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https://www.readbyqxmd.com/read/27922175/a-framework-to-quantify-karyotype-variation-associated-with-cho-production-instability
#1
Jong Youn Baik, Kelvin H Lee
Chinese hamster ovary (CHO) cells, major mammalian host cells for biomanufacturing of therapeutic proteins, have been extensively investigated to enhance productivity and product quality. However, cell line instability resulting in unexpected changes in productivity or product quality is challenging for biomanufacturing. Based on previous reports about causes and characteristics of production instability, we hypothesized that chromosomal rearrangements due to genomic instability are associated with production instability...
December 6, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27922023/systematic-site-directed-mutagenesis-of-the-helicobacter-pylori-cagl-protein-of-the-cag-type-iv-secretion-system-identifies-novel-functional-domains
#2
Tobias Bönig, Patrick Olbermann, Simon H Bats, Wolfgang Fischer, Christine Josenhans
The Cag Type IV secretion system, which contributes to inflammation and cancerogenesis during chronic infection, is one of the major virulence factors of the bacterial gastric pathogen Helicobacter pylori. We have generated and characterized a series of non-marked site-directed chromosomal mutants in H. pylori to define domains of unknown function of the essential tip protein CagL of the Cag secretion system. Characterizing the CagL mutants, we determined that their function to activate cells and transport the effector CagA was reduced to different extents...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921396/frequency-and-type-of-inheritable-mutations-induced-by-%C3%AE-rays-in-rice-as-revealed-by-whole-genome-sequencing
#3
Shan Li, Yun-Chao Zheng, Hai-Rui Cui, Hao-Wei Fu, Qing-Yao Shu, Jian-Zhong Huang
Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M2 rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M2 plant, resulting in genome coverage of >45 times for each plant...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27921343/complete-genome-sequence-of-streptococcus-troglodytae-tku31-isolated-from-an-oral-cavity-of-chimpanzee-pan-troglodytes
#4
Masaaki Okamoto, Mariko Naito, Mayu Miyanohara, Susumu Imai, Yoshiaki Nomura, Wataru Saito, Yasuko Momoi, Kazuko Takada, Takako Miyabe-Nishiwaki, Masaki Tomonaga, Nobuhiro Hanada
Streptococcus troglodytae TKU31 was isolated from an oral cavity of chimpanzee (Pan troglodytes), and it is the most closely related species to Streptococcus mutans among the mutans group streptococci. The complete sequence of TKU31 genome consisted of a single circular chromosome that was 2,097,874 base pairs in length, with a G + C content of 37.18%. It possessed a total of 2,082 coding sequences (CDSs), 65 tRNAs and five rRNA operons (15 rRNAs). Two clustered regularly interspaced short palindromic repeats (CRISPRs), six insertion sequences (IS) and two predicted prophage elements were identified...
December 6, 2016: Microbiology and Immunology
https://www.readbyqxmd.com/read/27921326/correlation-of-genetic-results-with-testicular-histology-hormones-and-sperm-retrieval-in-nonobstructive-azoospermia-patients-with-testis-biopsy
#5
W Liu, X Gao, G Ma, L Yan, T Chen, T Li, R-M Yu, J-L Ma
To investigate the frequency and types of genetic results in different testicular histology of patients with nonobstructive azoospermia (NOA), and correlated with hormones and sperm retrieval (SR), a retrospective study was conducted in 286 Chinese NOA patients who underwent testis biopsy and 100 age-matched fertile men as the control group. Chromosome karyotype analyses were performed by the peripheral blood chromosome G-band detection method. Screening of Y chromosome microdeletions of azoospermia factor (AZF) region was performed by polymerase chain reaction (PCR) amplification of 11 sequence-tagged sites (STS)...
December 6, 2016: Andrologia
https://www.readbyqxmd.com/read/27921283/choices-have-consequences-the-nexus-between-dna-repair-pathways-and-genomic-instability-in-cancer
#6
REVIEW
Sonali Bhattacharjee, Saikat Nandi
BACKGROUND: The genome is under constant assault from a multitude of sources that can lead to the formation of DNA double-stand breaks (DSBs). DSBs are cytotoxic lesions, which if left unrepaired could lead to genomic instability, cancer and even cell death. However, erroneous repair of DSBs can lead to chromosomal rearrangements and loss of heterozygosity, which in turn can also cause cancer and cell death. Hence, although the repair of DSBs is crucial for the maintenance of genome integrity the process of repair need to be well regulated and closely monitored...
December 2016: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/27921248/the-molecular-pathogenesis-of-schwannomatosis-a-paradigm-for-the-co-involvement-of-multiple-tumour-suppressor-genes-in-tumorigenesis
#7
REVIEW
Hildegard Kehrer-Sawatzki, Said Farschtschi, Victor-Felix Mautner, David N Cooper
Schwannomatosis is characterized by the predisposition to develop multiple schwannomas and, less commonly, meningiomas. Despite the clinical overlap with neurofibromatosis type 2 (NF2), schwannomatosis is not caused by germline NF2 gene mutations. Instead, germline mutations of either the SMARCB1 or LZTR1 tumour suppressor genes have been identified in 86% of familial and 40% of sporadic schwannomatosis patients. In contrast to patients with rhabdoid tumours, which are due to complete loss-of-function SMARCB1 mutations, individuals with schwannomatosis harbour predominantly hypomorphic SMARCB1 mutations which give rise to the synthesis of mutant proteins with residual function that do not cause rhabdoid tumours...
December 5, 2016: Human Genetics
https://www.readbyqxmd.com/read/27921120/the-potential-of-probabilistic-graphical-models-in-linkage-map-construction
#8
Huange Wang, Fred A van Eeuwijk, Johannes Jansen
Probabilistic graphical models show great potential for robust and reliable construction of linkage maps. We show how to use probabilistic graphical models to construct high-quality linkage maps in the face of data perturbations caused by genotyping errors and reciprocal translocations. It has been shown that linkage map construction can be hampered by the presence of genotyping errors and chromosomal rearrangements such as inversions and translocations. Here, we report a novel method for linkage map construction using probabilistic graphical models...
December 5, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27920999/frequency-of-y-chromosome-microdeletions-among-iranian-infertile-men-with-azoospermia-and-severe-oligozoospermia-a-meta-analysis
#9
Ehsan Yousefi-Razin, Mohammad Javad Nasiri, Mir Davood Omrani
BACKGROUND: While multiple factors can contribute to male infertility, genetic factors, such as chromosomal disorders or Y-chromosome microdeletion, are responsible for about 10% of male infertility. Considering the role of Y-chromosome micro-deletions in men with oligozoospermia who volunteer for in vitro fertilization (IVF), the prevalence of such microdeletions in each particular community needs to be exactly determined. Hence, the present study attempted to analyze the available literature on the frequency of chromosome microdeletion among Iranian infertile men...
October 2016: Journal of Reproduction & Infertility
https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#10
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920797/genome-wide-association-study-for-identifying-loci-that-affect-fillet-yield-carcass-and-body-weight-traits-in-rainbow-trout-oncorhynchus-mykiss
#11
Dianelys Gonzalez-Pena, Guangtu Gao, Matthew Baranski, Thomas Moen, Beth M Cleveland, P Brett Kenney, Roger L Vallejo, Yniv Palti, Timothy D Leeds
Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920770/the-use-of-transposon-insertion-sequencing-to-interrogate-the-core-functional-genome-of-the-legume-symbiont-rhizobium-leguminosarum
#12
Benjamin J Perry, Mir S Akter, Christopher K Yost
The free-living legume symbiont Rhizobium leguminosarum is of significant economic value because of its ability to provide fixed nitrogen to globally important leguminous food crops, such as peas and lentils. Discovery based research into the genetics and physiology of R. leguminosarum provides the foundational knowledge necessary for understanding the bacterium's complex lifestyle, necessary for augmenting its use in an agricultural setting. Transposon insertion sequencing (INSeq) facilitates high-throughput forward genetic screening at a genomic scale to identify individual genes required for growth in a specific environment...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920638/interstitial-1q21-1-microdeletion-is-associated-with-severe-skeletal-anomalies-dysmorphic-face-and-moderate-intellectual-disability
#13
Bruno F Gamba, Roseli M Zechi-Ceide, Nancy M Kokitsu-Nakata, Siulan Vendramini-Pittoli, Carla Rosenberg, Ana C V Krepischi Santos, Lucilene Ribeiro-Bicudo, Antonio Richieri-Costa
We report on a Brazilian patient with a 1.7-Mb interstitial microdeletion in chromosome 1q21.1. The phenotypic characteristics include microcephaly, a peculiar facial gestalt, cleft lip/palate, and multiple skeletal anomalies represented by malformed phalanges, scoliosis, abnormal modeling of vertebral bodies, hip dislocation, abnormal acetabula, feet anomalies, and delayed neuropsychological development. Deletions reported in this region are clinically heterogeneous, ranging from subtle phenotypic manifestations to severe congenital heart defects and/or neurodevelopmental findings...
November 2016: Molecular Syndromology
https://www.readbyqxmd.com/read/27920636/identifying-cnvs-in-15q11q13-and-16p11-2-of-patients-with-seizures-increases-the-rates-of-detecting-pathogenic-changes
#14
Gabrielle S Vianna, Mariana L Freitas, Valdirene T de Oliveira, Rafaella X Pietra, Michele da S Gonçalves, Patrícia P O Rocha, Rejane A C Monteiro, Luana C A Ferreira, Rosana R Xavier, Andréia M Carvalho, Patrícia R de M Lima, Maria Augusta N P Monteiro, Elvis C Mateo, Juliana G Giannetti, Giovana da C César, Joziele de S Lima, Paula F V Medeiros, Fernanda S Jehee
Chromosomal changes are frequently observed in patients with syndromic seizures. Understanding the genetic etiology of this pathology is crucial for the guidance and genetic counseling of families as well as for the establishment of appropriate treatment. A combination of MLPA kits was used to identify pathogenic CNVs in a group of 70 syndromic patients with seizures. Initially, a screening was performed for subtelomeric changes (MLPA P036 and P070 kits) and for the regions most frequently related to microdeletion/microduplication syndromes (MLPA P064)...
November 2016: Molecular Syndromology
https://www.readbyqxmd.com/read/27920471/identification-of-il11ra-and-melk-amplification-in-gastric-cancer-by-comprehensive-genomic-profiling-of-gastric-cancer-cell-lines
#15
Danielle Queiroz Calcagno, Sylvia Santomi Takeno, Carolina Oliveira Gigek, Mariana Ferreira Leal, Fernanda Wisnieski, Elizabeth Suchi Chen, Taíssa Maíra Thomaz Araújo, Eleonidas Moura Lima, Maria Isabel Melaragno, Samia Demachki, Paulo Pimentel Assumpção, Rommel Rodriguez Burbano, Marília Cardoso Smith
AIM: To identify common copy number alterations on gastric cancer cell lines. METHODS: Four gastric cancer cell lines (ACP02, ACP03, AGP01 and PG100) underwent chromosomal comparative genome hybridization and array comparative genome hybridization. We also confirmed the results by fluorescence in situ hybridization analysis using the bacterial artificial chromosome clone and quantitative real time PCR analysis. RESULTS: The amplification of 9p13...
November 21, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27920363/detection-of-imprinting-effects-for-qualitative-traits-on-x-chromosome-based-on-nuclear-families
#16
Ji-Yuan Zhou, Xiao-Ping You, Ran Yang, Wing Kam Fung
Methods for detecting imprinting effects have been developed primarily for autosomal markers. However, no method is available in the literature to test for imprinting effects on X chromosome. Therefore, it is necessary to suggest methods for detecting such imprinting effects. In this article, the parental-asymmetry test on X chromosome (XPAT) is first developed to test for imprinting for qualitative traits in the presence of association, based on family trios each with both parents and their affected daughter...
December 5, 2016: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/27920266/variability-of-ponto-cerebellar-fibers-by-diffusion-tensor-imaging-in-diverse-brain-malformations
#17
Nancy K Rollins, Timothy N Booth, Maria H Chahrour
To describe pontine axonal anomalies across diverse brain malformations. Institutional review board-approved review of magnetic resonance imaging (MRI) and genetic testing of 31 children with brain malformations and abnormal pons by diffusion tensor imaging. Anomalous dorsal pontocerebellar tracts were seen in mid-hindbrain anomalies and in diffuse malformations of cortical development including lissencephaly, gyral disorganization with dysplastic basal ganglia, presumed congenital fibrosis of extraocular muscles type 3, and in callosal agenesis without malformations of cortical development...
December 5, 2016: Journal of Child Neurology
https://www.readbyqxmd.com/read/27920250/renal-anemia-model-mouse-established-by-transgenic-rescue-with-erythropoietin-gene-lacking-kidney-specific-regulatory-elements
#18
Ikuo Hirano, Norio Suzuki, Shun Yamazaki, Hiroki Sekine, Naoko Minegishi, Ritsuko Shimizu, Masayuki Yamamoto
The erythropoietin (Epo) gene is under tissue-specific inducible regulation. Because kidney is the primary EPO-producing tissue in adults, impaired EPO production in chronic kidney disorders results in serious renal anemia. The Epo gene contains a liver-specific enhancer in the 3' region, but the kidney-specific enhancer for gene expression in renal EPO-producing (REP) cells remains elusive. Here, we examined a Conserved-Upstream-element for Renal-Epo-regulation (CURE) region that spans 17.4 kb to 3.6 kb upstream of the Epo gene and harbors several phylogenetically conserved elements...
December 5, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27920212/inhibition-of-antigen-specific-and-non-specific-stimulation-of-bovine-t-and-b-cells-by-lymphostatin-from-attaching-and-effacing-escherichia-coli
#19
Robin L Cassady-Cain, Elizabeth A Blackburn, Charlotte R Bell, Elizaveta Elshina, Jayne C Hope, Mark P Stevens
Enterohaemorrhagic E. coli (EHEC) and enteropathogenic E. coli (EPEC) are enteric bacterial pathogens of worldwide importance. Most EPEC and non-O157 EHEC strains express lymphostatin (also known as LifA), a chromosomally-encoded 365 kDa protein. We previously demonstrated that lymphostatin is a putative glycosyltransferase that is important in intestinal colonisation of cattle by EHEC serogroup O5, O111 and O26 strains. However, the nature and consequences of the interaction between lymphostatin and immune cells from the bovine host are ill-defined...
December 5, 2016: Infection and Immunity
https://www.readbyqxmd.com/read/27920086/a-role-for-mitotic-bookmarking-of-sox2-in-pluripotency-and-differentiation
#20
Cédric Deluz, Elias T Friman, Daniel Strebinger, Alexander Benke, Mahé Raccaud, Andrea Callegari, Marion Leleu, Suliana Manley, David M Suter
Mitotic bookmarking transcription factors remain bound to chromosomes during mitosis and were proposed to regulate phenotypic maintenance of stem and progenitor cells at the mitosis-to-G1 (M-G1) transition. However, mitotic bookmarking remains largely unexplored in most stem cell types, and its functional relevance for cell fate decisions remains unclear. Here we screened for mitotic chromosome binding within the pluripotency network of embryonic stem (ES) cells and show that SOX2 and OCT4 remain bound to mitotic chromatin through their respective DNA-binding domains...
December 5, 2016: Genes & Development
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