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https://www.readbyqxmd.com/read/27933535/systems-genetics-analysis-to-identify-the-genetic-modulation-of-a-glaucoma-associated-gene
#1
Sumana R Chintalapudi, Monica M Jablonski
Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933530/visualization-of-results-from-systems-genetics-studies-in-chromosomal-context
#2
Karen Y Oróstica, Ricardo A Verdugo
This chapter describes methods currently available for visualizing results from systems genetics experiments. Here, we abstract from the statistical methods used for genetic mapping, which are dependent on the specific resource being used, i.e. F2, RILs, or outbred populations among others. We use a public dataset with results from a mouse eQTL experiment for three examples of visualization: genome-wide dot plots of marker-by-gene association, karyotype-like plots, and circos plots. Dot plots give a first overview of the results from eQTL mapping, allowing detecting genome-wide patterns of cis- and trans-genetic association to transcription level...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933519/heterogeneous-stock-populations-for-analysis-of-complex-traits
#3
Leah C Solberg Woods, Richard Mott
Heterogeneous Stock (HS) populations allow for fine-resolution genetic mapping of a variety of complex traits. HS mice and rats were created from breeding together eight inbred strains, followed by maintaining the colony in a manner that minimizes inbreeding. After 50 or more generations of breeding, the resulting animals' chromosomes represent a genetic mosaic of the founders' haplotypes, with the average distance between recombination events in the centiMorgan range. This allows for genetic mapping to only a few Mb, a much smaller region than what can be identified using traditional F2 intercross or backcross mapping strategies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933412/genetic-diversity-study-on-12-x-str-loci-of-investigator%C3%A2-argus-x-str-kit-in-bangladeshi-population
#4
Abu Sufian, Md Ismail Hosen, Kaniz Fatema, Tania Hossain, Md Mahamud Hasan, Ashish Kumar Mazumder, Sharif Akhteruzzaman
The X-chromosome short tandem repeat (STR) loci are of particular interest for solving complex kinship and paternity cases. Here, we report the genetic data from 209 unrelated Bangladeshi individuals (102 males and 107 females) that were genotyped using the 12 X-chromosomal STR markers included in the Investigator® Argus X-12 kit (Qiagen). The 12 X-STR markers are located in four linkage groups (linkage group I: DXS10135, DXS10148, and DXS8378; linkage group II: DXS7132, DXS10079, and DXS10074; linkage group III: DXS10103, HPRTB, and DXS10101; and linkage group IV: DXS10146, DXS10134, and DXS7423)...
December 8, 2016: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/27933271/functional-significance-of-aurora-kinases-p53-protein-family-interactions-in-cancer
#5
REVIEW
Kaori Sasai, Warapen Treekitkarnmongkol, Kazuharu Kai, Hiroshi Katayama, Subrata Sen
Aurora kinases play critical roles in regulating spindle assembly, chromosome segregation, and cytokinesis to ensure faithful segregation of chromosomes during mitotic cell division cycle. Molecular and cell biological studies have revealed that Aurora kinases, at physiological levels, orchestrate complex sequential cellular processes at distinct subcellular locations through functional interactions with its various substrates. Aberrant expression of Aurora kinases, on the other hand, cause defects in mitotic spindle assembly, checkpoint response activation, and chromosome segregation leading to chromosomal instability...
2016: Frontiers in Oncology
https://www.readbyqxmd.com/read/27933089/a-rare-inherited-15q11-2-q13-1-interstitial-duplication-with-maternal-somatic-mosaicism-renal-carcinoma-and-autism
#6
Nora Urraca, Brian Potter, Rachel Hundley, Eniko K Pivnick, Kathryn McVicar, Ronald L Thibert, Christopher Ledbetter, Reed Chamberlain, Leticia Miravalle, Carissa L Sirois, Stormy Chamberlain, Lawrence T Reiter
Chromosome 15q11-q13.1 duplication is a common copy number variant associated with autism spectrum disorder (ASD). Most cases are de novo, maternal in origin and fully penetrant for ASD. Here, we describe a unique family with an interstitial 15q11.2-q13.1 maternal duplication and the presence of somatic mosaicism in the mother. She is typically functioning, but formal autism testing showed mild ASD. She had several congenital anomalies, and she is the first 15q Duplication case reported in the literature to develop unilateral renal carcinoma...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27933072/development-and-evaluation-of-chromosome-segment-substitution-lines-carrying-overlapping-chromosome-segments-of-the-whole-wild-rice-genome
#7
Dewei Yang, Xinfu Ye, Xianghua Zheng, Chaoping Cheng, Ning Ye, Fenghuang Huang
Common wild rice (Oryza rufipogon Griff.) represents an important resource for rice improvement. Genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) are most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, 146 CSSLs were produced; they were derived from the crossing and back-crossing of two rice cultivars: Dongnanihui 810 (Oryza sativa L.), an indica rice cultivar as the recipient, and ZhangPu wild rice, a wild rice cultivar as the donor...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933045/what-is-the-link-between-stringent-response-endoribonuclease-encoding-type-ii-toxin-antitoxin-systems-and-persistence
#8
Bhaskar C M Ramisetty, Dimpy Ghosh, Maoumita Roy Chowdhury, Ramachandran S Santhosh
Persistence is a transient and non-inheritable tolerance to antibiotics by a small fraction of a bacterial population. One of the proposed determinants of bacterial persistence is toxin-antitoxin systems (TASs) which are also implicated in a wide range of stress-related phenomena. Maisonneuve E, Castro-Camargo M, Gerdes K. 2013. Cell 154:1140-1150 reported an interesting link between ppGpp mediated stringent response, TAS, and persistence. It is proposed that accumulation of ppGpp enhances the accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxins...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27932995/genome-sizes-of-nine-insect-species-determined-by-flow-cytometry-and-k-mer-analysis
#9
Kang He, Kejian Lin, Guirong Wang, Fei Li
The flow cytometry method was used to estimate the genome sizes of nine agriculturally important insects, including two coleopterans, five Hemipterans, and two hymenopterans. Among which, the coleopteran Lissorhoptrus oryzophilus (Kuschel) had the largest genome of 981 Mb. The average genome size was 504 Mb, suggesting that insects have a moderate-size genome. Compared with the insects in other orders, hymenopterans had small genomes, which were averagely about ~200 Mb. We found that the genome sizes of four insect species were different between male and female, showing the organismal complexity of insects...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27932787/high-incidence-of-philadelphia-chromosome-like-acute-lymphoblastic-leukemia-ph-like-all-in-older-adults-with-b-all
#10
S K Tasian, C Hurtz, G B Wertheim, N G Bailey, M S Lim, R C Harvey, I-M Chen, C L Willman, R Astles, A Zebrowski, S C Reshmi, M M Li, N V Frey, S M Luger, M Carroll, A E Perl
Leukemia accepted article preview online, 09 December 2016. doi:10.1038/leu.2016.375.
December 9, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27932659/genome-sequence-of-pseudomonas-citronellolis-sjte-3-an-estrogen-and-polycyclic-aromatic-hydrocarbon-degrading-bacterium
#11
Daning Zheng, Xiuli Wang, Pingping Wang, Wanli Peng, Nannan Ji, Rubing Liang
Pseudomonas citronellolis SJTE-3, isolated from the active sludge of a wastewater treatment plant in China, can utilize a series of environmental estrogens and estrogen-like toxicants. Here, we report its whole-genome sequence, containing one circular chromosome and one circular plasmid. Genes involved in estrogen biodegradation in this bacterium were predicted.
December 8, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27932636/complete-genome-sequence-of-bacteriophage-ma12-which-infects-both-campylobacter-jejuni-and-salmonella-enterica-serovar-enteritidis
#12
Sunjin Lee, Taesoo Kwon, Su-Jin Chae, Jong-Hyun Kim, Yeon Ho Kang, Gyung Tae Chung, Dae-Won Kim, Deog-Yong Lee
Here, we announce the complete genome sequence of Salmonella enterica serovar Enteritidis (S Enteritidis) bacteriophage MA12, a 41-Kb chromosome. The strain can infect both Campylobacter jejuni (C. jejuni) and S Enteritidis and can be used in phage therapy experiments with poultry and poultry meat.
December 8, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27932541/cooperation-between-kinesin-motors-promotes-spindle-symmetry-and-chromosome-organization-in-oocytes
#13
Sarah J Radford, Allysa Marie M Go, Kim S McKim
The oocyte spindle in most animal species is assembled in the absence of the microtubule-organizing centers called centrosomes. Without the organization provided by centrosomes, acentrosomal meiotic spindle organization may rely heavily on the bundling of microtubules by kinesin motor proteins. Indeed, the minus-end directed kinesin-14 NCD and the plus-end directed kinesin-6 Subito are known to be required for oocyte spindle organization in Drosophila melanogaster How multiple microtubule-bundling kinesins interact to produce a functional acentrosomal spindle is not known...
December 7, 2016: Genetics
https://www.readbyqxmd.com/read/27932493/prdm9-interactions-with-other-proteins-provide-a-link-between-recombination-hotspots-and-the-chromosomal-axis-in-meiosis
#14
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/27932456/physico-chemical-fingerprinting-of-rna-genes
#15
Ankita Singh, Akhilesh Mishra, Ali Khosravi, Garima Khandelwal, B Jayaram
We advance here a novel concept for characterizing different classes of RNA genes on the basis of physico-chemical properties of DNA sequences. As knowledge-based approaches could yield unsatisfactory outcomes due to limitations of training on available experimental data sets, alternative approaches that utilize properties intrinsic to DNA are needed to supplement training based methods and to eventually provide molecular insights into genome organization. Based on a comprehensive series of molecular dynamics simulations of Ascona B-DNA consortium, we extracted hydrogen bonding, stacking and solvation energies of all combinations of DNA sequences at the dinucleotide level and calculated these properties for different types of RNA genes...
December 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27932447/unloading-of-homologous-recombination-factors-is-required-for-restoring-double-stranded-dna-at-damage-repair-loci
#16
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/27932423/integrated-genomic-analysis-of-survival-outliers-in-glioblastoma
#17
Sen Peng, Harshil Dhurv, Brock Armstrong, Bodour Salhia, Christophe Legendre, Jeffrey Kiefer, Julianna Parks, Selene Virk, Andrew E Sloan, Quinn T Ostrom, Jill S Barnholtz-Sloan, Nhan L Tran, Michael E Berens
BACKGROUND: To elucidate molecular features associated with disproportionate survival of glioblastoma (GB) patients, we conducted deep genomic comparative analysis of a cohort of patients receiving standard therapy (surgery plus concurrent radiation and temozolomide); "GB outliers" were identified: long-term survivor of 33 months (LTS; n = 8) versus short-term survivor of 7 months (STS; n = 10). METHODS: We implemented exome, RNA, whole genome sequencing, and DNA methylation for collection of deep genomic data from STS and LTS GB patients...
December 8, 2016: Neuro-oncology
https://www.readbyqxmd.com/read/27932023/molecular-cloning-and-expression-analysis-of-a-fish-specific-interferon-regulatory-factor-irf11-in-orange-spotted-grouper-epinephelus-coioides
#18
Wen Shu Huang, Mei Hua Zhu, Shan Chen, Zhi Xuan Wang, Ying Liang, Bei Huang, P Nie
Interferon regulatory factors (IRFs) are transcription mediators which play vital roles in multiple biological processes, such as antiviral defense, immune response, cell growth regulation and apoptosis. A fish specific IRF, termed IRF11, has been identified in previous study through searching fish genome databases. Herein, a transcript of IRF11, EcIRF11 was cloned from orange-spotted grouper, Epinephelus coioides. The EcIRF11 cDNA sequence has 1573 bp in length, encoding a putative protein of 261 amino acids, with a high degree of similarity found between EcIRF11 and its teleost counterparts...
December 5, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27931917/co-occurrence-of-marfan-syndrome-and-bipolar-disorder-a-fifteen-year-follow-up
#19
Vijendra Nath Jha, Manoj Kumar, Jatin Tarwani
INTRODUCTION: Marfan syndrome, a chromosomal disorder, has been commonly associated with schizophrenia but no association with Bipolar affective disorder has been reported in the scientific literature. CASE REPORT: This case depicts the occurrence of Bipolar affective disorder in a previously undiagnosed case of Marfan syndrome. DISCUSSION: In this case patient had all manic episodes without any depressive or schizophrenia-like episodes, suggesting a diagnostic stability over a long period of over fifteen years...
December 2016: Asian Journal of Psychiatry
https://www.readbyqxmd.com/read/27931810/evaluation-of-in-vivo-gene-mutation-with-etoposide-using-pig-a-and-pigret-assays
#20
Mika Yamamoto, Akihiro Wakata
The Pig-a assay detects the expression of the endogenous phosphatidylinositol glycan anchor biosynthesis, class A gene (Pig-a) as a reporter of mutations and shows promise for detecting mutations in vivo. This assay requires two to four weeks to detect mutations in erythrocytes after animals are administered a single dose of test compound. In contrast, the more recently developed PIGRET assay using reticulocytes detects mutation sensitively one week after dosing, which is an advantage for conducting short-term genotoxicity studies in vivo...
November 15, 2016: Mutation Research
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