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https://www.readbyqxmd.com/read/29679929/a-phylogenetic-framework-facilitates-y-str-variant-discovery-and-classification-via-massively-parallel-sequencing
#1
Tunde I Huszar, Mark A Jobling, Jon H Wetton
Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega's prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing...
April 12, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29679839/xenon-detection-in-human-blood-analytical-validation-by-accuracy-profile-and-identification-of-critical-storage-parameters
#2
Cécile Frampas, Julia Ney, Mark Coburn, Marc Augsburger, Vincent Varlet
Xenon is a rare, mostly inert, noble gas that has applications in a wide range of fields, including medicine. Xenon acts on the human body as a useful organ-protective and anesthetic agent and has also been previously studied for potential applications in fields such as optics, aerospace and medical imaging. Recently, it was discovered that xenon can boost erythropoietin production, and it has been used as a performance-enhancing agent in international sports competitions such as the Sochi Olympic Games. Therefore, screening methods to detect the misuse of xenon by analysis of biological samples and to monitor anesthesia kinetics and efficiency are being investigated...
April 13, 2018: Journal of Forensic and Legal Medicine
https://www.readbyqxmd.com/read/29679786/simultaneous-analysis-of-historical-emerging-and-novel-brominated-flame-retardants-in-food-and-feed-using-a-common-extraction-and-purification-method
#3
Emmanuelle Bichon, Ingrid Guiffard, Anaïs Vénisseau, Elodie Lesquin, Vincent Vaccher, Philippe Marchand, Bruno Le Bizec
Brominated Flame Retardants (BFRs) are still widely used for industrial purposes. These contaminants may enter the food chain where they mainly occur in food of animal origin. The aim of our work was to provide a unique method able to quantify the widest range of BFRs in feed and food items. After freeze-drying and grinding, a pressurized liquid extraction was carried out. The extract was purified on acidified silica, Florisil® and carbon columns, the four separated fractions were analyzed by gas and liquid chromatography coupled to high resolution and tandem mass spectrometry...
April 13, 2018: Chemosphere
https://www.readbyqxmd.com/read/29679754/serum-25-hydroxyvitamin-d-and-breast-cancer-risk-by-pathological-subtype-mcc-spain
#4
Virginia Lope, Adela Castelló, Antonio Mena-Bravo, Pilar Amiano, Nuria Aragonés, Tania Fernández-Villa, Marcela Guevara, Trinidad Dierssen-Sotos, Guillermo Fernandez-Tardón, Gemma Castaño-Vinyals, Rafael Marcos-Gragera, Víctor Moreno, Dolores Salas-Trejo, Marian Diaz-Santos, Madalen Oribe, Isabel Romieu, Manolis Kogevinas, Feliciano Priego-Capote, Beatriz Pérez-Gómez, Marina Pollán
Epidemiologic evidence on the association between vitamin D and breast cancer is still inconclusive. This study analyzes the association between serum 25-hydroxyvitamin D (25(OH)D) and breast cancer risk by pathologic subtype, stage at diagnosis and specific breast cancer risk factors. We conducted a population-based multicase-control study where 546 histologically-confirmed breast cancer cases and 558 population controls, frequently matched by geographic area, age and body mass index, were recruited in 12 Spanish provinces (MCC-Spain)...
April 18, 2018: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29679555/mass-spectrometric-measurement-of-urinary-kynurenine-to-tryptophan-ratio-in-children-with-and-without-urinary-tract-infection
#5
Melanie L Yarbrough, Kelleigh E Briden, John V Mitsios, Annette L Weindel, Cindy M Terrill, David A Hunstad, Dennis J Dietzen
BACKGROUND: Indoleamine-2,3-dioxygenase (IDO) catalyzes the first step of tryptophan (Trp) catabolism, yielding kynurenine (Kyn) metabolites. The kynurenine-to-tryptophan (K/T) ratio is used as a surrogate for biological IDO enzyme activity. IDO expression is increased during Escherichia coli urinary tract infection (UTI). Thus, our objective was to develop a method for measurement of Kyn/Trp ratio in human blood and urine and evaluate its use as a biomarker of UTI. METHODS: A mass spectrometric method was developed to measure Trp and Kyn in serum and urine specimens...
April 18, 2018: Clinical Biochemistry
https://www.readbyqxmd.com/read/29679499/quantification-of-metronidazole-in-healthy-subjects-feces-using-a-lc-ms-ms-method
#6
Pravin G Vanol, Mallika Sanyal, Priyanka A Shah, Pranav S Shrivastav
A highly selective and sensitive liquid chromatography-tandem mass spectrometry (LC MS/MS) method is developed for the quantification of metronidazole (MTZ) in human feces. The analyte was recovered from feces after liquid-liquid extraction with ethyl acetate and separated on Waters Symmetry® C18 (100 × 4.6 mm, 5 μm) column using 0.1 % formic acid in water and acetonitrile (40:60, v/v) as the mobile phase. A stable-deuterated internal standard metronidazole-d4 (MTZ-d4) was used in the study. Mass analysis was performed on a triple quadrupole mass spectrometer in the positive electrospray ionization mode...
April 21, 2018: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/29679453/simultaneous-analysis-of-multiple-urinary-biomarkers-for-the-evaluation-of-oxidative-stress-by-automated-on-line-in-tube-solid-phase-microextraction-coupled-with-negative-positive-ion-switching-mode-lc-ms-ms
#7
Akihiro Saito, Mariko Hamano, Hiroyuki Kataoka
This study described an automated on-line method for the simultaneous determination of 8-isoprostane, 8-hydroxy-2'-deoxyguanosine, and 3-nitro-l-tyrosine in human urine. The method involves in-tube solid-phase microextraction using a Carboxen 1006 PLOT capillary column as an extraction device, followed by liquid chromatography with tandem mass spectrometry using a CX column and detection in the negative/positive switching ion-mode by multiple reaction monitoring. Using their stable isotope-labeled internal standards, each of these oxidative stress biomarkers showed good linearity from 0...
April 20, 2018: Journal of Separation Science
https://www.readbyqxmd.com/read/29679387/the-pharmacokinetics-and-pharmacodynamics-of-carfentanil-after-recreational-exposure-a-case-report
#8
Uvaraj Uddayasankar, Colin Lee, Curtis Oleschuk, Gregg Eschun, Robert E Ariano
Carfentanil and related fentanyl analogues have been linked to a number of overdose deaths from drug users in several cities across North America. Diagnosis of carfentanil exposure requires a very high index of clinical suspicion, especially because available laboratory narcotic screens do not detect this agent. We describe a 34-year-old male admitted with depressed level of consciousness and in respiratory failure after recreational exposure to a white powder later inferred to contain carfentanil. Urine and whole blood samples were obtained for conventional preliminary drug screen immunoassays for unknown exposures; in addition to utilizing high pressure liquid chromatography tandem mass spectrometry assay for quantification of carfentanil and its metabolite...
April 20, 2018: Pharmacotherapy
https://www.readbyqxmd.com/read/29679287/the-first-ms-cleavable-photo-thiol-reactive-cross-linker-for-protein-structural-studies
#9
Claudio Iacobucci, Christine Piotrowski, Anne Rehkamp, Christian H Ihling, Andrea Sinz
Cleavable cross-linkers are gaining increasing importance for chemical cross-linking/mass spectrometry (MS) as they permit a reliable and automated data analysis in structural studies of proteins and protein assemblies. Here, we introduce 1,3-diallylurea (DAU) as the first CID-MS/MS-cleavable, photo-thiol-reactive cross-linker. DAU is a commercially available, inexpensive reagent that efficiently undergoes an anti-Markovnikov hydrothiolation with cysteine residues in the presence of a radical initiator upon UV-A irradiation...
April 20, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29679266/changes-in-content-of-triterpenoids-and-polysaccharides-in-ganoderma-lingzhi-at-different-growth-stages
#10
Toshinori Nakagawa, Qinchang Zhu, Sonam Tamrakar, Yhiya Amen, Yasuhiro Mori, Hiroto Suhara, Shuhei Kaneko, Hiroko Kawashima, Kotaro Okuzono, Yoshiyuki Inoue, Koichiro Ohnuki, Kuniyoshi Shimizu
Ganoderma lingzhi is a traditional medicinal mushroom, and its extract contains many bioactive compounds. Triterpenoids and polysaccharides are the primary bioactive components that contribute to its medicinal properties. In this study, we quantified 18 triterpenoids, total triterpenoid content and total polysaccharide content in the ethanol and water extracts of G. lingzhi at different growth stages. Triterpenoids were quantified by liquid chromatograph-tandem mass spectrometry in the multiple-reaction-monitoring mode...
April 20, 2018: Journal of Natural Medicines
https://www.readbyqxmd.com/read/29678859/gsyellow-a-swiss-knife-tag-for-functional-protein-analysis-in-monocot-and-dicot-plants
#11
Nienke Besbrugge, Jelle Van Leene, Dominique Eeckhout, Bernard Cannoot, Shubhada R Kulkarni, Nancy De Winne, Geert Persiau, Eveline Van De Slijke, Michiel Bontinck, Stijn Aesaert, Francis Impens, Kris Gevaert, Daniel van Damme, Mieke Van Lijsebettens, Dirk Inze, Klaas Vandepoele, Hilde Nelissen, Geert De Jaeger
The ability to tag proteins has boosted the emergence of generic molecular methods for protein functional analysis. Fluorescent protein tags are used to visualize protein localization and affinity tags enable the mapping of molecular interactions by, for example, tandem affinity purification (TAP) or chromatin immunoprecipitation (ChIP). To apply these widely used molecular techniques on a single transgenic plant line, we developed a multifunctional TAP tag, named GSyellow, which combines the streptavidin-binding peptide (SBP) tag with citrine yellow fluorescent protein (cYFP)...
April 20, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29678717/a-tandem-mass-tag-tmt-proteomic-analysis-during-the-early-phase-of-experimental-pancreatitis-reveals-new-insights-in-the-disease-pathogenesis
#12
Violeta García-Hernández, Carmen Sánchez-Bernal, Domitille Schvartz, José J Calvo, Jean-Charles Sanchez, Jesús Sánchez-Yagüe
Changes in the protein expression occurring within the initiation phase of acute pancreatitis (AP) might be vital in the development of this complex disease. However, the exact mechanisms involved in the onset of AP remains elusive and most of our knowledge about the pathobiology of AP comes from animal models. We performed in a rat pancreatitic model a high-throughput shotgun proteomic profiling of the soluble and whole membrane fractions from the pancreas during the early phase of cerulein (Cer)-induced AP...
April 17, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29678600/when-a-new-technological-product-launching-fails-a-multi-method-approach-of-facial-recognition-and-e-wom-sentiment-analysis
#13
Dra Asunción Hernández-Fernández, Elísabet Mora, Dña María Isabel Vizcaíno Hernández
The dual aim of this research is, firstly, to analyze the physiological and unconscious emotional response of consumers to a new technological product and, secondly, link this emotional response to consumer conscious verbal reports of positive and negative product perceptions. In order to do this, biometrics and self-reported measures of emotional response are combined. On the one hand, a neuromarketing experiment based on the facial recognition of emotions of 10 subjects, when physical attributes and economic information of a technological product are exposed, shows the prevalence of the ambivalent emotion of surprise...
April 17, 2018: Physiology & Behavior
https://www.readbyqxmd.com/read/29678407/determination-of-nine-bisphenols-in-sewage-and-sludge-using-dummy-molecularly-imprinted-solid-phase-extraction-coupled-with-liquid-chromatography-tandem-mass-spectrometry
#14
Xiaoli Sun, Junyu Peng, Muhua Wang, Jincheng Wang, Chunlan Tang, Luoxing Yang, Hua Lei, Fang Li, Xueli Wang, Jiping Chen
This paper describes the determination of bisphenol A (BPA), bisphenol S (BPS), bisphenol F (BPF), bisphenol E (BPE), bisphenol B (BPB), bisphenol AF (BPAF), bisphenol AP (BPAP), bisphenol Z (BPZ) and tetrabromobisphenol A (TBBPA) in sewage and sludge samples. A highly class-selective dummy molecularly imprinted polymer was used for solid phase extraction (SPE) and clean-up of the samples. Bisphenols was quantified by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The developed method had acceptable recoveries (43...
April 3, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29678161/an-unusually-high-frequency-of-scad-deficiency-caused-by-two-pathogenic-variants-in-the-acads-gene-and-its-relationship-to-the-ethnic-structure-in-slovakia
#15
Jana Lisyová, Ján Chandoga, Petra Jungová, Marcel Repiský, Mária Knapková, Martina Machková, Svetozár Dluholucký, Darina Behúlová, Jana Šaligová, Ľudmila Potočňáková, Miroslava Lysinová, Daniel Böhmer
BACKGROUND: Short-chain acyl-CoA dehydrogenase deficiency (SCADD) represents a rare autosomal recessive inborn metabolic disorder of mitochondrial β-oxidation of monocarboxylic acids. Clinical symptoms can vary from a severe life-threatening condition to an asymptomatic state, reported in the majority of cases. Since the expansion of newborn screenings, more than three hundred probands were admitted for molecular-genetic analysis, most selected because of elevated values of C4-acylcarnitine detected in newborn screenings in Slovakia...
April 20, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29678149/comparative-mitochondrial-genomics-of-cryptophyte-algae-gene-shuffling-and-dynamic-mobile-genetic-elements
#16
Jong Im Kim, Hwan Su Yoon, Gangman Yi, Woongghi Shin, John M Archibald
BACKGROUND: Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. RESULTS: To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29677633/differences-in-the-bovine-milk-whey-proteome-between-early-pregnancy-and-the-estrous-cycle
#17
D Johnston, I Malo Estepa, H A Ebhardt, M A Crowe, M G Diskin
Current bovine pregnancy detection methods are not reliable until at least day 28 post artificial insemination (AI). The bovine estrous cycle is approximately 21 days; consequently, producers miss an opportunity to rebreed at the next estrous event. Therefore, commercial interest exists for the discovery of novel biomarkers of pregnancy which could reliably detect pregnancy status at or before day 21 of pregnancy. The objective of the present study was to use liquid chromatography tandem mass spectrometry (LC-MS/MS) to perform a global, label-free, proteomics study on (i) milk whey and (ii) extracellular vesicle (EV) enriched milk whey samples, from day 21 of pregnancy, compared with day 21 of the estrous cycle, in order to identify potential protein biomarkers of early pregnancy...
April 12, 2018: Theriogenology
https://www.readbyqxmd.com/read/29677481/mutation-analysis-of-short-tandem-repeats-in-a-population-sample-from-upper-silesia-southern-poland
#18
Kornelia Droździok, Jadwiga Kabiesz, Marcin Tomsia, Rafał Skowronek, Krzysztof Rębała
In paternity testing, DNA polymorphism analysis not only settles explicitly disputed paternity issue but also provides information on mutation frequencies in STR loci. In this study, insertion or deletion of one repetitive unit was observed in 38 of 32,391 meiotic transfers analysed in 953 paternity testing cases. Parentage samples from Upper Silesia (southern Poland) were examined in 2008-2014 with the use of three commercially available amplification kits: AmpFlSTR Identifiler (Applied Biosystems), PowerPlex 16 HS (Promega) and PowerPlex ESX 17 (Promega)...
April 1, 2018: Legal Medicine
https://www.readbyqxmd.com/read/29677216/plasma-metabolomic-biomarkers-accurately-classify-acute-mild-traumatic-brain-injury-from-controls
#19
Massimo S Fiandaca, Mark Mapstone, Amin Mahmoodi, Thomas Gross, Fabio Macciardi, Amrita K Cheema, Kian Merchant-Borna, Jeffrey Bazarian, Howard J Federoff
Past and recent attempts at devising objective biomarkers for traumatic brain injury (TBI) in both blood and cerebrospinal fluid have focused on abundance measures of time-dependent proteins. Similar independent determinants would be most welcome in diagnosing the most common form of TBI, mild TBI (mTBI), which remains difficult to define and confirm based solely on clinical criteria. There are currently no consensus diagnostic measures that objectively define individuals as having sustained an acute mTBI. Plasma metabolomic analyses have recently evolved to offer an alternative to proteomic analyses, offering an orthogonal diagnostic measure to what is currently available...
2018: PloS One
https://www.readbyqxmd.com/read/29677121/prophylactic-neuroprotection-of-total-glucosides-of-paeoniae-radix-alba-against-semen-strychni-induced-neurotoxicity-in-rats-suppressing-oxidative-stress-and-reducing-the-absorption-of-toxic-components
#20
Shujuan Li, Yanjie Chu, Ruowen Zhang, Linjia Sun, Xiaohui Chen
Strychnos alkaloids (SAs) are the main toxic constituents in Semen Strychni, a traditional Chinese medicine, which is known for its fatal neurotoxicity. Hence, the present study was carried out to evaluate the neurotoxicity induced by SAs and the pre-protective effects of the total glucosides of Paeoniae Radix Alba (TGP). An SA brain damage model was firstly established. The neurotoxicity induced by SAs and the pre-protective effects of TGP were confirmed by physical and behavioral testing, biochemical assay, and histological examination...
April 20, 2018: Nutrients
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