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short tandem repeats

Kimiko Aoki, Hiroyuki Tanaka, Makoto Ueki
When the tampering of a urine sample is suspected in doping control, personal identification of the sample needs to be determined by short tandem repeat (STR) analysis using DNA. We established a method for extracting DNA from urine samples stored at -20 °C without using any additives or procedures, which is consistent with how samples are required to be managed for doping control. The method, using the Puregene® Blood Core kit followed by NucleoSpin® gDNA Clean-up or NucleoSpin® gDNA Clean-up XS kit, does not need any special instrument and can provide a purified extract with high-quality DNA from up to 40 mL of urine suitable for STR analysis using an AmpFlSTR® Identifiler® PCR amplification kit...
October 24, 2016: Drug Testing and Analysis
Monica Dalva, Khadija El Jellas, Solrun J Steine, Bente B Johansson, Monika Ringdal, Janniche Torsvik, Heike Immervoll, Dag Hoem, Felix Laemmerhirt, Peter Simon, Markus M Lerch, Stefan Johansson, Pål R Njølstad, Frank U Weiss, Karianne Fjeld, Anders Molven
BACKGROUND/OBJECTIVES: We have recently described copy number variants (CNVs) of the human carboxyl-ester lipase (CEL) gene, including a recombined deletion allele (CEL-HYB) that is a genetic risk factor for chronic pancreatitis. Associations with pancreatic disease have also been reported for the variable number of tandem repeat (VNTR) region located in CEL exon 11. Here, we examined if CEL CNVs and VNTR length polymorphisms affect the risk for developing pancreatic cancer. METHODS: CEL CNVs and VNTR were genotyped in a German family with non-alcoholic chronic pancreatitis and pancreatic cancer, in 265 German and 197 Norwegian patients diagnosed with pancreatic adenocarcinoma, and in 882 controls...
October 11, 2016: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
Brandon L Thompson, Christopher Birch, Daniel A Nelson, Jingyi Li, Jacquelyn A DuVall, Delphine Le Roux, An-Chi Tsuei, Daniel L Mills, Brian E Root, James P Landers
Current conventional methods utilized for forensic DNA analysis are time consuming and labor-intensive requiring large and expensive equipment and instrumentation. While more portable Rapid DNA systems have been developed, introducing them to a working laboratory still necessitates a high cost of initiation followed by the recurrent cost of the devices. This has highlighted the need for an inexpensive, rapid and portable DNA analysis tool for human identification in a forensic setting. In order for an integrated DNA analysis system such as this to be realized, device operations must always be concluded by a rapid separation of short-tandem repeat (STR) DNA fragments...
October 21, 2016: Lab on a Chip
Jem Ma Ahn, Chang Ha Kim, Soon Ho Um, Kyung Mee Kim, Tae Hyung Kim, Sun Young Yim, Hyuk Soon Choi, Eun Sun Kim, Bora Keum, Yeon Seok Seo, Hyung Joon Yim, Yoon Tae Jeen, Hong Sik Lee, Hoon Jai Chun, Chang Duck Kim, Ho Sang Ryu
BACKGROUND AND AIM: In a recent study, microsatellite variations (GCA tandem repeats) in the promoter region of the (kidney-type) glutaminase gene were associated with the development of hepatic encephalopathy (HE) in Spanish patients with cirrhosis. The objective of this study was to validate the relation between microsatellite variations in the glutaminase promoter region and the development of overt HE in Korean patients with liver cirrhosis. METHODS: We performed a prospective cohort study of 154 cirrhotic patients who underwent a glutaminase microsatellite study without previous overt HE history at baseline...
October 17, 2016: Journal of Gastroenterology and Hepatology
Jennifer Weida, Avinash S Patil, Frank P Schubert, Gail Vance, Holli Drendel, Angela Reese, Stephen Dlouhy, Shaochun Bai, Men-Jean Lee
PURPOSE: The purpose of this study is to evaluate the incidence of maternal cell contamination (MCC) in the first few milliliters of amniotic fluid withdrawn during amniocentesis. METHODS: A prospective observational study was performed. The initial 2-3 ml of amniotic fluid withdrawn during amniocentesis was divided into direct analysis (uncultured) and cultured samples. A matching maternal buccal swab was obtained for MCC testing. MCC was determined by short-tandem repeat analysis...
October 17, 2016: Journal of Maternal-fetal & Neonatal Medicine
Zhizhen Qi, Yujun Cui, Qingwen Zhang, Ruifu Yang
This chapter summarized the taxonomy and typing works of Yersinia pestis since it's firstly identified in Hong Kong in 1894. Phenotyping methods that based on phenotypic characteristics, including biotyping, serotyping, antibiogram analysis, bacteriocin typing, phage typing, and plasmid typing, were firstly applied in classification of Y. pestis in subspecies level. And then, with the advancement of molecular biological technology, the methods based on outer membrane protein profiles, fatty acid composition, and bacterial mass fingerprinting were also used to identify the populations within Y...
2016: Advances in Experimental Medicine and Biology
Daisuke Hagiwara, Akira Watanabe, Katsuhiko Kamei, Gustavo H Goldman
Invasive aspergillosis is a life-threatening mycosis caused by the pathogenic fungus Aspergillus. The predominant causal species is Aspergillus fumigatus, and azole drugs are the treatment of choice. Azole drugs approved for clinical use include itraconazole, voriconazole, posaconazole, and the recently added isavuconazole. However, epidemiological research has indicated that the prevalence of azole-resistant A. fumigatus isolates has increased significantly over the last decade. What is worse is that azole-resistant strains are likely to have emerged not only in response to long-term drug treatment but also because of exposure to azole fungicides in the environment...
2016: Frontiers in Microbiology
F F Coelho, F K Marques, M S Gonçalves, V C O Almeida, E C C Mateo, A C S Ferreira
Approximately 10-15% of all pregnancies end in spontaneous abortions. Many factors can lead to embryonic loss; however, it has been well established that over 50% of all miscarriages result from chromosomal abnormalities, primarily aneuploidies (>96%). Identifying the cause of miscarriage can significantly reduce the psychological stress in women, and enable better genetic counseling for a future pregnancy. Quantitative fluorescent polymerase chain reaction (QF-PCR) has been previously used in the study of chromosomal abnormalities...
September 23, 2016: Genetics and Molecular Research: GMR
U R Pagel, R S Reis, V P Carvalho, E V W Santos, E Zandonade, I D Louro, F Paula
Short tandem repeats (STRs) are commonly used as genetic markers. The detection and analysis of STRs can be used to gather information on polymorphisms of interest to forensic geneticists. Denaturing polyacrylamide gel electrophoresis (PAGE) is an affordable method for the detection of minor sequence changes in DNA, while capillary electrophoresis (CE) is the gold standard for genotyping analysis. This appears to be the first study to directly compare data obtained using the two electrophoretic techniques. We analyzed genomic DNA from 209 individuals to compare genotyping results from seven Combined DNA Index System (CODIS) STR markers obtained by both techniques...
September 9, 2016: Genetics and Molecular Research: GMR
Rocio Garcia-Rubio, Horacio Gil, Maria Candida Monteiro, Teresa Pelaez, Emilia Mellado
Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed...
2016: PloS One
Qiu-Ling Liu, Li Xue, Wei-Wei Wu, Xin He, Kai-Yan Liu, Hu Zhao, De-Jian Lu
In this study, a panel of 13 STR loci locate on chromosome 3, 4, and 17 (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2404, D4S2364, AC001348A, AC001348B, D17S975, and D17S1294) were assessed for pairwise kinship analysis. Map distances between these STR loci ranged from 0.07 cM to 97.03 cM. The population genetic study of Chinese Han population showed that linkage disequilibrium exists in two clusters of closely linked markers (D4S2404-D4S2364 and D17S975-D17S1294), in which the recombination fractions were 0...
October 4, 2016: Electrophoresis
Nicole M M Novroski, Jonathan L King, Jennifer D Churchill, Lay Hong Seah, Bruce Budowle
Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups...
September 28, 2016: Forensic Science International. Genetics
Jiří Drábek, Michaela Smolíková, Ruslan Kalendar, Fernando A Lopes Pinto, Pavel Pavloušek, Karel Klepárník, Ivo Frébort
Although the analysis of length polymorphism at short tandem repeat (STR) loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and capillary electrophoresis with laser induced fluorescence, and tested it on 90 grape cultivars...
October 2, 2016: Electrophoresis
Frank R Wendt, David H Warshauer, Xiangpei Zeng, Jennifer D Churchill, Nicole M M Novroski, Bing Song, Jonathan L King, Bobby L LaRue, Bruce Budowle
Short tandem repeat (STR) loci are the traditional markers used for kinship, missing persons, and direct comparison human identity testing. These markers hold considerable value due to their highly polymorphic nature, amplicon size, and ability to be multiplexed. However, many STRs are still too large for use in analysis of highly degraded DNA. Small bi-allelic polymorphisms, such as insertions/deletions (INDELs), may be better suited for analyzing compromised samples, and their allele size differences are amenable to analysis by capillary electrophoresis...
September 20, 2016: Forensic Science International. Genetics
Kevin Bihan, Qin Lu, Manon Enjalbert, Maxime Apparuit, Olivier Langeron, Jean-Jacques Rouby, Christian Funck-Brentano, Noel Zahr
BACKGROUND: Colistin is a polypeptide antibiotic from the polymyxin E group used for the treatment of infections caused by multidrug resistant gram-negative bacteria. The main constituents, accounting for approximately 85% of this mixture, are colistinA (polymyxin E1) and colistin B (polymyxin E2). The aim of this study was to develop and validate new and fast methods of quantification of colistin A&B and its precursors (CMS A&B) by Liquid Chromatography-tandem Mass Spectrometry (UPLC-MS) in plasma and urine with short pre-treatment and run times...
September 27, 2016: Therapeutic Drug Monitoring
Jing Chen, Bingbing Xie, Yaran Yang, Meng Yang, Chao Liu, Yuexin Lv, Chuguang Chen, Xiu Liu, Xiangdong Fang, Huijuan Wu, Jiangwei Yan
BACKGROUND: Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential prerequisite in forensic application. AIM: In the present study, we obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. SUBJECTS AND METHODS: Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of Chinese Li ethnic group...
September 26, 2016: Annals of Human Biology
Joshua Elmore, Ora Dillon-Carter, John Partilla, Kayla N Ellefsen, Marta Concheiro, Masaki Suzuki, Kenner C Rice, Marilyn A Huestis, Michael H Baumann
3,4-Methylenedioxy-N-methylcathinone (methylone) is a new psychoactive substance and the β-keto analog of 3,4-methylenedioxy-N-methylamphetamine (MDMA). It is well established that MDMA metabolism produces bioactive metabolites. Here we tested the hypothesis that methylone metabolism in rats can form bioactive metabolites. First, we examined the pharmacokinetics (PK) of methylone and its metabolites after subcutaneous (sc) methylone administration (3, 6, 12 mg/kg) to male rats fitted with intravenous (iv) catheters for repeated blood sampling...
September 23, 2016: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
Danuta Piniewska, Marek Sanak, Marta Wojtas, Nina Polanska
Advances in forensic identification using molecular genetics are helpful in resolving some historical mysteries. The aim of this study was to confirm the authenticity of shrunken-head artifacts exhibited by two Polish museums. Shrunken heads, known as tsantsas, were headhunting trophies of South American Indians (Jivaroan). A special preparation preserved their hair and facial appearance. However, it was quite common to offer counterfeit shrunken heads of sloths or monkeys to collectors of curiosities. We sampled small skin specimens of four shrunken-head skin from the museum collection from Warsaw and Krakow, Poland...
September 18, 2016: International Journal of Legal Medicine
Terence J Colgan, Martin C Chang, Shabin Nanji, Elena Kolomietz
The diagnosis of partial hydatidiform mole (PM) is especially difficult early in gestation as the morphology of nonmolar abortus (NMA) may mimic PM. Molecular genotyping analysis can definitively identify diandric triploidy, the genetic basis for PM, whereas NMA cases show a biparental inheritance. This 4-year retrospective study sought to determine what proportion of NMA cases which were initially suspected as being PM was aneuploid, and whether this knowledge of aneuploidy status is clinically useful. Cases with atypical villous morphology on histopathology suggestive of PM were subjected to molecular genotyping...
September 15, 2016: International Journal of Gynecological Pathology
Somayeh Reiisi, Mohammad Amin Tabatabaiefar, Mohammad Hosein Sanati, Morteza Hashemzadeh Chaleshtori
OBJECTIVES: Non-syndromic sensorineural hearing loss (NSHL) is a common disorder affecting approximately 1 in 500 newborns. This type of hearing loss is extremely heterogeneous and includes over 100 loci. Mutations in the GJB2 gene have been implicated in about half of autosomal recessive non-syndromic hearing loss (ARNSHL) cases, making this the most common cause of ARNSHL. For the latter form of deafness, most frequent genes proposed include GJB2, SLC26A4, MYO15A, OTOF, and CDH23 worldwide...
July 2016: Iranian Journal of Basic Medical Sciences
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