 (ACE2) is a monocarboxypeptidase that cleaves angiotensin II (1-8) to form angiotensin (1-7). Therefore, we examined the renal effects of murine recombinant ACE2 in mice with streptozotocin-induced diabetic nephropathy as well as that of amplification of circulating ACE2 using minicircle DNA delivery prior to induction of experimental diabetes...
December 4, 2016: Kidney International
https://www.readbyqxmd.com/read/27926907/mammalian-meiotic-recombination-a-toolbox-for-genome-evolution
#11
Laia Capilla, Montserrat Garcia Caldés, Aurora Ruiz-Herrera
Meiotic recombination is a process that increases genetic diversity and is fundamental for sexual reproduction. Determining by which mechanisms genetic variation is generated and maintained across different phylogenetic groups provides the basis for our understanding of biodiversity and evolution. In this review, we go through different aspects of this essential phenomenon, paying special attention to mammals. We provide a comprehensive view on the organization of meiotic chromosomes and the mechanisms involved in the formation and genomic distribution of recombination hotspots, focusing on the factors influencing the formation and repair of the massive amount of self-induced DNA breaks in early stages of meiosis...
December 8, 2016: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/27926866/inflammation-induced-oxidative-stress-mediates-gene-fusion-formation-in-prostate-cancer
#12
Ram S Mani, Mohammad A Amin, Xiangyi Li, Shanker Kalyana-Sundaram, Brendan A Veeneman, Lei Wang, Aparna Ghosh, Adam Aslam, Susmita G Ramanand, Bradley J Rabquer, Wataru Kimura, Maxwell Tran, Xuhong Cao, Sameek Roychowdhury, Saravana M Dhanasekaran, Nallasivam Palanisamy, Hesham A Sadek, Payal Kapur, Alisa E Koch, Arul M Chinnaiyan
Approximately 50% of prostate cancers are associated with gene fusions of the androgen-regulated gene TMPRSS2 to the oncogenic erythroblast transformation-specific (ETS) transcription factor ERG. The three-dimensional proximity of TMPRSS2 and ERG genes, in combination with DNA breaks, facilitates the formation of TMPRSS2-ERG gene fusions. However, the origins of DNA breaks that underlie gene fusion formation in prostate cancers are far from clear. We demonstrate a role for inflammation-induced oxidative stress in the formation of DNA breaks leading to recurrent TMPRSS2-ERG gene fusions...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27924011/roles-for-aprin-pds5b-in-homologous-recombination-and-in-ovarian-cancer-prediction
#13
Anthony M Couturier, Hubert Fleury, Anne-Marie Patenaude, Victoria L Bentley, Amélie Rodrigue, Yan Coulombe, Joshi Niraj, Joris Pauty, Jason N Berman, Graham Dellaire, Javier M Di Noia, Anne-Marie Mes-Masson, Jean-Yves Masson
APRIN (PDS5 cohesin associated factor B) interacts with both the cohesin complex and the BRCA2 tumor suppressor. How APRIN influences cohesion and DNA repair processes is not well understood. Here, we show that APRIN is recruited to DNA damage sites. We find that APRIN interacts directly with RAD51, PALB2 and BRCA2. APRIN stimulates RAD51-mediated DNA strand invasion. APRIN also binds DNA with an affinity for D-loop structures and single-strand (ss) DNA. APRIN is a new homologous recombination (HR) mediator as it counteracts the RPA inhibitory effect on RAD51 loading to ssDNA...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924006/the-homologous-recombination-protein-rad51d-protects-the-genome-from-large-deletions
#14
Wade A Reh, Rodney S Nairn, Megan P Lowery, Karen M Vasquez
Homologous recombination (HR) is a DNA double-strand break (DSB) repair pathway that protects the genome from chromosomal instability. RAD51 mediator proteins (i.e. paralogs) are critical for efficient HR in mammalian cells. However, how HR-deficient cells process DSBs is not clear. Here, we utilized a loss-of-function HR-reporter substrate to simultaneously monitor HR-mediated gene conversion and non-conservative mutation events. The assay is designed around a heteroallelic duplication of the Aprt gene at its endogenous locus in isogenic Chinese hamster ovary cell lines...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923995/homologous-recombination-in-budding-yeast-expressing-the-human-rad52-gene-reveals-a-rad51-independent-mechanism-of-conservative-double-strand-break-repair
#15
Glenn M Manthey, Alissa D Clear, Lauren C Liddell, Maria C Negritto, Adam M Bailis
RAD52 is a homologous recombination (HR) protein that is conserved from bacteriophage to humans. Simultaneously attenuating expression of both the RAD52 gene, and the HR and tumor suppressor gene, BRCA2, in human cells synergistically reduces HR - indicating that RAD52 and BRCA2 control independent mechanisms of HR. We have expressed the human RAD52 gene (HsRAD52) in budding yeast strains lacking the endogenous RAD52 gene and found that HsRAD52 supports repair of DNA double-strand breaks (DSB) by a mechanism of HR that conserves genome structure...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923977/absence-of-renal-enlargement-in-fructose-fed-proximal-tubule-select-insulin-receptor-ir-insulin-like-growth-factor-receptor-igf1r-double-knockout-mice
#16
Lijun Li, Marcus Byrd, Kwame Doh, Patrice D Dixon, Hwal Lee, Swasti Tiwari, Carolyn M Ecelbarger
The major site of fructose metabolism in the kidney is the proximal tubule (PT). To test whether insulin and/or IGF1 signaling in the PT is involved in renal structural/functional responses to dietary fructose, we bred mice with dual knockout (KO) of the insulin receptor (IR) and the IGF1 receptor (IGF1R) in PT by Cre-lox recombination, using a γ-glutamyl transferase promoter. KO mice had slightly (~10%) reduced body and kidney weights, as well as, a reduction in mean protein-to-DNA ratio in kidney cortex suggesting smaller cell size...
December 2016: Physiological Reports
https://www.readbyqxmd.com/read/27923922/mechanisms-of-evolution-in-high-consequence-drug-resistance-plasmids
#17
Susu He, Michael Chandler, Alessandro M Varani, Alison B Hickman, John P Dekker, Fred Dyda
: The dissemination of resistance among bacteria has been facilitated by the fact that resistance genes are usually located on a diverse and evolving set of transmissible plasmids. However, the mechanisms generating diversity and enabling adaptation within highly successful resistance plasmids have remained obscure, despite their profound clinical significance. To understand these mechanisms, we have performed a detailed analysis of the mobilome (the entire mobile genetic element content) of a set of previously sequenced carbapenemase-producing Enterobacteriaceae (CPE) from the National Institutes of Health Clinical Center...
December 6, 2016: MBio
https://www.readbyqxmd.com/read/27923845/numerical-and-spatial-patterning-of-yeast-meiotic-dna-breaks-by-tel1
#18
Neeman Mohibullah, Scott Keeney
The Spo11-generated double-strand breaks (DSBs) that initiate meiotic recombination are dangerous lesions that can disrupt genome integrity, so meiotic cells regulate their number, timing, and distribution. Mechanisms of this regulation remain poorly understood. Here, we use Spo11-oligonucleotide complexes, a byproduct of DSB formation, to reveal aspects of the contribution of the Saccharomyces cerevisiae DNA damage-responsive kinase Tel1 (ortholog of mammalian ATM). A tel1Δ mutant has globally increased amounts of Spo11-oligonucleotide complexes and altered Spo11-oligonucleotide lengths, consistent with conserved roles for Tel1 in control of DSB number and processing...
December 6, 2016: Genome Research
https://www.readbyqxmd.com/read/27923769/recombination-in-hepatitis-c-virus-is-not-uncommon-among-people-who-inject-drugs-in-kolkata-india
#19
Debanjali Gupta, Kallol Saha, Aritra Biswas, Rushna Firdaus, Monika Ghosh, Provash Chandra Sadhukhan
Recombination in RNA virus is a rare event in the survival and evolution to evade host immune system. This is increasing within high risk group population (HRG) due to super infection that occurs by continuous sharing of common drug equipment by HCV infected or HIV-HCV co-infected recurrent drug users. Recombination causes impediment to vaccine development and therapeutic intervention as standard HCV treatment is still genotype specific. Blood samples of 194 people who inject drugs (PWID) were collected from an Opioid Substitution Therapy Centre in Kolkata,India...
December 3, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27923713/when-transcription-goes-on-holliday-double-holliday-junctions-block-rna-polymerase-ii-transcription-in-vitro
#20
Anne Pipathsouk, Boris P Belotserkovskii, Philip C Hanawalt
Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJ), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact...
December 3, 2016: Biochimica et Biophysica Acta
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