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short tandem repeats

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https://www.readbyqxmd.com/read/28633355/how-proteins-bind-to-dna-target-discrimination-and-dynamic-sequence-search-by-the-telomeric-protein-trf1
#1
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
https://www.readbyqxmd.com/read/28631292/validation-of-reduced-reagent-volumes-in-the-implementation-of-the-quantifiler-%C3%A2-trio-quantification-kit
#2
Yoonjung Cho, Hyo Sook Kim, Min-Hee Kim, Moonhee Park, Hansol Kwon, Yang Han Lee, Dong Sub Lee
The Quantifiler(®) Trio Quantification Kit has been developed to quantify the total amount of amplifiable and human male DNA in samples and to estimate the extent of DNA degradation. To minimize the cost of DNA quantification, we evaluated kit performance using a reduced volume of reagents (1/10-volume) using DNA samples of varying types and concentrations. Our results demonstrated concordance between the manufacturer's method and the low-volume method for DNA quantification, DNA degradation index estimation, and human male DNA quantification...
June 20, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28630379/the-association-between-telomere-length-and-mortality-in-bangladesh
#3
Samantha G Dean, Chenan Zhang, Jianjun Gao, Shantanu Roy, Justin Shinkle, Mekala Sabarinathan, Maria Argos, Lin Tong, Alauddin Ahmed, Md Tariqul Islam, Tariqul Islam, Muhammad Rakibuz-Zaman, Golam Sarwar, Hasan Shahriar, Mahfuzar Rahman, Md Yunus, Joseph H Graziano, Lin S Chen, Farzana Jasmine, Muhammad G Kibriya, Habibul Ahsan, Brandon L Pierce
Telomeres are tandem repeat sequences at the end of chromosomes that bind proteins to protect chromosome ends. Telomeres shorten with age, and shorter leukocyte telomere length (TL) has been associated with overall mortality in numerous studies. However, this association has not been tested in populations outside of Europe and the U.S. We assessed the association between TL and subsequent mortality using data on 744 mortality cases and 761 age-/sex-matched controls sampled from >27,000 participants from three longitudinal Bangladeshi cohorts: Health Effects of Arsenic Longitudinal Study (HEALS), HEALS Expansion (HEALS-E), and Bangladesh Vitamin E and Selenium Trial (BEST)...
June 15, 2017: Aging
https://www.readbyqxmd.com/read/28623801/dna-analysis-of-root-canal-filled-teeth
#4
Hikaru Izawa, Hirofumi Tsutsumi, Sayaka Maruyama, Toshinobu Komuro
Teeth are markedly useful as samples for DNA analysis; however, intact teeth are not always available. This study examined the possibility of identifying autosomal and Y-chromosome short tandem repeat (STR) types in samples from 34 teeth (15 intact and 19 root canal filled) that had been preserved for 10-33years after dental extraction. The aim was to explore the feasibility of individual identification by DNA analysis of samples obtained from highly decomposed and skeletonized corpses. Only one out of 24 autosomal STR loci was not identified in two of the 15 intact teeth, whereas all 23 loci of the Y chromosome STR were detected...
May 10, 2017: Legal Medicine
https://www.readbyqxmd.com/read/28622802/rapid-multiplex-dna-amplification-on-an-inexpensive-microdevice-for-human-identification-via-short-tandem-repeat-analysis
#5
Jacquelyn A DuVall, Delphine Le Roux, Brandon L Thompson, Christopher Birch, Daniel A Nelson, Jingyi Li, Daniel L Mills, An-Chi Tsuei, Martin G Ensenberger, Cindy Sprecher, Douglas R Storts, Brian E Root, James P Landers
Forensic DNA analysis requires several steps, including DNA extraction, PCR amplification, and separation of PCR fragments. Intuitively, there are numerous situations where it would be beneficial to speed up the overall DNA analysis process; in this work, we focus on the most time-consuming component in the analysis pipeline, namely the polymerase chain reaction (PCR). Primers were specially designed to target 10 human genomic loci, all yielding amplicons shorter than 350 bases, for ease of downstream integration with on-board microchip electrophoresis...
August 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28619083/on-marker-based-parentage-verification-via-non-linear-optimization
#6
Vinzent Boerner
BACKGROUND: Parentage verification by molecular markers is mainly based on short tandem repeat markers. Single nucleotide polymorphisms (SNPs) as bi-allelic markers have become the markers of choice for genotyping projects. Thus, the subsequent step is to use SNP genotypes for parentage verification as well. Recent developments of algorithms such as evaluating opposing homozygous SNP genotypes have drawbacks, for example the inability of rejecting all animals of a sample of potential parents...
June 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28617865/a-human-genotyping-trial-to-estimate-the-post-feeding-time-from-mosquito-blood-meals
#7
Yuuji Hiroshige, Masaaki Hara, Atsushi Nagai, Tomoyuki Hikitsuchi, Mitsuo Umeda, Yumi Kawajiri, Koji Nakayama, Koichi Suzuki, Aya Takada, Akira Ishii, Toshimichi Yamamoto
Mosquitoes occur almost worldwide, and females of some species feed on blood from humans and other animals to support ovum maturation. In warm and hot seasons, such as the summer in Japan, fed mosquitoes are often observed at crime scenes. The current study attempted to estimate the time that elapsed since feeding from the degree of human DNA digestion in mosquito blood meals and also to identify the individual human sources of the DNA using genotyping in two species of mosquito: Culex pipiens pallens and Aedes albopictus...
2017: PloS One
https://www.readbyqxmd.com/read/28613230/oligonucleotides-and-nd-fish-displaying-different-arrangements-of-tandem-repeats-and-identification-of-dasypyrum-villosum-chromosomes-in-wheat-backgrounds
#8
Zhiqiang Xiao, Shuyao Tang, Ling Qiu, Zongxiang Tang, Shulan Fu
Oligonucleotide probes and the non-denaturing fluorescence in situ hybridization (ND-FISH) technique are widely used to analyze plant chromosomes because they are convenient tools. New oligonucleotide probes, Oligo-Ku, Oligo-3B117.1, Oligo-3B117.2, Oligo-3B117.2.1, Oligo-3B117.3, Oligo-3B117.4, Oligo-3B117.5, Oligo-3B117.6, Oligo-pTa71A-1, Oligo-pTa71A-2, Oligo-pTa71B-1, Oligo-pTa71B-2, Oligo-pTa71C-1, Oligo-pTa71C-2, Oligo-pTa71C-3 and Oligo-pTa71D were designed based on the repetitive sequences KU.D15.15, pSc119...
June 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28613042/allele-frequencies-of-15-str-loci-in-bosnian-and-herzegovinian-population
#9
Amela Pilav, Naris Pojskić, Anesa Ahatović, Mirela Džehverović, Jasmina Čakar, Damir Marjanović
AIM: To determine newest the most accurate allele frequencies for 15 short tandem repeat (STR) loci in the Bosnian and Herzegovinian population, calculate statistical parameters, and compare them with the relevant data for seven neighboring populations. METHODS: Genomic DNA was obtained from buccal swabs of 1000 unrelated individuals from all regions of Bosnia and Herzegovina. Genotyping was performed using PowerPlex® 16 System to obtain allele frequencies for 15 polymorphic STR loci including D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX, and FGA...
June 14, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/28613038/investigation-of-the-str-loci-noise-distributions-of-powerseq%C3%A2-auto-system
#10
Xiangpei Zeng, Jonathan L King, Bruce Budowle
AIM: To characterize the noise and stutter distribution of 23 short tandem repeats (STRs) included in the PowerSeqTM Auto System. METHODS: Raw FASTQ files were analyzed using STRait Razor v2s to display alleles and coverage. The sequence noise was divided into several categories: noise at allele position, noise at -1 repeat position, and artifact. The average relative percentages of locus coverage for each noise, stutter, and allele were calculated from the samples used for this locus noise analysis...
June 14, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/28608349/identification-and-evolutionary-characterization-of-argonaute-binding-platforms
#11
Joshua T Trujillo, Rebecca A Mosher
ARGONAUTE (AGO) proteins are eukaryotic RNA silencing effectors that interact with their binding partners via short peptide motifs known as AGO hooks. AGO hooks tend to cluster in one region of the protein to create an AGO-binding platform. In addition to the presence of AGO hooks, AGO-binding platforms are intrinsically disordered, contain tandem repeat arrays, and have weak sequence conservation even between close relatives. These characteristics make it difficult to identify and perform evolutionary analysis of these regions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28607805/simplified-microsatellite-instability-detection-protocol-provides-equivalent-sensitivity-to-robust-detection-strategies-in-lynch-syndrome-patients
#12
Hadi Babaei, Mehrdad Zeinalian, Mohammad Hassan Emami, Mortaza Hashemzadeh, Najmeh Farahani, Rasoul Salehi
OBJECTIVE: : Germline mutations in mismatch repair (MMR) genes cause Lynch syndrome (LS). LS is an inherited disease, and an important consequence of MMR deficiency is microsatellite instability (MSI) phenotype. MSI phenotype influences the efficacy of 5 fluorouracil (5-FU) chemotherapy. Reproducible, cost effective, and easy to perform laboratory tests are required to include MSI detection in routine laboratory practice. Evaluation of CAT25 as monomorphic short tandem repeat sequence enables CAT25 to be an efficient screening tool among hereditary nonpolyposis colorectal cancer (HNPCC) patients compared with other methods used currently...
May 2017: Cancer Biology & Medicine
https://www.readbyqxmd.com/read/28605651/fast-str-allele-identification-with-strait-razor-3-0
#13
August E Woerner, Jonathan L King, Bruce Budowle
The short tandem repeat allele identification tool (STRait Razor), a program used to characterize the haplotypes of short tandem repeats (STRs) in massively parallel sequencing (MPS) data, was redesigned. STRait Razor v3.0 performs ∼660× faster allele identification than its previous version (v2s), a speedup that is largely due to a novel indexing strategy used to perform "fuzzy" (approximate) string matching of anchor sequences. Written in a portable compiled language, C++, STRait Razor v3.0 functions on all major operating systems including Microsoft Windows, and it has cross-platform multithreading support...
June 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28603070/clinical-utility-of-quantitative-pcr-for-chimerism-and-engraftment-monitoring-after-allogeneic-stem-cell-transplantation-for-hematologic-malignancies
#14
Müberra Ahci, Karin Stempelmann, Ulrike Buttkereit, Pietro Crivello, Mirko Trilling, Andreas Heinold, Nina Kristin Steckel, Michael Koldehoff, Peter A Horn, Dietrich W Beelen, Katharina Fleischhauer
Although quantitative PCR (qPCR) has been explored for chimerism monitoring after allogeneic stem cell transplantation (SCT), evidence regarding its clinical utility compared to standard short tandem repeat (STR) is still limited. We retrospectively studied commercial qPCR and STR chimerism with respective positivity thresholds of 0.1% and 1%, in 359 peripheral blood (PB) and 95 bone marrow (BM) samples from 30 adult patients after first HLA-matched SCT for myeloid malignancies or acute lymphatic leukemia. Concordance between the two methods was 79...
June 8, 2017: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/28600828/allogeneic-mscs-and-recycled-autologous-chondrons-mixed-in-a-one-stage-cartilage-cell-transplantion-a-first-in-man-trial-in-35-patients
#15
Tommy S de Windt, Lucienne A Vonk, Ineke C M Slaper-Cortenbach, Razmara Nizak, Mattie H P van Rijen, Daniel B F Saris
MSCs are known as multipotent mesenchymal stem cells that have been found capable of differentiating into various lineages including cartilage. However, recent studies suggest MSCs are pericytes that stimulate tissue repair through trophic signaling. Aimed at articular cartilage repair in an one-stage cell transplantation, this study provides first clinical evidence that MSCs stimulate autologous cartilage repair in the knee without engrafting in the host tissue. A phase I (first-in-man) clinical trial studied the one-stage application of allogeneic MSCs mixed with 10% or 20% recycled defect derived autologous chondrons for the treatment of cartilage defects in 35 patients...
June 10, 2017: Stem Cells
https://www.readbyqxmd.com/read/28600436/accurate-quantification-of-chromosomal-lesions-via-short-tandem-repeat-analysis-using-minimal-amounts-of-dna
#16
Johann-Christoph Jann, Daniel Nowak, Florian Nolte, Stephanie Fey, Verena Nowak, Julia Obländer, Jovita Pressler, Iris Palme, Christina Xanthopoulos, Alice Fabarius, Uwe Platzbecker, Aristoteles Giagounidis, Katharina Götze, Anne Letsch, Detlef Haase, Richard Schlenk, Gesine Bug, Michael Lübbert, Arnold Ganser, Ulrich Germing, Claudia Haferlach, Wolf-Karsten Hofmann, Maximilian Mossner
BACKGROUND: Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings...
June 9, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28600257/search-for-more-effective-microsatellite-markers-for-forensics-with-next-generation-sequencing
#17
Bowen Tan, Zicheng Zhao, Zhe Zhang, Shengbin Li, Shuai Cheng Li
Published by the Combined DNA Index System (CODIS) program of the Federal Bureau of Investigation (FBI) in 1997, the 13 core short tandem repeat (STR) loci are widely adopted as genetic markers in forensic applications, e.g., identity testing and paternity testing. However, these loci may be biased and suffer from reduced sensitivities towards specific population groups. In addition, the rapid growth of entries in forensic databases raises the chance of random hits, which can cause false recognitions of criminal suspects...
June 7, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28594853/the-unexpected-co-occurrence-of-grn-and-mapt-p-a152t-in-basque-families-clinical-and-pathological-characteristics
#18
Fermin Moreno, Begoña Indakoetxea, Myriam Barandiaran, María Cristina Caballero, Ana Gorostidi, Francesc Calafell, Alazne Gabilondo, Mikel Tainta, Miren Zulaica, José F Martí Massó, Adolfo López de Munain, Pascual Sánchez-Juan, Suzee E Lee
BACKGROUND: The co-occurrence of the c.709-1G>A GRN mutation and the p.A152T MAPT variant has been identified in 18 Basque families affected by frontotemporal dementia (FTD). We aimed to investigate the influence of the p.A152T MAPT variant on the clinical and neuropathological features of these Basque GRN families. METHODS AND FINDINGS: We compared clinical characteristics of 14 patients who carried the c.709-1G>A GRN mutation (GRN+/A152T-) with 21 patients who carried both the c...
2017: PloS One
https://www.readbyqxmd.com/read/28589897/phylogenic-analysis-and-forensic-genetic-characterization-of-chinese-uyghur-group-via-autosomal-multi-str-markers
#19
Xiaoye Jin, Yuanyuan Wei, Jiangang Chen, Tingting Kong, Yuling Mu, Yuxin Guo, Qian Dong, Tong Xie, Haotian Meng, Meng Zhang, Jianfei Li, Xiaopeng Li, Bofeng Zhu
We investigated the allelic frequencies and forensic descriptive parameters of 23 autosomal short tandem repeat loci in a randomly selected sample of 1218 unrelated healthy Uyghur individuals residing in the Xinjiang Uyghur Autonomous Region, northwest China. A total of 281 alleles at these loci were identified and their corresponding allelic frequencies ranged from 0.0004 to 0.5390. The combined match probability and combined probability of exclusion of all loci were 5.192 × 10-29 and 0.9999999996594, respectively...
May 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28589562/the-complete-genome-sequence-of-exiguobacterium-arabatum-w-01-reveals-potential-probiotic-functions
#20
Meinan Cong, Qingling Jiang, Xiaojin Xu, Lixing Huang, Yongquan Su, Qingpi Yan
Shrimp is extensively cultured worldwide. Shrimp farming is suffering from a variety of diseases. Probiotics are considered to be one of the effective methods to prevent and cure shrimp diseases. Exiguobacterium arabatum W-01, a gram-positive and orange-pigmented bacterium, was isolated from the intestine of a healthy Penaeus vannamei specimen. Whole-genome sequencing revealed a genome of 2,914,854 bp, with 48.02% GC content. In total, 3,083 open reading frames (ORFs) were identified, with an average length of 843...
June 6, 2017: MicrobiologyOpen
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