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https://www.readbyqxmd.com/read/27919619/microsatellite-polymorphism-located-immediately-upstream-of-the-phosphatidylinositol-glycan-class-k-gene-pigk-affects-its-expression-which-correlates-with-tyrosinase-activity-in-human-melanocytes
#1
Ken Okamura, Masahiro Hayashi, Yuko Abe, Yuta Araki, Yutaka Hozumi, Tamio Suzuki
BACKGROUND: Glycosylphosphatidylinositol (GPI) acts as a membrane anchor and a post-translational modifier for more than 150 proteins (called GPI-anchored proteins: GPI-APs). However, little study has been done to explore the role of GPI-APs in melanocytes. METHODS: The relationship between the mRNA expression of the genes which play essential roles in GPI anchoring system [phosphatidylinositol glycan, class A, and class K gene (PIGA, PIGK)] and melanogenesis-related genes (MITF, TYRP1, TYRP2, and TYR) as well as DOPA oxidase activities were evaluated in 13 different normal human epidermal melanocytes (NHEMs)...
November 27, 2016: Journal of Dermatological Science
https://www.readbyqxmd.com/read/27916431/2016-scct-str-guidelines-for-coronary-artery-calcium-scoring-of-noncontrast-noncardiac-chest-ct-scans-a-report-of-the-society-of-cardiovascular-computed-tomography-and-society-of-thoracic-radiology
#2
Harvey S Hecht, Paul Cronin, Michael J Blaha, Matthew J Budoff, Ella A Kazerooni, Jagat Narula, David Yankelevitz, Suhny Abbara
The Society of Cardiovascular Computed Tomography (SCCT) and the Society of Thoracic Radiology (STR) have jointly produced this document. Experts in this subject have been selected from both organizations to examine subject-specific data and write this guideline in partnership. A formal literature review, weighing the strength of evidence has been performed. When available, information from studies on cost was considered. Computed tomography (CT) acquisition, CAC scoring methodologies and clinical outcomes are the primary basis for the recommendations in this guideline...
November 10, 2016: Journal of Cardiovascular Computed Tomography
https://www.readbyqxmd.com/read/27914554/comparative-performance-of-ampflstr%C3%A2-identifiler%C3%A2-plus-pcr-amplification-kit-and-qiagen%C3%A2-investigator%C3%A2-idplex-plus-kit
#3
Dalad Mattayat, Thitika Kitpipit, Sukanya Phetpeng, Watee Asawutmangkul, Phuvadol Thanakiatkrai
Many forensic STR kits are currently available in the market. The AmpFLSTR® Identifiler® Plus kit, which targets 15 STRs, is commonly used worldwide. The Thai forensic DNA community is built around it in terms of instrument, databases, and interpretation. QIAGEN's IDplex Plus kit targets the same loci, but the PCR cycling time is shorter by about 90min. A direct comparison that assesses forensic parameters and applicability to casework between the two kits has never been carried out. In this study, we performed a direct comparison between the two kits using serial dilutions of two control DNA samples and 60 randomly selected casework samples, including samples taken from improvised explosive devices and terrorist raids...
December 2016: Science & Justice: Journal of the Forensic Science Society
https://www.readbyqxmd.com/read/27914278/fdstools-a-software-package-for-analysis-of-massively-parallel-sequencing-data-with-the-ability-to-recognise-and-correct-str-stutter-and-other-pcr-or-sequencing-noise
#4
Jerry Hoogenboom, Kristiaan J van der Gaag, Rick H de Leeuw, Titia Sijen, Peter de Knijff, Jeroen F J Laros
Massively parallel sequencing (MPS) is on the advent of a broad scale application in forensic research and casework. The improved capabilities to analyse evidentiary traces representing unbalanced mixtures is often mentioned as one of the major advantages of this technique. However, most of the available software packages that analyse forensic short tandem repeat (STR) sequencing data are not well suited for high throughput analysis of such mixed traces. The largest challenge is the presence of stutter artefacts in STR amplifications, which are not readily discerned from minor contributions...
November 27, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27912743/str-realigner-a-realignment-method-for-short-tandem-repeat-regions
#5
Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori, Masao Nagasaki
BACKGROUND: In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27910883/the-mechanism-of-transactivation-regulation-due-to-polymorphic-short-tandem-repeats-strs-using-igf1-promoter-as-a-model
#6
Holly Y Chen, Suk Ling Ma, Wei Huang, Lindan Ji, Vincent H K Leung, Honglin Jiang, Xiaoqiang Yao, Nelson L S Tang
Functional short tandem repeats (STR) are polymorphic in the population, and the number of repeats regulates the expression of nearby genes (known as expression STR, eSTR). STR in IGF1 promoter has been extensively studied for its association with IGF1 concentration in blood and various clinical traits and represents an important eSTR. We previously used an in-vitro luciferase reporter model to examine the interaction between STRs and SNPs in IGF1 promoter. Here, we further explored the mechanism how the number of repeats of the STR regulates gene transcription...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27909867/developmental-validation-of-the-homygene19-14y-system
#7
Weian Du, Ling Chen, Hong Liu, Pingming Qiu, Fayuan Li, Jing Gao, Yu Zhou, Bangchao Wang, Chao Liu
The HomyGene19+14Y System (HG19+14Y) is a PCR-based amplification kit that enables typing of 18 autosomal short tandem repeat (STR) loci (i.e., CSF1PO, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, Penta E, TPOX, TH01, vWA), 14 widely used Y chromosome STR (Y-STR) loci (Y_GATA_H4, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439, DYS456, DYS458, DYS635), and amelogenin. This multiplex system was designed for the simultaneous analysis of amelogenin-Y allele mutation, single-source searches, kinship (including familial searching), mixture profiles, international data sharing, and other forensic applications...
December 1, 2016: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/27908490/y-chromosomal-haplogroup-distribution-in-the-tuzla-canton-of-bosnia-and-herzegovina-a-concordance-study-using-four-different-in-silico-assignment-algorithms-based-on-y-str-data
#8
S Dogan, N Babic, C Gurkan, A Goksu, D Marjanovic, V Hadziavdic
Y-chromosomal haplogroups are sets of ancestrally related paternal lineages, traditionally assigned by the use of Y-chromosomal single nucleotide polymorphism (Y-SNP) markers. An increasingly popular and a less labor-intensive alternative approach has been Y-chromosomal haplogroup assignment based on already available Y-STR data using a variety of different algorithms. In the present study, such in silico haplogroup assignments were made based on 23-loci Y-STR data for 100 unrelated male individuals from the Tuzla Canton, Bosnia and Herzegovina (B&H) using the following four different algorithms: Whit Athey's Haplogroup Predictor, Jim Cullen's World Haplogroup & Haplogroup-I Subclade Predictor, Vadim Urasin's YPredictor and the NevGen Y-DNA Haplogroup Predictor...
November 1, 2016: Homo: Internationale Zeitschrift Für die Vergleichende Forschung Am Menschen
https://www.readbyqxmd.com/read/27907810/prediction-of-autosomal-str-typing-success-in-ancient-and-second-world-war-bone-samples
#9
Irena Zupanič Pajnič, Tomaž Zupanc, Jože Balažic, Živa Miriam Geršak, Oliver Stojković, Ivan Skadrić, Matija Črešnar
Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded...
November 19, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27907169/crystal-structure-of-chitinase-chiw-from-paenibacillus-sp-str-fpu-7-reveals-a-novel-type-of-bacterial-cell-surface-expressed-multi-modular-enzyme-machinery
#10
Takafumi Itoh, Takao Hibi, Fumiko Suzuki, Ikumi Sugimoto, Akihiro Fujiwara, Koji Inaka, Hiroaki Tanaka, Kazunori Ohta, Yutaka Fujii, Akira Taketo, Hisashi Kimoto
The Gram-positive bacterium Paenibacillus sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 Å resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed β-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st β/α-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd β/α-barrel catalytic domain (GH-18)...
2016: PloS One
https://www.readbyqxmd.com/read/27905141/first-case-of-sterility-associated-with-sex-chromosomal-abnormalities-in-a-jenny
#11
J Dorado, G Anaya, M Bugno-Poniewierska, A Molina, A Mendez-Sanchez, I Ortiz, M Moreno-Millán, M Hidalgo, P Peral García, S Demyda-Peyrás
Chromosomal abnormalities are one of the main causes of genetic infertility in horses. Currently, their detection rate is rising due to the use of new diagnostic tools employing molecular markers linked to the sex chromosome pair. Despite genetic similarities, there are no previous reports of sterility associated with chromosomal abnormalities in the domestic donkey (Equus asinus). Hereby, we determined the presence of a chromosomal mosaicism in a female donkey with reproductive problems using molecular methodologies developed for horses...
December 1, 2016: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/27903261/discrete-phenotypes-are-not-underpinned-by-genome-wide-genetic-differentiation-in-the-squat-lobster-munida-gregaria-crustacea-decapoda-munididae-a-multi-marker-study-covering-the-patagonian-shelf
#12
Chen Wang, Shobhit Agrawal, Jürgen Laudien, Vreni Häussermann, Christoph Held
BACKGROUND: DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27900418/rapid-microfluidic-analysis-of-a-y-str-multiplex-for-screening-of-forensic-samples
#13
Georgiana Gibson-Daw, Patricia Albani, Marcus Gassmann, Bruce McCord
In this paper, we demonstrate a rapid analysis procedure for use with a small set of rapidly mutating Y chromosomal short tandem repeat (Y-STR) loci that combines both rapid polymerase chain reaction (PCR) and microfluidic separation elements. The procedure involves a high-speed polymerase and a rapid cycling protocol to permit PCR amplification in 16 min. The resultant amplified sample is next analysed using a short 1.8-cm microfluidic electrophoresis system that permits a four-locus Y-STR genotype to be produced in 80 s...
November 30, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27899851/cutoff-value-of-admission-n-terminal-pro-brain-natriuretic-peptide-which-predicts-poor-myocardial-perfusion-after-primary-percutaneous-coronary-intervention-for-st-segment-elevation-myocardial-infarction
#14
Khairy Abdel-Dayem, Inas I Eweda, Ashraf El-Sherbiny, Marc O Dimitry, Wail Nammas
BACKGROUND: We explored the value of admission levels of N-terminal pro-brain natriuretic peptide (NTProBNP) that best predicts poor myocardial tissue perfusion following primary percutaneous coronary intervention (PPCI) in patients admitted with acute ST-segment-elevation myocardial infarction (STEMI). METHODS: We enrolled 90 consecutive patients admitted with acute STEMI who underwent PPCI and achieved post-procedural TIMI flow grade 3 in the infarct-related artery...
November 2016: Acta Cardiologica Sinica
https://www.readbyqxmd.com/read/27898725/spatially-explicit-models-to-investigate-geographic-patterns-in-the-distribution-of-forensic-strs-application-to-the-north-eastern-mediterranean
#15
Francesco Messina, Andrea Finocchio, Nejat Akar, Aphrodite Loutradis, Emmanuel I Michalodimitrakis, Radim Brdicka, Carla Jodice, Andrea Novelletto
Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies...
2016: PloS One
https://www.readbyqxmd.com/read/27895910/proteomic-identification-of-cryostress-in-epididymal-spermatozoa
#16
Sung Jae Yoon, Md Saidur Rahman, Woo Sung Kwon, Do Yeal Ryu, Yoo Jin Park, Myung Geol Pang
BACKGROUND: Cryopreservation of epididymal spermatozoa is important in cases in which it is not possible to collect semen using normal methods, as the sudden death of an animal or a catastrophic injury. However, the freezing and thawing processes cause stress to spermatozoa, including cold shock, osmotic damage, and ice crystal formation, thereby reducing sperm quality. We assessed the motility (%), motion kinematics, capacitation status, and viability of spermatozoa using computer-assisted sperm analysis and Hoechst 33258/chlortetracycline fluorescence staining...
2016: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/27895624/visualizing-evolutionary-relationships-of-multidomain-proteins-an-example-from-receiver-rec-domains-of-sensor-histidine-kinases-in-the-candidatus-maribeggiatoa-str-orange-guaymas-draft-genome
#17
Barbara J MacGregor
For multidomain proteins, evolutionary changes may occur at the domain as well as the whole-protein level. An example is presented here, with suggestions for how such complicated relationships might be visualized. Earlier analysis of the Candidatus Maribeggiatoa str. Orange Guaymas (BOGUAY; Gammaproteobacteria) single-filament draft genome found evidence of gene exchange with the phylogenetically distant Cyanobacteria, particularly for sensory and signal transduction proteins. Because these are modular proteins, known to undergo frequent duplication, domain swapping, and horizontal gene transfer, a single domain was chosen for analysis...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27895236/a-review-of-single-tablet-regimens-for-the-treatment-of-hiv-1-infection
#18
REVIEW
Jamielynn C Sebaaly, Denise Kelley
OBJECTIVE: To review the pharmacokinetics, safety, drug-drug interactions, and advantages and disadvantages of currently available single-tablet regimens (STRs) for HIV-1 infection. DATA SOURCES: A search using PubMed was conducted (up to September 2016) using the following keywords: single tablet regimen AND HIV Additionally, a PubMed search was conducted for each individual STR using the generic names of the agents. Articles were evaluated for content, and additional references were identified from a review of literature citations...
November 27, 2016: Annals of Pharmacotherapy
https://www.readbyqxmd.com/read/27891181/whole-genome-sequencing-and-comparative-genomic-analysis-of-escherichia-coli-o91-strains-isolated-from-symptomatic-and-asymptomatic-human-carriers
#19
Taesoo Kwon, Young-Seok Bak, Young-Hee Jung, Young-Bin Yu, Jong Tae Choi, Cheorl-Ho Kim, Jung-Beom Kim, Won Kim, Seung-Hak Cho
BACKGROUND: The Shiga toxin-producing Escherichia coli (STEC) O91:H21 strains NCCP15736 and NCCP15737 were isolated during a single outbreak in Korea, NCCP15736 from a symptomatic carrier and NCCP15737 from an asymptomatic carrier. To investigate genomic differences between the two strains, we performed whole-genome sequencing of both strains and conducted a comparative genomic analysis. RESULTS: Using the Illumina HiSeq 2000 platform and Rapid Annotation using the Subsystem Technology (RAST) server, whole-genome sequences of NCCP15736 and NCCP15737 were obtained and annotated...
2016: Gut Pathogens
https://www.readbyqxmd.com/read/27890109/ascorbic-acid-and-vitamin-c-containing-beverages-delay-the-leucomalachite-green-reaction-to-detect-latent-bloodstains
#20
Haeyong Lee, Myung Jin Park, Seol Hee Sun, Dong-Ho Choi, Yang-Han Lee, Ki-Won Park, Byung Won Chun
The leucomalachite green (LMG) test is one of catalytic tests for the detection of latent bloodstains and generally used in forensic field because of convenience and cost/time-effectiveness. However, contamination of latent bloodstains at crime scenes can interfere with the LMG reaction, resulting in false-negative or false-positive decisions. Herein, we examined if ascorbic acid and vitamin C (l-ascorbic acid or ascorbate)-containing beverages affect the LMG reaction. Ascorbic acid showed the inhibitory activities on the LMG reaction in a dose-dependent manner...
November 2016: Legal Medicine
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