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short tandem repeats

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https://www.readbyqxmd.com/read/28730502/establishment-of-11-linked-x-str-loci-within-1-1-mb-to-assist-with-kinship-testing
#1
James Chun-I Lee, Chun-Yen Lin, Li-Chin Tsai, Yu-Jen Yu, Keng-Hsien Liao, Adrian Linacre, Hsing-Mei Hsieh
This report identifies and characterizes 10 novel short tandem repeat (STR) loci on the human X chromosome, all of which are within a range of 1.1 Mb. These newly characterized loci were developed to aid in kinship assignment when the X chromosome is specifically required. The repeat DNA sequences were identified initially using data in GenBank and are located immediately upstream and downstream from the previously described locus DXS6807. Only those loci with seven or more observed alleles were used for further study resulting in the identification of 10 new loci...
July 20, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28724489/population-genetic-structure-of-the-cayo-santiago-colony-of-rhesus-macaques-macaca-mulatta
#2
Sreetharan Kanthaswamy, Robert F Oldt, Jillian Ng, Angelina V Ruiz-Lambides, Elizabeth Maldonado, Melween I Martínez, Carlos A Sariol
The rhesus macaque population at Cayo Santiago increases annually and is in urgent need of control. In-depth assessments of the colony's population genetic and pedigree structures provide a starting point for improving the colony's long-term management program. We evaluated the degree of genetic variation and coefficients of inbreeding and kinship of the Cayo Santiago colony by using pedigree and short tandem repeat (STR) data from 4738 rhesus macaques, which represent 7 extant social groups and a group of migrant males...
July 1, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28724409/hybrid-assembly-with-long-and-short-reads-improves-discovery-of-gene-family-expansions
#3
Jason R Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P Walenz, Junqi Liu, Robert M Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G Maron, Susan R McCouch, W Richard McCombie, Michael C Schatz, Peter Tiffin, Nevin D Young, Kevin A T Silverstein
BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28723299/support-for-disease-only-genotypes-and-excess-of-homozygosity-at-the-cyth4-primate-specific-gttt-repeat-in-schizophrenia
#4
Ehteram Khademi, Elham Alehabib, Ehsan Esmaili Shandiz, Azadeh Ahmadifard, Monavvar Andarva, Javad Jamshidi, Simin Rahimi-Aliabadi, Ramin Pouriran, Farhad Ramezani Nejad, Nader Mansoori, Neda Shahmohammadibeni, Shaghyegh Taghavi, Parasto Shokraeian, Haleh Akhavan-Niaki, Coro Paisán-Ruiz, Hossein Darvish, Mina Ohadi
OBJECTIVE: The role of short tandem repeats (STRs) in the control of gene expression among species is being increasingly understood following the identification of several instances in which certain STRs occur identically, or expand differentially, in primates versus nonprimates. These STRs may regulate genes that participate in characteristics that have diverged primates from other species (e.g., brain higher order functions). The CYTH4 gene contains the longest tetranucleotide STR in its core promoter, at 7-repeats, and links to the evolution of human and nonhuman primates...
July 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28721719/imprinted-nanovelcro-microchips-for-isolation-and-characterization-of-circulating-fetal-trophoblasts-toward-noninvasive-prenatal-diagnostics
#5
Shuang Hou, Jie-Fu Chen, Min Song, Yazhen Zhu, Yu Jen Jan, Szu Hao Chen, Tzu-Hua Weng, Dean-An Ling, Shang-Fu Chen, Tracy Ro, An-Jou Liang, Tom Lee, Helen Jin, Man Li, Lian Liu, Yu-Sheng Hsiao, Peilin Chen, Hsiao-Hua Yu, Ming-Song Tsai, Margareta D Pisarska, Angela Chen, Li-Ching Chen, Hsian-Rong Tseng
Circulating fetal nucleated cells (CFNCs) in maternal blood offer an ideal source of fetal genomic DNA for noninvasive prenatal diagnostics (NIPD). We developed a class of nanoVelcro microchips to effectively enrich a subcategory of CFNCs, i.e., circulating trophoblasts (cTBs) from maternal blood, which can then be isolated with single-cell resolution by a laser capture microdissection (LCM) technique for downstream genetic testing. We first established a nanoimprinting fabrication process to prepare the LCM-compatible nanoVelcro substrates...
July 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28717961/determining-the-optimal-forensic-dna-analysis-procedure-following-investigation-of-sample-quality
#6
Ronny Hedell, Johannes Hedman, Petter Mostad
Crime scene traces of various types are routinely sent to forensic laboratories for analysis, generally with the aim of addressing questions about the source of the trace. The laboratory may choose to analyse the samples in different ways depending on the type and quality of the sample, the importance of the case and the cost and performance of the available analysis methods. Theoretically well-founded guidelines for the choice of analysis method are, however, lacking in most situations. In this paper, it is shown how such guidelines can be created using Bayesian decision theory...
July 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28717960/population-genetic-analysis-of-the-globalfiler-str-loci-in-3032-individuals-from-the-altay-han-population-of-xinjiang-in-northwest-china
#7
XueBo Li, Liangliang Li, Qingshan Wang, Jianzhong Zhang, Wendong Ge, Rufeng Bai, Xiaojun Yu, Meisen Shi
The genetic polymorphisms of 21 autosomal short tandem repeat (STR) loci included in the GlobalFiler™ PCR Amplification Kit were evaluated in 3032 unrelated individuals Altay Han of Xinjiang, northwest China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. SE33 showed the greatest power of discrimination in Altay Han population, whereas TPOX showed the lowest. The combined discrimination power and probability of excluding paternity of the 21 autosomal STR loci were 0...
July 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28712775/simple-sequence-repeats-showing-length-preference-have-regulatory-functions-in-humans
#8
Jaya Krishnan, Fathima Athar, Tirupaati Swaroopa Rani, Rakesh Kumar Mishra
Simple sequence repeats (SSRs), simple tandem repeats (STRs) or microsatellites are short tandem repeats of 1-6 nucleotide motifs. They are twice as abundant as the protein coding DNA in the human genome and yet little is known about their functional relevance. Analysis of genomes across various taxa show that despite the instability associated with longer stretches of repeats, few SSRs with specific longer repeat lengths are enriched in the genomes indicating a positive selection. This conserved feature of length dependent enrichment hints at not only sequence but also length dependent functionality for SSRs...
July 13, 2017: Gene
https://www.readbyqxmd.com/read/28706611/a-novel-variant-in-the-pah-gene-causing-phenylketonuria-in-an-iranian-pedigree
#9
Elaheh Alavinejad, Seyede Zahra Sajedi, Masoumeh Razipour, Mona Entezam, Neda Mohajer, Aria Setoodeh, Saeed Talebi, Mohammad Keramatipour
BACKGROUND: Phenylalanine hydroxylase (PAH) gene is the well-known causative gene for classic Phenylketonuria (PKU) (OMIM#261600) disease, with more than 500 reported mutations. Through this study, a novel mutation in the PAH gene in an Iranian pedigree with phenylketonuria was introduced. METHODS: A consanguineous family with a 10-year old affected girl was referred for genetic analysis. Mutation screening of all exons and exon-intron boundaries was performed by Sanger sequencing, and mini haplotype analysis was carried out by genotyping of Short Tandem Repeat (STR) and Variable Number Tandem Repeat (VNTR) alleles...
July 2017: Avicenna Journal of Medical Biotechnology
https://www.readbyqxmd.com/read/28705464/diversity-of-pneumocystis-jirovecii-across-europe-a-multicentre-observational-study
#10
Alexandre Alanio, Maud Gits-Muselli, Nicolas Guigue, Marie Desnos-Ollivier, Enrique J Calderon, David Di Cave, Damien Dupont, Axel Hamprecht, Philippe M Hauser, Jannik Helweg-Larsen, Marta Kicia, Katrien Lagrou, Martina Lengerova, Olga Matos, Willem J G Melchers, Florent Morio, Gilles Nevez, Anne Totet, Lewis P White, Stéphane Bretagne
Pneumocystis jirovecii is an airborne human-specific ascomycetous fungus responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients, affecting >500,000 patients per year (www.gaffi.org). The understanding of its epidemiology is limited by the lack of standardised culture. Recent genotyping data suggests a limited genetic diversity of P. jirovecii. The objective of the study was to assess the diversity of P. jirovecii across European hospitals and analyse P. jirovecii diversity in respect to clinical data obtained from the patients...
June 29, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28690679/trichoderma-reesei-complete-genome-sequence-repeat-induced-point-mutation-and-partitioning-of-cazyme-gene-clusters
#11
Wan-Chen Li, Chien-Hao Huang, Chia-Ling Chen, Yu-Chien Chuang, Shu-Yun Tung, Ting-Fang Wang
BACKGROUND: Trichoderma reesei (Ascomycota, Pezizomycotina) QM6a is a model fungus for a broad spectrum of physiological phenomena, including plant cell wall degradation, industrial production of enzymes, light responses, conidiation, sexual development, polyketide biosynthesis, and plant-fungal interactions. The genomes of QM6a and its high enzyme-producing mutants have been sequenced by second-generation-sequencing methods and are publicly available from the Joint Genome Institute. While these genome sequences have offered useful information for genomic and transcriptomic studies, their limitations and especially their short read lengths make them poorly suited for some particular biological problems, including assembly, genome-wide determination of chromosome architecture, and genetic modification or engineering...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28679522/next-generation-sequence-analysis-reveals-methicillin-resistance-transfer-to-a-methicillin-susceptible-staphylococcus-aureus-mssa-strain-that-subsequently-caused-a-methicillin-resistant-staphylococcus-aureus-mrsa-outbreak-a-descriptive-study
#12
Veronica Weterings, Thijs Bosch, Sandra Witteveen, Fabian Landman, Leo Schouls, Jan Kluytmans
Resistance to methicillin in Staphylococcus aureus is primarily caused by the mecA gene, which is carried on a mobile genetic element: the staphylococcal cassette chromosome mec (SCCmec). Horizontal transfer of this element is supposed to play an important factor in the emergence of new clones of methicillin-resistant Staphylococcus aureus (MRSA), but has been rarely observed in real-time.In 2012, an outbreak occurred involving a healthcare worker (HCW) and three patients all carrying a fusidic-acid resistant MRSA strain...
July 5, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28677539/an-integration-free-virus-free-rhesus-macaque-induced-pluripotent-stem-cell-line-ripsc90-from-embryonic-fibroblasts
#13
Enrique Sosa, Rachel Kim, Ernesto J Rojas, Linzi Hosohama, Jon D Hennebold, Kyle E Orwig, Amander T Clark
The rhesus macaque induced pluripotent stem cell (riPSC) line, UCLAi090-A (riPSC90), was generated from rhesus embryonic fibroblast (REF) cells called REF90. REF90 cells and the riPSC90 line were authenticated by short tandem repeat analysis and had a normal male (42, XY) karyotype. The riPSC90 line expressed markers of self-renewal including OCT4, NANOG, TRA-1-81 and SSEA4, and generated teratomas after transplantation into immunocompromised mice. riPSC90 could be used in parallel with riPSC89, which was derived from REFs cultured from a different rhesus macaque embryo (Sosa et al...
May 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28667380/variants-in-the-non-coding-region-of-the-tlr2-gene-associated-with-infectious-subphenotypes-in-pediatric-sickle-cell-anemia
#14
Susana David, Pedro Aguiar, Liliana Antunes, Alexandra Dias, Anabela Morais, Anavaj Sakuntabhai, João Lavinha
Sickle cell anemia (SCA) is characterized by chronic hemolysis, severe vasoocclusive crises (VOCs), and recurrent often severe infections. A cohort of 95 SCA pediatric patients was the background for genotype-to-phenotype association of the patient's infectious disease phenotype and three non-coding polymorphic regions of the TLR2 gene, the -196 to -174 indel, SNP rs4696480, and a (GT)n short tandem repeat. The infectious subphenotypes included (A) recurrent respiratory infections and (B) severe bacterial infection at least once during the patient's follow-up...
June 30, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28666376/a-massively-parallel-strategy-for-str-marker-development-capture-and-genotyping
#15
Logan Kistler, Stephen M Johnson, Mitchell T Irwin, Edward E Louis, Aakrosh Ratan, George H Perry
Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery...
June 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28664933/frequent-homozygosity-in-both-mature-and-immature-ovarian-teratomas-a-shared-genetic-basis-of-tumorigenesis
#16
Olivia L Snir, Maura DeJoseph, Serena Wong, Natalia Buza, Pei Hui
Although homozygosity is well documented in mature teratomas, the genetic zygosity of ovarian immature teratomas and mixed germ cell tumors is less well studied. Ten cases of mature cystic teratomas, eleven cases of grade 2 or 3 immature teratomas, and seven cases of mixed germ cell tumors with an immature teratoma component were investigated by short tandem repeat genotyping to interrogate their genetic zygosity. DNA genotyping was informative in eight mature teratomas, seven immature teratomas and six cases of mixed germ cell tumors...
June 30, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28662107/highly-mutable-tandem-dna-repeats-generate-a-cell-wall-protein-variant-more-frequent-in-disease-causing-candida-albicans-isolates-than-in-commensal-isolates
#17
Zhuo Zhou, Zoe Jordens, Shuguang Zhang, Ningxin Zhang, Jan Schmid
During adaptation to host environments, many microorganisms alter their cell surface. One mechanism for doing so is variation in the number of amino acid repeats in cell surface proteins encoded by hypermutable DNA tandem repeats. In the yeast Candida albicans, an opportunistic human pathogen, the gene SSR1 encodes a GPI-anchored cell wall protein with a structural role. It contains two regions consisting of tandem repeats, almost exclusively encoding the amino acid pair Ser-Ala. As expected, the repeat regions make SSR1 highly mutable...
2017: PloS One
https://www.readbyqxmd.com/read/28660852/population-genetic-structure-of-the-cayo-santiago-colony-of-rhesus-macaques-macaca-mulatta
#18
Sreetharan Kanthaswamy, Robert F Oldt, Jillian Ng, Angelina V Ruiz-Lambides, Elizabeth Maldonado, Melween I Martínez, Carlos A Sariol
The rhesus macaque population at Cayo Santiago increases annually and is in urgent need of control. In-depth assessmentsof the colony's population genetic and pedigree structures provide a starting point for improving the colony's long-termmanagement program. We evaluated the degree of genetic variation and coefficients of inbreeding and kinship of the CayoSantiago colony by using pedigree and short tandem repeat (STR) data from 4738 rhesus macaques, which represent 7 extantsocial groups and a group of migrant males...
June 28, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28652746/association-between-serotonin-transporter-polymorphisms-5-httlpr-and-the-madrs-dysphoria-retardation-and-vegetative-subscale-scores-in-the-treatment-of-depression
#19
Hitoshi Takahashi, Hisashi Higuchi, Kazuhiro Sato, Mitsuhiro Kamata, Keizo Yoshida, Katsuji Nishimura
OBJECTIVE: We investigated the association between serotonin- or 5-hydroxytryptamine (5-HT)-related gene polymorphisms and response to antidepressant treatment in a specific symptom cluster of major depression by using the three-factor model of the Montgomery-Åsberg Depression Rating Scale (MADRS), ie, dysphoria (items of sadness, pessimistic thoughts, and suicidal thoughts), retardation (items of lassitude, inability to feel, apparent sadness, and concentration difficulties), and vegetative symptoms (items of reduced sleep, reduced appetite, and inner tension)...
2017: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/28633355/how-proteins-bind-to-dna-target-discrimination-and-dynamic-sequence-search-by-the-telomeric-protein-trf1
#20
Milosz Wieczór, Jacek Czub
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA...
June 15, 2017: Nucleic Acids Research
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