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Allelic exclusion

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https://www.readbyqxmd.com/read/28346493/aberrant-neuronal-activity-induced-signaling-and-gene-expression-in-a-mouse-model-of-rasopathy
#1
Franziska Altmüller, Santosh Pothula, Anil Annamneedi, Saeideh Nakhei-Rad, Carolina Montenegro-Venegas, Eneko Pina-Fernández, Claudia Marini, Monica Santos, Denny Schanze, Dirk Montag, Mohammad R Ahmadian, Oliver Stork, Martin Zenker, Anna Fejtova
Noonan syndrome (NS) is characterized by reduced growth, craniofacial abnormalities, congenital heart defects, and variable cognitive deficits. NS belongs to the RASopathies, genetic conditions linked to mutations in components and regulators of the Ras signaling pathway. Approximately 50% of NS cases are caused by mutations in PTPN11. However, the molecular mechanisms underlying cognitive impairments in NS patients are still poorly understood. Here, we report the generation and characterization of a new conditional mouse strain that expresses the overactive Ptpn11D61Y allele only in the forebrain...
March 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28345808/molecular-genetic-analysis-of-the-melanoma-regulatory-locus-in-xiphophorus-interspecies-hybrids
#2
Yuan Lu, Mikki Boswell, William Boswell, Susanne Kneitz, Michael Hausmann, Barbara Klotz, Janine Regneri, Markita Savage, Angel Amores, John Postlethwait, Wesley Warren, Manfred Schartl, Ronald Walter
Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC1 ) hybrids and 13 fifth generation (BC5 ) hybrids...
March 27, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28342798/allele-frequencies-and-other-forensic-parameters-of-the-hid-ion-ampliseq%C3%A2-identity-panel-markers-in-basques-using-the-ion-torrent-pgm%C3%A2-platform
#3
O García, A Soto, I Yurrebaso
The HID-Ion AmpliSeq™ Identity Panel amplifies 90 autosomal SNPs and 34 Y- SNPs with massively parallel sequencing (MPS) using the Ion Torrent PGM™ platform. In the present study, 105 Basques were analyzed to assess this panel. All loci were in Hardy-Weinberg equilibrium and no association between them was detected. Forensic parameters were calculated as 5.74×10(-36) for combined match probability and 99.99998% for combined power of exclusion. In conclusion, the HID Identity panel and the use of this new MPS technology are very promising tools for paternity testing and human identification in routine casework in the forensic field...
March 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28342005/genetic-polymorphisms-for-19-autosomal-str-loci-of-chongqing-han-ethnicity-and-phylogenetic-structure-exploration-among-28-chinese-populations
#4
Xing Zou, YongGuo Li, Ping Li, QianYun Nie, Ting Wang, Yue Hu, Ying Zhu, JianBo Li, RenKuan Tang
The allele frequencies and forensic statistical parameters of 19 autosomal short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, THOl, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, D6S1043, Penta D, Penta E, and D12S391) included in the Goldeneye™ DNA ID system 20A kit were obtained in 671 Chinese Han individuals residing in Chongqing, Southwest China. All 19 STR loci were identified in agreement with the Hardy-Weinberg equilibrium. A total of 238 alleles were observed with corresponding allele frequencies that varied from 0...
March 24, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28338502/sellar-atypical-teratoid-rhabdoid-tumor-at-rt-a-clinicopathologically-and-genetically-distinct-variant-of-at-rt
#5
Satoshi Nakata, Sumihito Nobusawa, Takanori Hirose, Shinji Ito, Naoko Inoshita, Shunsuke Ichi, Vishwa J Amatya, Yukio Takeshima, Kazuhiko Sugiyama, Yukihiko Sonoda, Hironori Haga, Junko Hirato, Yoichi Nakazato, Hideaki Yokoo
Atypical teratoid/rhabdoid tumors (AT/RTs) are rare aggressive tumors of the central nervous system that predominantly affect infants. Although adult AT/RT are rare, accumulated cases have revealed adult-specific AT/RT in the sellar region. Twelve previously reported cases of sellar AT/RT exclusively occurred in adult females, suggesting biological differences from conventional infant AT/RT. We herein investigated a series of 6 sellar AT/RT for histopathologic features, the molecular status of the INI1/SMARCB1 gene, and clinical courses...
March 23, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28334821/in-vivo-cleavage-specificity-of-trypanosoma-brucei-editosome-endonucleases
#6
Jason Carnes, Suzanne McDermott, Atashi Anupama, Brian G Oliver, D Noah Sather, Kenneth Stuart
RNA editing is an essential post-transcriptional process that creates functional mitochondrial mRNAs in Kinetoplastids. Multiprotein editosomes catalyze pre-mRNA cleavage, uridine (U) insertion or deletion, and ligation as specified by guide RNAs. Three functionally and compositionally distinct editosomes differ by the mutually exclusive presence of the KREN1, KREN2 or KREN3 endonuclease and their associated partner proteins. Because endonuclease cleavage is a likely point of regulation for RNA editing, we elucidated endonuclease specificity in vivo...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28329770/antigen-presentation-profiling-reveals-recognition-of-lymphoma-immunoglobulin-neoantigens
#7
Michael S Khodadoust, Niclas Olsson, Lisa E Wagar, Ole A W Haabeth, Binbin Chen, Kavya Swaminathan, Keith Rawson, Chih Long Liu, David Steiner, Peder Lund, Samhita Rao, Lichao Zhang, Caleb Marceau, Henning Stehr, Aaron M Newman, Debra K Czerwinski, Victoria E H Carlton, Martin Moorhead, Malek Faham, Holbrook E Kohrt, Jan Carette, Michael R Green, Mark M Davis, Ronald Levy, Joshua E Elias, Ash A Alizadeh
Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28324054/ccdc141-mutations-in-idiopathic-hypogonadotropic-hypogonadism
#8
Ihsan Turan, B Ian Hutchins, Bulent Hacihamdioglu, L Damla Kotan, Fatih Gurbuz, Ayca Ulubay, Eda Mengen, Bilgin Yuksel, Susan Wray, A Kemal Topaloglu
Context: GnRH neurons originate outside the central nervous system in the olfactory placode and migrate into the CNS, becoming integral components of the hypothalamic-pituitary-gonadal axis. Failure of this migration can lead to Idiopathic Hypogonadotropic Hypogonadism (IHH)/Kallmann Syndrome (KS). We have previously shown that CCDC141 knockdown leads to impaired migration of GnRH neurons but not of olfactory receptor neurons. Objective: The aim of this study was to further describe the phenotype and prevalence of CCDC141 mutations in IHH/KS...
January 23, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28322274/a-rare-missense-variant-in-rcl1-segregates-with-depression-in-extended-families
#9
N Amin, F M S de Vrij, M Baghdadi, R W W Brouwer, J G J van Rooij, O Jovanova, A G Uitterlinden, A Hofman, H L A Janssen, S Darwish Murad, R Kraaij, J Stedehouder, M C G N van den Hout, J M Kros, W F J van IJcken, H Tiemeier, S A Kushner, C M van Duijn
Depression is the most prevalent psychiatric disorder with a complex and elusive etiology that is moderately heritable. Identification of genes would greatly facilitate the elucidation of the biological mechanisms underlying depression, however, its complex etiology has proved to be a major bottleneck in the identification of its genetic risk factors, especially in genome-wide association-like studies. In this study, we exploit the properties of a genetic isolate and its family-based structure to explore whether relatively rare exonic variants influence the burden of depressive symptoms in families...
March 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28320875/gata3-abundance-is-a-critical-determinant-of-t-cell-receptor-beta-allelic-exclusion
#10
Chia-Jui Ku, JoAnn M Sekiguchi, Bharat Panwar, Yuanfang Guan, Satoru Takahashi, Keigyou Yoh, Ivan Maillard, Tomonori Hosoya, James Douglas Engel
Allelic exclusion describes the essential immunological process by which feedback repression of sequential DNA rearrangements ensures that only one autosome expresses a functional T or B cell receptor. In wild type mammals, approximately 60% of cells have recombined the DNA of one Tcrb V-to-DJ-joined allele in a functional configuration, while the second allele has only recombined the DJ sequences; the other 40% of the cells have recombined the V- to the DJ segments on both alleles, with only one of the two predicting a functional TCRβ protein...
March 20, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28315511/deletion-of-gstm1-and-gstt1-genes-and-lung-cancer-survival-a-systematic-review
#11
Cristina Ramos Hernández, Cecilia Mouronte-Roibás, Juan Miguel Barros-Dios, Alberto Fernández-Villar, Alberto Ruano-Ravina
PURPOSE: The mechanisms of lung carcinogenesis are not fully understood. Not all smokers develop lung cancer, indicating that genetic variations and other environmental factors may play an important role in its development. The human glutathione S-transferases (GSTs) have been associated with an increased risk of lung cancer. Glutathione S-transferases are phase II biotransformation enzymes that play a role in detoxifying a wide range of exogenous agents including carcinogens but also anticarcinogenic drugs...
March 18, 2017: Tumori
https://www.readbyqxmd.com/read/28296739/ugt1a1-28-relationship-with-abnormal-total-bilirubin-levels-in-chronic-hepatitis-c-patients-outcomes-from-a-case-control-study
#12
Marcelo Moreira Tavares de Souza, Victor Van Vaisberg, Rodrigo Martins Abreu, Aline Siqueira Ferreira, Camila daSilvaFerreira, Paulo Dominguez Nasser, Helena Scavone Paschoale, Flair José Carrilho, Suzane Kioko Ono
Gilbert syndrome (GS) is a frequent benign clinical condition, marked by intermittent unconjugated hyperbilirubinemia, mostly due to the polymorphism uridine diphosphate-glucuronosyltransferase 1A1*28 (UGT1A1*28). Hyperbilirubinemia has been reported in a GS patient undergoing hepatitis C treatment, and other UGT isoforms polymorphisms have been linked to worse outcomes in viral hepatitis. Yet, little is known to GS contributions' to the liver disease scenario. Our aim was to assess UGT1A1 genotypes' frequency in chronic hepatitis C (CHC) patients and correlate with total bilirubin (TB)...
March 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28295812/hybridization-between-two-cryptic-filamentous-brown-seaweeds-along-the-shore-analysing-pre-and-post-zygotic-barriers-in-populations-of-individuals-with-varying-ploidy-levels
#13
Alejandro E Montecinos, Marie-Laure Guillemin, Lucia Couceiro, Akira F Peters, Solenn Stoeckel, Myriam Valero
We aimed to study the importance of hybridization between two cryptic species of the genus Ectocarpus, a group of filamentous algae with haploid-diploid life cycles that include the principal genetic model organism for the brown algae. In haploid-diploid species, the genetic structure of the two phases of the life cycle can be analysed separately in natural populations. Such life cycles provide a unique opportunity to estimate the frequency of hybrid genotypes in diploid sporophytes and meiotic recombinant genotypes in haploid gametophytes allowing the effects of reproductive barriers preventing fertilization or preventing meiosis to be untangle...
March 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28292857/awake1-an-abc-type-transporter-reveals-an-essential-role-for-suberin-in-the-control-of-seed-dormancy
#14
Fabio Fedi, Carmel O'Neil, Guillaume Menard, Martin Trick, Francoise Corbineau, Christophe Bailly, Peter J Eastmond, Steven Penfield
The mother plant plays an important dynamic role in the control of dormancy of her progeny seed, in response to environmental signals. In order to further understand the mechanisms by which this dormancy control takes place we conducted a forward genetic screen to isolate mutants which fail to enter dormancy in response to variation in temperature during seed set. We show that for the first of these mutants, designated AWAKE1, the maternal allele is required for entry into strongly dormant states, and that awake1 mutants show seed phenotypes previously shown to be associated with loss of suberin the seed...
March 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28291786/association-of-lifelong-exposure-to-cognitive-reserve-enhancing-factors-with-dementia-risk-a-community-based-cohort-study
#15
Hui-Xin Wang, Stuart W S MacDonald, Serhiy Dekhtyar, Laura Fratiglioni
BACKGROUND: Variation in the clinical manifestation of dementia has been associated with differences in cognitive reserve, although less is known about the cumulative effects of exposure to cognitive reserve factors over the life course. We examined the association of cognitive reserve-related factors over the lifespan with the risk of dementia in a community-based cohort of older adults. METHODS AND FINDINGS: Information on early-life education, socioeconomic status, work complexity at age 20, midlife occupation attainment, and late-life leisure activities was collected in a cohort of dementia-free community dwellers aged 75+ y residing in the Kungsholmen district of Stockholm, Sweden, in 1987-1989...
March 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28283040/functional-variation-in-allelic-methylomes-underscores-a-strong-genetic-contribution-and-reveals-novel-epigenetic-alterations-in-the-human-epigenome
#16
Warren A Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Marie-Michelle Simon, Elodie Boulier, Adriana Redensek, Stephen Watt, Avik Datta, Laura Clarke, Paul Flicek, Daniel Mead, Dirk S Paul, Stephan Beck, Guillaume Bourque, Mark Lathrop, André Tchernof, Marie-Claude Vohl, Florence Demenais, Isabelle Pin, Kate Downes, Hendrick G Stunnenberg, Nicole Soranzo, Tomi Pastinen, Elin Grundberg
BACKGROUND: The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have only been carried out in a limited set of samples. RESULTS: We describe a large-scale coordinated study of allelic and non-allelic effects on DNA methylation, histone mark deposition, and gene expression, detecting the interrelations between epigenetic and functional features at unprecedented resolution...
March 10, 2017: Genome Biology
https://www.readbyqxmd.com/read/28282489/systematic-functional-testing-of-rare-variants-contributions-of-cfi-to-age-related-macular-degeneration
#17
Perciliz L Tan, Melanie E Garrett, Jason R Willer, Peter A Campochiaro, Betsy Campochiaro, Donald J Zack, Allison E Ashley-Koch, Nicholas Katsanis
Purpose: Genome-wide association (GWAS) and sequencing studies for AMD have highlighted the importance of coding variants at loci that encode components of the complement pathway. However, assessing the contribution of such alleles to AMD, especially when they are rare, remains coarse, in part because of the persistent challenge in establishing their functional relevance. Others and we have shown previously that rare alleles in complement factor I (CFI) can be tested functionally using a surrogate in vivo assay of retinal vascularization in zebrafish embryos...
March 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28275220/lipoprotein-lipase-lpl-polymorphism-and-the-risk-of-coronary-artery-disease-a-meta-analysis
#18
Li Xie, You-Mei Li
BACKGROUND: In recent years, the lipoprotein lipase (LPL) polymorphism has been extensively investigated as a potential risk factor for coronary artery disease (CAD). However, the results of these studies have been inconsistent. Therefore, we performed this meta-analysis to explore the association between LPL polymorphism and CAD risk. METHODS: The literature was searched from electronic databases such as Embase, China Biological Medicine Database, PubMed, Knowledge Infrastructure, and China National Web of Science by the key words "coronary artery disease", "lipoprotein lipase" and "polymorphism"...
January 16, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28274756/common-genetic-variation-and-risk-of-gallbladder-cancer-in-india-a-case-control-genome-wide-association-study
#19
Sharayu Mhatre, Zhaoming Wang, Rajini Nagrani, Rajendra Badwe, Shubhada Chiplunkar, Balraj Mittal, Saurabh Yadav, Haoyu Zhang, Charles C Chung, Prachi Patil, Stephen Chanock, Rajesh Dikshit, Nilanjan Chatterjee, Preetha Rajaraman
BACKGROUND: Gallbladder cancer is highly lethal, with notable differences in incidence by geography and ethnic background. The aim of this study was to identify common genetic susceptibility alleles for gallbladder cancer. METHODS: In this case-control genome-wide association study (GWAS), we did a genome-wide scan of gallbladder cancer cases and hospital visitor controls, both of Indian descent, followed by imputation across the genome. Cases were patients aged 20-80 years with microscopically confirmed primary gallbladder cancer diagnosed or treated at Tata Memorial Hospital, Mumbai, India, and enrolled in the study between Sept 12, 2010, and June 8, 2015...
March 3, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28244489/chromosome-choice-for-initiation-of-v-d-j-recombination-is-not-governed-by-genomic-imprinting
#20
Claudia Gebert, Lauren Correia, Zhenhu Li, Howard T Petrie, Paul E Love, Karl Pfeifer
V-(D)-J recombination generates the antigen receptor diversity necessary for immune cell function, while allelic exclusion ensures that each cell expresses a single antigen receptor. V-(D)-J recombination of the Ig, Tcrb, Tcrg and Tcrd antigen receptor genes is ordered and sequential so that only one allele generates a productive rearrangement. The mechanism controlling sequential rearrangement of antigen receptor genes, in particular how only one allele is selected to initiate recombination while at least temporarily leaving the other intact, remains unresolved...
February 28, 2017: Immunology and Cell Biology
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