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https://www.readbyqxmd.com/read/28531371/wing-1-of-protein-hop2-is-as-important-as-helix-3-in-dna-binding-by-md-simulation
#1
Hem Moktan, Donghua H Zhou
The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28531348/plant-derived-transcription-factors-for-orthologous-regulation-of-gene-expression-in-the-yeast-saccharomyces-cerevisiae
#2
Gita Naseri, Salma Balazadeh, Fabian Machens, Iman Kamranfar, Katrin Messerschmidt, Bernd Mueller-Roeber
Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects where tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harbouring cognate cis-regulatory motifs driving a yEGFP reporter...
May 22, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28531187/multi-scale-computational-study-of-the-mechanical-regulation-of-cell-mitotic-rounding-in-epithelia
#3
Ali Nematbakhsh, Wenzhao Sun, Pavel A Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J Zartman, Mark Alber
Mitotic rounding during cell division is critical for preventing daughter cells from inheriting an abnormal number of chromosomes, a condition that occurs frequently in cancer cells. Cells must significantly expand their apical area and transition from a polygonal to circular apical shape to achieve robust mitotic rounding in epithelial tissues, which is where most cancers initiate. However, how cells mechanically regulate robust mitotic rounding within packed tissues is unknown. Here, we analyze mitotic rounding using a newly developed multi-scale subcellular element computational model that is calibrated using experimental data...
May 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28531132/effects-of-%C3%AE-carotene-and-its-cleavage-products-in-primary-pneumocyte-type-ii-cells
#4
Cornelia Haider, Franziska Ferk, Ekramije Bojaxhi, Giuseppe Martano, Hanno Stutz, Nikolaus Bresgen, Siegfried Knasmüller, Avdulla Alija, Peter M Eckl
β-Carotene has been shown to increase the risk of developing lung cancer in smokers and asbestos workers in two large scale trails, the Beta-Carotene and Retinol Efficacy Trial (CARET) and the Alpha-Tocopherol Beta-carotene Cancer Prevention Trial (ATBC). Based on this observation, it was proposed that genotoxic oxidative breakdown products may cause this effect. In support of this assumption, increased levels of sister chromatid exchanges, micronuclei, and chromosomal aberrations were found in primary hepatocyte cultures treated with a mixture of cleavage products (CPs) and the major product apo-8'carotenal...
May 21, 2017: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/28530678/the-complex-genetics-of-hypoplastic-left-heart-syndrome
#5
Xiaoqin Liu, Hisato Yagi, Shazina Saeed, Abha S Bais, George C Gabriel, Zhaohan Chen, Kevin A Peterson, You Li, Molly C Schwartz, William T Reynolds, Manush Saydmohammed, Brian Gibbs, Yijen Wu, William Devine, Bishwanath Chatterjee, Nikolai T Klena, Dennis Kostka, Karen L de Mesy Bentley, Madhavi K Ganapathiraju, Phillip Dexheimer, Linda Leatherbury, Omar Khalifa, Anchit Bhagat, Maliha Zahid, William Pu, Simon Watkins, Paul Grossfeld, Stephen A Murray, George A Porter, Michael Tsang, Lisa J Martin, D Woodrow Benson, Bruce J Aronow, Cecilia W Lo
Congenital heart disease (CHD) affects up to 1% of live births. Although a genetic etiology is indicated by an increased recurrence risk, sporadic occurrence suggests that CHD genetics is complex. Here, we show that hypoplastic left heart syndrome (HLHS), a severe CHD, is multigenic and genetically heterogeneous. Using mouse forward genetics, we report what is, to our knowledge, the first isolation of HLHS mutant mice and identification of genes causing HLHS. Mutations from seven HLHS mouse lines showed multigenic enrichment in ten human chromosome regions linked to HLHS...
May 22, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28529873/white-matter-hyperintensities-are-seen-only-in-grn-mutation-carriers-in-the-genfi-cohort
#6
Carole H Sudre, Martina Bocchetta, David Cash, David L Thomas, Ione Woollacott, Katrina M Dick, John van Swieten, Barbara Borroni, Daniela Galimberti, Mario Masellis, Maria Carmela Tartaglia, James B Rowe, Caroline Graff, Fabrizio Tagliavini, Giovanni Frisoni, Robert Laforce, Elizabeth Finger, Alexandre de Mendonça, Sandro Sorbi, Sébastien Ourselin, M Jorge Cardoso, Jonathan D Rohrer
Genetic frontotemporal dementia is most commonly caused by mutations in the progranulin (GRN), microtubule-associated protein tau (MAPT) and chromosome 9 open reading frame 72 (C9orf72) genes. Previous small studies have reported the presence of cerebral white matter hyperintensities (WMH) in genetic FTD but this has not been systematically studied across the different mutations. In this study WMH were assessed in 180 participants from the Genetic FTD Initiative (GENFI) with 3D T1- and T2-weighed magnetic resonance images: 43 symptomatic (7 GRN, 13 MAPT and 23 C9orf72), 61 presymptomatic mutation carriers (25 GRN, 8 MAPT and 28 C9orf72) and 76 mutation negative non-carrier family members...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28529612/adipoq-rs266729-g-c-gene-polymorphism-and-plasmatic-adipocytokines-connect-metabolic-syndrome-to-colorectal-cancer
#7
Rosa Divella, Antonella Daniele, Antonio Mazzocca, Ines Abbate, Porzia Casamassima, Cosimo Caliandro, Eustachio Ruggeri, Emanuele Naglieri, Carlo Sabbà, Raffaele De Luca
Background: ADIPOQ gene, which encode for Adiponectin (APN), is sited on chromosome 3q27 and linked to a susceptibility locus for metabolic syndrome (MetS). The ADIPOQ rs266729 G/C gene polymorphism is significantly associated with low APN levels and linked to susceptibility to develop cancer. In addition, decreased APN serum levels are linked with tumor development and progression and inversely associated with markers of inflammation. Here, we investigate the influence of APN rs266729 G/C polymorphism on adipocytokine circulating levels and their association with MetS in colorectal cancer patients (CRC)...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28529600/prospective-evaluation-of-fluorescence-in-situ-hybridization-for-diagnosing-urothelial-carcinoma
#8
Tianhai Lin, Zhenhua Liu, Liangren Liu, Lu Yang, Ping Han, Peng Zhang, Qiang Wei
Urothelial carcinoma (UC) is the most common type of cancer of the bladder and upper urinary tract, and is characterized by a high risk of recurrence and progression. Urine fluorescence in situ hybridization (FISH) is a technique that detects genetic aberrations in exfoliated cells in the urine, with specific probes for chromosomes 3, 7 and 17 and the p16 gene. To evaluate the diagnostic value of FISH in UC, 119 patients from November 2010 to June 2012 with suspected UC were recruited into a prospective, cross-sectional study and were followed up for 12-30 months...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28529470/microdissection-of-the-ah01-chromosome-in-upland-cotton-and-microcloning-of-resistance-gene-anologs-from-the-single-chromosome
#9
Xinchuan Cao, Yuling Liu, Zhen Liu, Fang Liu, Yalei Wu, Zhongli Zhou, Xiaoyan Cai, Xingxing Wang, Zhenmei Zhang, Yuhong Wang, Zhimin Luo, Renhai Peng, Kunbo Wang
BACKGROUND: Chromosome microdissection is one of the most important techniques in molecular cytogenetic research. Cotton (Gossypium Linnaeus, 1753) is the main natural fiber crop in the world. The resistance gene analog (RGA) cloning after its single chromosome microdissection can greatly promote cotton genome research and breeding. RESULTS: Using the linker adaptor PCR (LA-PCR) with the primers of rice disease-resistance homologues, three nucleotide sequences PS016 (KU051681), PS054 (KU051682), and PS157 (KU051680) were obtained from the chromosome Ah01 of upland cotton (cv...
2017: Hereditas
https://www.readbyqxmd.com/read/28529243/over-expression-of-mir-21-and-lower-pten-levels-in-wilms-tumor-with-aggressive-behavior
#10
Mingyu Cui, Wei Liu, Lijuan Zhang, Feng Guo, Yang Liu, Fang Chen, Ting Liu, Rui Ma, Rongde Wu
Wilms' tumor (WT) is the most common pediatric kidney tumor. MiR-21 is one of the most frequently overexpressed microRNAs in solid tumors, while phosphatase and tensin homolog deleted from chromosome 10 (PTEN) is the most highly mutated tumor suppressor gene. The aim of this study was to investigate the relationship between miR-21 and PTEN in WT. The expression levels of miR-21 and the PTEN protein were determined by qRT-PCR and Western blot analyses in WT specimens, respectively. In WT tissues, the miR-21 expression levels were significantly higher and the PTEN protein levels were significantly lower, compared to the adjacent non-tumorous renal tissues...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28528769/complete-genome-sequence-and-analysis-of-three-kinds-of-%C3%AE-agarase-of-cellulophaga-lytica-dau203-isolated-from-marine-sediment
#11
Yong-Suk Lee, Yong-Lark Choi
Cellulophaga lytica DAU203 (KACC 19187), isolated from the marine sediment in Korea, has a strong ability to degrade agar. The genome of C. lytica DAU203 contains a single chromosome that is 3,952,957bp in length, with 32.02% G+C contents. The genomic information predicted that the DAU203 has the potential to be utilized in various enzymatic industries.
May 18, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28528545/discovery-and-biosynthesis-of-gladiolin-a-burkholderia-gladioli-antibiotic-with-promising-activity-against-mycobacterium-tuberculosis
#12
Lijiang Song, Matthew Jenner, Joleen Masschelein, Cerith Jones, Matthew J Bull, Simon R Harris, Ruben C Hartkoorn, Anthony Vocat, Isolda Romero-Canelón, Paul Coupland, Gordon Webster, Matthew Dunn, Rebecca Weiser, Christopher Paisey, Stewart T Cole, Julian Parkhill, Eshwar Mahenthiralingam, Gregory L Challis
An antimicrobial activity screen of Burkholderia gladioli BCC0238, a clinical isolate from a cystic fibrosis patient, led to the discovery of gladiolin, a novel macrolide antibiotic with potent activity against Mycobacterium tuberculosis H37Rv. Gladiolin is structurally-related to etnangien, a highly unstable antibiotic from Sorangium cellulosum that is also active against Mycobacteria. Like etnangien, gladiolin was found to inhibit RNA polymerase, a validated drug target in M. tuberculosis. However, gladiolin lacks the highly labile hexaene moiety of etnangien and was thus found to possess significantly increased chemical stability...
May 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28528441/herpesvirus-latency-on-the-importance-of-positioning-oneself
#13
Patrick Lomonte
The nucleus is composed of multiple compartments and domains, which directly or indirectly influence many cellular processes including gene expression, RNA splicing and maturation, protein post-translational modifications, and chromosome segregation. Nuclear-replicating viruses, especially herpesviruses, have co-evolved with the cell, adopting strategies to counteract and eventually hijack this hostile environment for their own benefit. This allows them to persist in the host for the entire life of an individual and to ensure their maintenance in the target species...
2017: Advances in Anatomy, Embryology, and Cell Biology
https://www.readbyqxmd.com/read/28528201/x-linked-carriers-of-chronic-granulomatous-disease-illness-lyonization-and-stability
#14
Beatriz E Marciano, Christa S Zerbe, E Liana Falcone, Li Ding, Suk See DeRavin, Janine Daub, Samantha Kreuzburg, Lynne Yockey, Sally Hunsberger, Ladan Foruraghi, Lisa A Barnhart, Kabir Matharu, Victoria Anderson, Dirk N Darnell, Cathleen Frein, Danielle L Fink, Karen P Lau, Debra A Long Priel, John I Gallin, Harry L Malech, Gulbu Uzel, Alexandra F Freeman, Douglas B Kuhns, Sergio D Rosenzweig, Steven M Holland
BACKGROUND: Chronic granulomatous disease (CGD) is characterized by recurrent life-threatening bacterial and fungal infections and aberrant inflammation. Mutations in CYBB cause X-linked CGD and account for 65%-70% of cases in western countries. OBJECTIVE: To understand the clinical manifestations associated with the X-linked CGD carrier state. METHODS: We undertook a comprehensive retrospective study of 162 affected females. We examined dihydrorhodamine oxidation (DHR) data for percent (%) X chromosome inactivation...
May 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28528003/acinetobacter-baumannii-k11-and-k83-capsular-polysaccharides-have-the-same-6-deoxy-l-talose-containing-pentasaccharide-k-units-but-different-linkages-between-the-k-units
#15
Johanna J Kenyon, Alexander S Shashkov, Sof'ya N Senchenkova, Mikhail M Shneider, Bin Liu, Anastasiya V Popova, Nikolay P Arbatsky, Konstantin A Miroshnikov, Lei Wang, Yuriy A Knirel, Ruth M Hall
Acinetobacter baumannii produces a variety of capsular polysaccharides (CPS) via genes located at the chromosomal K locus and some KL gene clusters include genes for the synthesis of specific sugars. The structures of K11 and K83 CPS produced by isolates LUH5545 and LUH5538, which carry related KL11a and KL83 gene clusters, respectively, were established by sugar analysis and one- and two-dimensional (1)H and (13)C NMR spectroscopy. Both CPS contain L-rhamnose (L-Rha) and 6-deoxy-L-talose (L-6dTal), and both KL gene clusters include genes for dTDP-L-Rhap synthesis and a tle (talose epimerase) gene encoding an epimerase that converts dTDP-L-Rhap to dTDP-L-6dTalp...
May 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28527972/genetic-and-epigenetic-alterations-in-meningiomas
#16
REVIEW
Vasiliki Galani, Evangeli Lampri, Anna Varouktsi, George Alexiou, Antigoni Mitselou, Athanasios P Kyritsis
Meningiomas originate from the arachnoid layer of the meninges and divided histologically into three grades: benign (grade I), atypical (grade II), and malignant meningiomas (grade III). Genetic alterations in grade I meningiomas include frequent deletions of chromosomal locus 22q12 and NF2 gene mutations and uncommon somatic SMARCB1 and SMARCE1gene mutations; In grade II meningiomas, chromosomal losses occur on 1p, 22q, 14q, 18q, 10, and 6q, and gains on 20q, 12q, 15q, 1q, 9q, and 17q; In grade III meningiomas, losses have been recognized on 6q, 10, and 14q and alterations of PTEN, CDKN2A and CDKN2B genes...
May 3, 2017: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/28527764/differential-stress-response-of-saccharomyces-hybrids-revealed-by-monitoring-hsp104-aggregation-and-disaggregation
#17
Claudia Kempf, Klaus Lengeler, Jürgen Wendland
Proteotoxic stress may occur upon exposure of yeast cells to different stress conditions. The induction of stress response mechanisms is important for cells to adapt to changes in the environment and ensure survival. For example, during exposure to elevated temperatures the expression of heat shock proteins such as Hsp104 is induced in yeast. Hsp104 extracts misfolded proteins from aggregates to promote their refolding. We used an Hsp104-GFP reporter to analyze the stress profiles of Saccharomyces species hybrids...
July 2017: Microbiological Research
https://www.readbyqxmd.com/read/28527624/understanding-aerobic-anaerobic-metabolism-in-caldibacillus-debilis-through-a-comparison-with-model-organisms
#18
Scott Wushke, Victor Spicer, Xiang Li Zhang, Brian Fristensky, Oleg V Krokhin, David B Levin, Nazim Cicek, Richard Sparling
Caldibacillus debilis GB1 is a facultative anaerobe isolated from a thermophilic aero-tolerant cellulolytic enrichment culture. There is a lack of representative proteomes of facultative anaerobic thermophilic Bacillaceae, exploring aerobic/anaerobic expression. The C. debilis GB1 genome was sequenced and annotated, and the proteome characterized under aerobic and anaerobic conditions while grown on cellobiose. The draft sequence of C. debilis GB1 contains a 3,340,752 bp chromosome and a 5,386 bp plasmid distributed over 49 contigs...
April 13, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28527524/c9orf72-hexanucleotide-repeat-expansions-and-ataxin-2-intermediate-length-repeat-expansions-in-indian-patients-with-amyotrophic-lateral-sclerosis
#19
Priyam Narain, James Gomes, Rohit Bhatia, Inder Singh, Perumal Vivekanandan
Repeat expansions in the chromosome 9 open reading frame 72 (C9orf72) gene have been recognized as a major contributor to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia in the Caucasian population. Intermediate length repeat expansions of CAG (polyQ) repeat in the ATXN2 gene have also been reported to increase the risk of developing ALS in North America and Europe. We screened 131 ALS patients and 127 healthy controls from India for C9orf72 and ATXN2 repeat expansions. We found pathogenic hexanucleotide expansions in 3 of the 127 sporadic ALS patients, in 1 of the 4 familial ALS patients, and in none of the healthy controls...
April 26, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28527403/interplay-between-bacillus-subtilis-recd2-and-the-recg-or-ruvab-helicase-in-recombinational-repair
#20
Rubén Torres, Hector Romero, Violeta Rodríguez-Cerrato, Juan C Alonso
Bacillus subtilis AddAB, RecS, RecQ, PcrA, HelD, DinG, RecG, RuvAB, PriA and RecD2 are genuine recombinational repair enzymes, but the biological role of RecD2 is poorly defined. A ΔrecD2 mutation sensitizes cells to DNA-damaging agents that stall or collapse replication forks. We found that this ΔrecD2 mutation impaired growth, and that a mutation in the pcrA gene (pcrA596) relieved this phenotype. The ΔrecD2 mutation was not epistatic to ΔaddAB, ΔrecQ, ΔrecS, ΔhelD, pcrA596 and ΔdinG, but epistatic to recA...
May 12, 2017: DNA Repair
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