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https://www.readbyqxmd.com/read/28408723/nucleic-acid-detection-with-crispr-cas13a-c2c2
#1
Jonathan S Gootenberg, Omar O Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J Dy, Julia Joung, Vanessa Verdine, Nina Donghia, Nichole M Daringer, Catherine A Freije, Cameron Myhrvold, Roby P Bhattacharyya, Jonathan Livny, Aviv Regev, Eugene V Koonin, Deborah T Hung, Pardis C Sabeti, James J Collins, Feng Zhang
Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided, RNA-targeting CRISPR effector Cas13a (previously known as C2c2) exhibits a "collateral effect" of promiscuous RNAse activity upon target recognition. We combine the collateral effect of Cas13a with isothermal amplification to establish a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity...
April 13, 2017: Science
https://www.readbyqxmd.com/read/28376236/inland-waters-and-their-role-in-the-carbon-cycle-of-alaska
#2
Sarah M Stackpoole, David E Butman, David W Clow, Kristine L Verdin, Benjamin V Gaglioti, Hélène Genet, Robert G Striegl
The magnitude of Alaska (AK) inland waters carbon (C) fluxes is likely to change in the future due to amplified climate warming impacts on the hydrology and biogeochemical processes in high latitude regions. Although current estimates of major aquatic C fluxes represent an essential baseline against which future change can be compared, a comprehensive assessment for AK has not yet been completed. To address this gap, we combined available datasets and applied consistent methodologies to estimate river lateral C export to the coast, river and lake carbon dioxide (CO2 ) and methane (CH4 ) emissions, and C burial in lakes for the six major hydrologic regions in the state...
April 4, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28195575/a-land-data-assimilation-system-for-sub-saharan-africa-food-and-water-security-applications
#3
Amy McNally, Kristi Arsenault, Sujay Kumar, Shraddhanand Shukla, Pete Peterson, Shugong Wang, Chris Funk, Christa D Peters-Lidard, James P Verdin
Seasonal agricultural drought monitoring systems, which rely on satellite remote sensing and land surface models (LSMs), are important for disaster risk reduction and famine early warning. These systems require the best available weather inputs, as well as a long-term historical record to contextualize current observations. This article introduces the Famine Early Warning Systems Network (FEWS NET) Land Data Assimilation System (FLDAS), a custom instance of the NASA Land Information System (LIS) framework. The FLDAS is routinely used to produce multi-model and multi-forcing estimates of hydro-climate states and fluxes over semi-arid, food insecure regions of Africa...
February 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28181251/iv-results-links-between-spatial-assembly-later-spatial-skills-and-concurrent-and-later-mathematical-skills
#4
Brian N Verdine, Roberta Michnick Golinkoff, Kathy Hirsh-Pasek, Nora S Newcombe
No abstract text is available yet for this article.
March 2017: Monographs of the Society for Research in Child Development
https://www.readbyqxmd.com/read/28181250/causal-inference-and-the-spatial-math-link-in-early-childhood
#5
Drew H Bailey
Verdine et al. (2017) present compelling evidence for a causal effect of spatial skills on children's mathematics achievement in early childhood. In additional analyses of the correlation matrix reported by Verdine et al., I present evidence that the spatial-math link is not merely an epiphenomenon of general cognitive demands of both tasks. However, the question of whether the link is due to a causal effect of spatial skills on mathematics skills, a causal effect of mathematics skills on spatial skills, or common factors influencing both during this developmental period is a more difficult one to answer...
March 2017: Monographs of the Society for Research in Child Development
https://www.readbyqxmd.com/read/28181249/v-results-individual-difference-factors-in-spatial-and-mathematical-skills
#6
Brian N Verdine, Roberta Michnick Golinkoff, Kathy Hirsh-Pasek, Nora S Newcombe
No abstract text is available yet for this article.
March 2017: Monographs of the Society for Research in Child Development
https://www.readbyqxmd.com/read/28181248/i-spatial-skills-their-development-and-their-links-to-mathematics
#7
Brian N Verdine, Roberta Michnick Golinkoff, Kathy Hirsh-Pasek, Nora S Newcombe
Understanding the development of spatial skills is important for promoting school readiness and improving overall success in STEM (science, technology, engineering, and mathematics) fields (e.g., Wai, Lubinski, Benbow, & Steiger, 2010). Children use their spatial skills to understand the world, including visualizing how objects fit together, and can practice them via spatial assembly activities (e.g., puzzles or blocks). These skills are incorporated into measures of overall intelligence and have been linked to success in subjects like mathematics (Mix & Cheng, 2012) and science (Pallrand & Seeber, 1984; Pribyl & Bodner, 1987)...
March 2017: Monographs of the Society for Research in Child Development
https://www.readbyqxmd.com/read/28181247/vi-discussion-and-implications-how-early-spatial-skills-predict-later-spatial-and-mathematical-skills
#8
Brian N Verdine, Roberta Michnick Golinkoff, Kathy Hirsh-Pasek, Nora S Newcombe
No abstract text is available yet for this article.
March 2017: Monographs of the Society for Research in Child Development
https://www.readbyqxmd.com/read/28181246/ii-methods-for-longitudinal-study-of-preschool-spatial-and-mathematical-skills
#9
Brian N Verdine, Roberta Michnick Golinkoff, Kathy Hirsh-Pasek, Nora S Newcombe
No abstract text is available yet for this article.
March 2017: Monographs of the Society for Research in Child Development
https://www.readbyqxmd.com/read/28181245/iii-results-considering-the-2-d-and-3-d-trials-of-the-tosa-separately-and-together
#10
Brian N Verdine, Roberta Michnick Golinkoff, Kathy Hirsh-Pasek, Nora S Newcombe
No abstract text is available yet for this article.
March 2017: Monographs of the Society for Research in Child Development
https://www.readbyqxmd.com/read/28130451/structural-basis-for-the-lesion-scanning-mechanism-of-the-muty-dna-glycosylase
#11
Lan Wang, Srinivas Chakravarthy, Gregory L Verdine
The highly mutagenic A:8-oxoguanine (oxoG) base pair is generated mainly by misreplication of the C:oxoG base pair, the oxidation product of the C:G base pair. The A:oxoG base pair is particularly insidious because neither base in it carries faithful information to direct the repair of the other. The bacterial MutY (MUTYH in humans) adenine DNA glycosylase is able to initiate the repair of A:oxoG by selectively cleaving the A base from the A:oxoG base pair. The difference between faithful repair and wreaking mutagenic havoc on the genome lies in the accurate discrimination between two structurally similar base pairs: A:oxoG and A:T...
March 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28076787/impdh2-is-an-intracellular-target-of-the-cyclophilin-a-and-sanglifehrin-a-complex
#12
Khian Hong Pua, Dylan T Stiles, Mathew E Sowa, Gregory L Verdine
Natural products have demonstrated utility in the clinic and can also act as probes to understand complex cellular pathways. Sanglifehrin A (SFA) is a mixed polyketide and non-ribosomal peptide synthase natural product with sub-nano-molar affinity for its receptor cyclophilin A (PPIA). It has been shown to behave in vitro as an immune suppressant. Here, we identify inosine-5'-monophosphate dehydrogenase 2 (IMPDH2) as an intracellular target of the PPIA-SFA binary complex. The formation of this ternary complex does not inhibit the enzymatic activity of IMPDH2...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28061412/nature-of-fly-ash-amendments-differently-influences-oxidative-stress-alleviation-in-four-forest-tree-species-and-metal-trace-element-phytostabilization-in-aged-contaminated-soil-a-long-term-field-experiment
#13
Sonia Labidi, Stéphane Firmin, Anthony Verdin, Géraldine Bidar, Frédéric Laruelle, Francis Douay, Pirouz Shirali, Joël Fontaine, Anissa Lounès-Hadj Sahraoui
Aided phytostabilization using coal fly ashes (CFAs) is an interesting technique to clean-up polluted soils and valorizing industrial wastes. In this context, our work aims to study the effect of two CFAs: silico-aluminous (CFA1) and sulfo-calcic (CFA2) ones, 10 years after their addition, on the phytostabilization of a highly Cd (cadmium), Pb (lead) and Zn (zinc) contaminated agricultural soil, with four forest tree species: Robinia pseudoacacia, Alnus glutinosa, Acer pseudoplatanus and Salix alba. To assess the effect of CFAs on trees, leaf fatty acid composition, malondialdehyde (MDA), oxidized and reduced glutathione contents ratio (GSSG: GSH), 8-hydroxy-2'-deoxyguanosine (8-OHdG), Peroxidase (PO) and Superoxide dismutase (SOD) activities were examined...
April 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/27978436/the-mtor-complex-controls-hiv-latency
#14
Emilie Besnard, Shweta Hakre, Martin Kampmann, Hyung W Lim, Nina N Hosmane, Alyssa Martin, Michael C Bassik, Erik Verschueren, Emilie Battivelli, Jonathan Chan, J Peter Svensson, Andrea Gramatica, Ryan J Conrad, Melanie Ott, Warner C Greene, Nevan J Krogan, Robert F Siliciano, Jonathan S Weissman, Eric Verdin
A population of CD4 T lymphocytes harboring latent HIV genomes can persist in patients on antiretroviral therapy, posing a barrier to HIV eradication. To examine cellular complexes controlling HIV latency, we conducted a genome-wide screen with a pooled ultracomplex shRNA library and in vitro system modeling HIV latency and identified the mTOR complex as a modulator of HIV latency. Knockdown of mTOR complex subunits or pharmacological inhibition of mTOR activity suppresses reversal of latency in various HIV-1 latency models and HIV-infected patient cells...
December 14, 2016: Cell Host & Microbe
https://www.readbyqxmd.com/read/27914859/fine-and-ultrafine-atmospheric-particulate-matter-at-a-multi-influenced-urban-site-physicochemical-characterization-mutagenicity-and-cytotoxicity
#15
Yann Landkocz, Frédéric Ledoux, Véronique André, Fabrice Cazier, Paul Genevray, Dorothée Dewaele, Perrine J Martin, Capucine Lepers, Anthony Verdin, Lucie Courcot, Saâd Boushina, François Sichel, Maurizio Gualtieri, Pirouz Shirali, Dominique Courcot, Sylvain Billet
Particulate Matter (PM) air pollution is one of the major concerns for environment and health. Understanding the heterogeneity and complexity of fine and ultrafine PM is a fundamental issue notably for the assessment of PM toxicological effects. The aim of this study was to evaluate mutagenicity and cytotoxicity of a multi-influenced urban site PM, with or without the ultrafine fraction. For this purpose, PM2.5-0.3 (PM with aerodynamic diameter ranging from 0.3 to 2.5 μm) and PM2.5 were collected in Dunkerque, a French coastal industrial city and were extensively characterized for their physico-chemical properties, including inorganic and organic species...
February 2017: Environmental Pollution
https://www.readbyqxmd.com/read/27843757/comparison-between-manual-and-automated-methods-for-ki-67-immunoexpression-quantification-in-ameloblastomas
#16
COMPARATIVE STUDY
Rogelio González-González, Nelly Molina-Frechero, Ramón G Carreón-Burciaga, Sandra López-Verdín, Carlos Robles-Bonilla, Vanesa Pereira-Prado, Ronell Bologna-Molina
Ameloblastoma is a common and unpredictable odontogenic tumor with high relapse rates. Several studies assessing the proliferative capacity of these neoplasms have been published, mainly using the protein Ki-67. Cell counts must be completed to determine the cell proliferation rate. Multiple methods have been developed for this purpose. The most widely used method is the labeling index, which has undergone changes over time to better facilitate cell counting. Here, we compared manual cell counting methods with automated cell counting (ImmunoRatio) to determine the relative effectiveness of these methods...
2016: Analytical Cellular Pathology (Amsterdam)
https://www.readbyqxmd.com/read/27815257/sirt3-blocks-myofibroblast-differentiation-and-pulmonary-fibrosis-by-preventing-mitochondrial-dna-damage
#17
Samik Bindu, Vinodkumar B Pillai, Abhinav Kanwal, Sadhana Samant, Gökhan M Mutlu, Eric Verdin, Nickolai Dulin, Mahesh P Gupta
Myofibroblast differentiation is a key process in the pathogenesis of fibrotic diseases. Transforming growth factor-β1 (TGF-β1) is a powerful inducer of myofibroblast differentiation and is implicated in pathogenesis of tissue fibrosis. This study was undertaken to determine the role of mitochondrial deacetylase SIRT3 in TGF-β1-induced myofibroblast differentiation in vitro and lung fibrosis in vivo. Treatment of human lung fibroblasts with TGF-β1 resulted in increased expression of fibrosis markers, smooth muscle α-actin (α-SMA), collagen-1, and fibronectin...
January 1, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/27801941/non-coding-variation-in-disorders-of-sex-development
#18
REVIEW
D Baetens, B B Mendonça, H Verdin, M Cools, E De Baere
Genetic studies in Disorders of Sex Development (DSD), representing a wide spectrum of developmental or functional conditions of the gonad, have mainly been oriented towards the coding genome. Application of genomic technologies, such as whole-exome sequencing, result in a molecular genetic diagnosis in ∼50% of cases with DSD. Many of the genes mutated in DSD encode transcription factors such as SRY, SOX9, NR5A1, and FOXL2, characterized by a strictly regulated spatiotemporal expression. Hence, it can be hypothesized that at least part of the missing genetic variation in DSD can be explained by non-coding mutations in regulatory elements that alter gene expression, either by reduced, mis- or overexpression of their target genes...
February 2017: Clinical Genetics
https://www.readbyqxmd.com/read/27748153/rectal-cancer-treatment-in-a-teaching-hospital
#19
Vanessa Verdin, Joseph Weerts, David Francart, Constant Jehaes, David Magis, Paul Magotteaux, Laurine Mattart, Benoit Monami, Christian Wahlen, Serge Markiewicz
BACKGROUND: Rectal adenocarcinomas surgery morbidity and mortality might be impaired by neoadjuvant therapy. We performed this retropsective study to be compared with the PROCARE study running afterwards. METHODS: We performed a retrospective study of 95 patients operated on for rectal adenocarcinoma in a single institution during the period of 2007-2009. We used logistic regression to estimate the relationship between possible predictive parameters of anastomotic leakage (AL)...
February 2017: Acta Chirurgica Belgica
https://www.readbyqxmd.com/read/27455144/associations-between-school-difficulties-and-health-related-problems-and-risky-behaviours-in-early-adolescence-a-cross-sectional-study-in-middle-school-adolescents-in-france
#20
Kénora Chau, Bernard Kabuth, Odile Causin-Brice, Yves Delacour, Catherine Richoux-Picard, Monique Verdin, Isabelle Armand, Nearkasen Chau
Health-related problems and risky behaviours (substance use) are frequent in adolescents, may alter their physical and mental capabilities, and may thus generate school absenteeism, low academic performance, and school dropout ideation. This study assessed their associations and the contribution of socioeconomic factors among 1559 middle-school adolescents (mean age 13.5+1.3) from north-eastern France. They completed a questionnaire including socioeconomic characteristics, health-related problems (poor physical health, psychological health, social relationships, and living environment) assessed with the World Health Organization's quality of life measure (score<25th percentile), risky behaviours, school absences during the present school year, last-trimester academic performance, and school dropout ideation...
October 30, 2016: Psychiatry Research
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