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https://www.readbyqxmd.com/read/28088766/staphylococcus-aureus-cc395-harbours-a-novel-composite-staphylococcal-cassette-chromosome-mec-element
#1
Jesper Larsen, Paal S Andersen, Volker Winstel, Andreas Peschel
BACKGROUND: CoNS species are likely reservoirs of the staphylococcal cassette chromosome mec (SCCmec) in Staphylococcus aureus S aureus CC395 is unique as it is capable of exchanging DNA with CoNS via bacteriophages, which are also known to mediate transfer of SCCmec OBJECTIVES: To analyse the structure and putative origin of the SCCmec element in S aureus CC395. METHODS: The only MRSA CC395 strain described in the literature, JS395, was subjected to WGS, and its SCCmec element was compared with those found in CoNS species and other S...
January 14, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28087673/rdna-stability-is-supported-by-many-buffer-genes-introduction-to-the-yeast-rdna-stability-database
#2
Takehiko Kobayashi, Mariko Sasaki
The ribosomal RNA gene (rDNA) is the most abundant gene in yeast and other eukaryotic organisms. Due to its heavy transcription, repetitive structure and programmed replication fork pauses, the rDNA is one of the most unstable regions in the genome. Thus, the rDNA is the best region to study the mechanisms responsible for maintaining genome integrity. Recently, we screened a library of ∼4,800 budding yeast gene knockout strains to identify mutants defective in the maintenance of rDNA stability. The results of this screen are summarized in the Yeast rDNA Stability Database, in which the stability and copy number of rDNA in each mutant are presented...
January 12, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28087584/emergence-of-klebsiella-variicola-positive-for-ndm-9-a-variant-of-new-delhi-metallo-%C3%AE-lactamase-in-an-urban-river-in-south-korea
#3
Doris Y W Di, Jeonghwan Jang, Tatsuya Unno, Hor-Gil Hur
OBJECTIVES: To examine the presence of pathogenic bacteria carrying New Delhi metallo-β-lactamase in the environment and to characterize the genome structures of these strains. METHODS: Phenotypic screening of antimicrobial susceptibility and WGS were conducted on three Klebsiella variicola strains possessing NDM-9 isolated from an urban river. RESULTS: Three carbapenem-resistant K. variicola isolated from Gwangju tributary were found to possess blaNDM-9 genes...
January 12, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28087167/lingering-questions-about-enhancer-rna-and-enhancer-transcription-coupled-genomic-instability
#4
REVIEW
Gerson Rothschild, Uttiya Basu
Intergenic and intragenic enhancers found inside topologically associated regulatory domains (TADs) express noncoding RNAs, known as enhancer RNAs (eRNAs). Recent studies have indicated these eRNAs play a role in gene regulatory networks by controlling promoter and enhancer interactions and topology of higher-order chromatin structure. Misregulation of enhancer and promoter associated noncoding RNAs (ncRNAs) could stabilize deleterious secondary DNA structures, noncoding RNA associated DNA/RNA hybrid formation, and promote collisions of transcription complexes with replisomes...
January 10, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28081371/gwas-identifies-new-loci-for-painful-temporomandibular-disorder
#5
A E Sanders, D Jain, T Sofer, K F Kerr, C C Laurie, J R Shaffer, M L Marazita, L M Kaste, G D Slade, R B Fillingim, R Ohrbach, W Maixner, T Kocher, O Bernhardt, A Teumer, C Schwahn, K Sipilä, R Lähdesmäki, M Männikkö, P Pesonen, M Järvelin, C M Rizzatti-Barbosa, C B Meloto, M Ribeiro-Dasilva, L Diatchenko, P Serrano, S B Smith
Temporomandibular disorder (TMD) is a musculoskeletal condition characterized by pain and reduced function in the temporomandibular joint and/or associated masticatory musculature. Prevalence in the United States is 5% and twice as high among women as men. We conducted a discovery genome-wide association study (GWAS) of TMD in 10,153 participants (769 cases, 9,384 controls) of the US Hispanic Community Health Study/Study of Latinos (HCHS/SOL). The most promising single-nucleotide polymorphisms (SNPs) were tested in meta-analysis of 4 independent cohorts...
January 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28081277/comparative-genomic-hybridization-analysis-of-rice-dwarf-mutants-induced-by-gamma-irradiation
#6
J E Hwang, S-H Kim, I J Jung, S M Han, J-W Ahn, S-J Kwon, S H Kim, S-Y Kang, D S Kim, J-B Kim
Comparative genomic hybridization (CGH) is a powerful tool used to analyze changes in copy number, polymorphisms, and structural variations in the genome. Gene copy number variation (CNV) is a common form of natural diversity in the genome, which can create new genes and alter gene structure. Thus, CNVs may influence phenotypic variation and gene expression. In this study, to detect CNVs, we irradiated rice seeds with gamma rays (300 Gy) and selected two dwarf mutagenized plants, GA-III-189 and -1052, in the M3 generation...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28078516/dense-gene-physical-maps-of-the-non-model-species-drosophila-subobscura
#7
Dorcas J Orengo, Eva Puerma, Montserrat Papaceit, Carmen Segarra, Montserrat Aguadé
The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28078515/capturing-genomic-relationships-that-matter
#8
REVIEW
Cameron S Osborne, Borbála Mifsud
There is a strong interrelationship within the cell nucleus between form and function of the genome. This connection is exhibited across multiple hierarchies, ranging from grand-scale positioning of chromosomes and their intersection with specific nuclear functional activities, the segregation of chromosome structure into distinct domains and long-range regulatory contacts that drive spatial and temporal expression patterns of genes. Fifteen years ago, the development of the chromosome conformation capture method placed the nature of specific, long-range regulatory interactions under scrutiny...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#9
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28077560/mechanistic-insights-into-type-i-toxin-antitoxin-systems-in-helicobacter-pylori-the-importance-of-mrna-folding-in-controlling-toxin-expression
#10
Hélène Arnion, Dursun Nizam Korkut, Sara Masachis Gelo, Sandrine Chabas, Jérémy Reignier, Isabelle Iost, Fabien Darfeuille
Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial expression in H. pylori induces cell death. The synthesis of this toxin is prevented by the transcription of an antitoxin RNA, named IsoA1, expressed on the opposite strand of the toxin gene. We further reveal additional layers of post-transcriptional regulation that control toxin expression: (i) transcription of the aapA1 gene generates a full-length transcript whose folding impedes translation (ii) a 3' end processing of this message generates a shorter transcript that, after a structural rearrangement, becomes translatable (iii) but this rearrangement also leads to the formation of two stem-loop structures allowing formation of an extended duplex with IsoA1 via kissing-loop interactions...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28076990/outcomes-in-the-absence-of-the-ductus-venosus-diagnosed-in-the-first-trimester
#11
Hiroko Takita, Junichi Hasegawa, Tatsuya Arakaki, Shoko Hamada, Mayumi Tokunaka, Masamitsu Nakamura, Ryu Matsuoka, Akihiko Sekizawa
PURPOSE: To clarify the outcomes of the absence of the ductus venosus diagnosed in fetuses suspected to have a structural abnormality during a morphological assessment in the first trimester. METHODS: Infants in whom ultrasound fetal morphological assessments were attempted in the first trimester (11 to 13-6 weeks of gestation) and who were subsequently delivered between 2013 and 2015 at Showa University Hospital were enrolled. In cases in which the absence of the ductus venosus was diagnosed in the first trimester, the prognosis was assessed...
January 11, 2017: Journal of Maternal-fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/28074435/plk1-inhibition-leads-to-a-failure-of-mitotic-division-during-the-first-mitotic-division-in-pig-embryos
#12
Zixiao Zhang, Changchao Chen, Panpan Cui, Yaya Liao, Lingyun Yao, Yue Zhang, Rong Rui, Shiqiang Ju
PURPOSE: This study was conducted to examine the dynamic distribution of polo-like 1 kinase (Plk1) and the possible role it plays in first mitotic division during early porcine embryo development. METHODS: Indirect immunofluorescence and confocal microscopy imaging techniques combined with western blot analyses were used to study the dynamic expression and subcellular localization of Plk1 protein in pig parthenogenetic embryos. Finally, a selective Plk1 inhibitor, GSK461364, was used to evaluate the potential role of Plk1 during this special stage...
January 10, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28073183/a-liver-specific-long-non-coding-rna-with-a-role-in-cell-viability-is-elevated-in-human-non-alcoholic-steatohepatitis
#13
Biljana Atanasovska, Sander S Rensen, Marijke R van der Sijde, Glenn Marsman, Vinod Kumar, Iris Jonkers, Sebo Withoff, Ronit Shiri-Sverdlov, Jan Willem M Greve, Klaas Nico Faber, Han Moshage, Cisca Wijmenga, Bart van de Sluis, Marten H Hofker, Jingyuan Fu
: Hepatocyte apoptosis in non-alcoholic steatohepatitis (NASH) can lead to fibrosis and cirrhosis, which permanently damage the liver. Understanding the regulation of hepatocyte apoptosis is therefore important to identify therapeutic targets that may prevent the progression of NASH to fibrosis. Recently, increasing evidence has shown that lncRNAs are involved in various biological processes and that their dysregulation underlies a number of complex human diseases. By performing gene expression profiling of 4,383 lncRNAs in 82 liver samples from individuals with NASH (n=48), simple steatosis but no NASH (n=11) and healthy controls (n=23), we discovered a liver-specific lncRNA (RP11-484N16...
January 10, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28073088/characterization-of-the-iberian-y-chromosome-haplogroup-r-df27-in-northern-spain
#14
Patricia Villaescusa, María José Illescas, Laura Valverde, Miriam Baeta, Carolina Nuñez, Begoña Martínez-Jarreta, Maria Teresa Zarrabeitia, Francesc Calafell, Marian M de Pancorbo
The European paternal lineage R-DF27 has been proposed as a haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28072833/accurate-breakpoint-mapping-in-apparently-balanced-translocation-families-with-discordant-phenotypes-using-whole-genome-mate-pair-sequencing
#15
Constantia Aristidou, Costas Koufaris, Athina Theodosiou, Mads Bak, Mana M Mehrjouy, Farkhondeh Behjati, George Tanteles, Violetta Christophidou-Anastasiadou, Niels Tommerup, Carolina Sismani
Familial apparently balanced translocations (ABTs) segregating with discordant phenotypes are extremely challenging for interpretation and counseling due to the scarcity of publications and lack of routine techniques for quick investigation. Recently, next generation sequencing has emerged as an efficacious methodology for precise detection of translocation breakpoints. However, studies so far have mainly focused on de novo translocations. The present study focuses specifically on familial cases in order to shed some light to this diagnostic dilemma...
2017: PloS One
https://www.readbyqxmd.com/read/28071788/chromosome-inversions-and-ecological-plasticity-in-the-main-african-malaria-mosquitoes
#16
Diego Ayala, Pelayo Acevedo, Marco Pombi, Ibrahima Dia, Daniela Boccolini, Carlo Costantini, Frédéric Simard, Didier Fontenille
Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range...
January 10, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28070912/role-of-testosterone-and-y-chromosome-genes-for-the-masculinization-of-the-human-brain
#17
Ivanka Savic, Louise Frisen, Amirhossein Manzouri, Anna Nordenstrom, Angelica Lindén Hirschberg
: Women with complete androgen insensitivity syndrome (CAIS) have a male (46,XY) karyotype but no functional androgen receptors. Their condition, therefore, offers a unique model for studying testosterone effects on cerebral sex dimorphism. We present MRI data from 16 women with CAIS and 32 male (46,XY) and 32 female (46,XX) controls. METHODS: FreeSurfer software was employed to measure cortical thickness and subcortical structural volumes. Axonal connections, indexed by fractional anisotropy, (FA) were measured with diffusion tensor imaging, and functional connectivity with resting state fMRI...
January 10, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28070687/predicting-chromatin-architecture-from-models-of-polymer-physics
#18
REVIEW
Simona Bianco, Andrea M Chiariello, Carlo Annunziatella, Andrea Esposito, Mario Nicodemi
We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches...
January 9, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28069312/centromeres-drive-a-hard-bargain
#19
REVIEW
Leah F Rosin, Barbara G Mellone
Centromeres are essential chromosomal structures that mediate the accurate distribution of genetic material during meiotic and mitotic cell divisions. In most organisms, centromeres are epigenetically specified and propagated by nucleosomes containing the centromere-specific H3 variant, centromere protein A (CENP-A). Although centromeres perform a critical and conserved function, CENP-A and the underlying centromeric DNA are rapidly evolving. This paradox has been explained by the centromere drive hypothesis, which proposes that CENP-A is undergoing an evolutionary tug-of-war with selfish centromeric DNA...
January 6, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28069135/epigenetic-control-of-gene-expression-in-maize
#20
J Huang, J S Lynn, L Schulte, S Vendramin, K McGinnis
Epigenetic gene regulation is important for proper development and gene expression in eukaryotes. Maize has a large and complex genome that includes abundant repetitive sequences which are frequently silenced by epigenetic mechanisms, making it an ideal organism to study epigenetic gene regulation. Epigenetic modifications are chromosome-bound, heritable changes to the genome that do not affect the DNA sequence, and can include DNA methylation, histone modification, and RNA processing. Our appreciation and understanding of epigenetic regulation has grown with the field since its inception ∼65 years ago...
2017: International Review of Cell and Molecular Biology
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