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https://www.readbyqxmd.com/read/28792927/genome-scale-activation-screen-identifies-a-lncrna-locus-regulating-a-gene-neighbourhood
#1
Julia Joung, Jesse M Engreitz, Silvana Konermann, Omar O Abudayyeh, Vanessa K Verdine, Francois Aguet, Jonathan S Gootenberg, Neville E Sanjana, Jason B Wright, Charles P Fulco, Yuen-Yi Tseng, Charles H Yoon, Jesse S Boehm, Eric S Lander, Feng Zhang
Mammalian genomes contain thousands of loci that transcribe long noncoding RNAs (lncRNAs), some of which are known to carry out critical roles in diverse cellular processes through a variety of mechanisms. Although some lncRNA loci encode RNAs that act non-locally (in trans), there is emerging evidence that many lncRNA loci act locally (in cis) to regulate the expression of nearby genes-for example, through functions of the lncRNA promoter, transcription, or transcript itself. Despite their potentially important roles, it remains challenging to identify functional lncRNA loci and distinguish among these and other mechanisms...
August 11, 2017: Nature
https://www.readbyqxmd.com/read/28758782/shape-up-an-eye-tracking-study-of-preschoolers-shape-name-processing-and-spatial-development
#2
Brian N Verdine, Ann Bunger, Angeliki Athanasopoulou, Roberta Michnick Golinkoff, Kathy Hirsh-Pasek
Learning the names of geometric shapes is at the intersection of early spatial, mathematical, and language skills, all important for school-readiness and predictors of later abilities in science, technology, engineering, and mathematics (STEM). We investigated whether socioeconomic status (SES) influenced children's processing of shape names and whether differences in processing were predictive of later spatial skills. Three-year-olds (N = 79) with mothers of varying education levels participated in an eye-tracking task that required them to look at named shapes...
July 31, 2017: Developmental Psychology
https://www.readbyqxmd.com/read/28751388/rhizospheric-microbiome-profiling-of-capsicum-annuum-l-cultivated-in-amended-soils-by-16s-and-internal-transcribed-spacer-2-rrna-amplicon-metagenome-sequencing
#3
Ali Asaff-Torres, Mariana Armendáriz-Ruiz, Manuel Kirchmayr, Raúl Rodríguez-Heredia, Marcos Orozco, Juan Carlos Mateos-Díaz, Luis Figueroa-Yáñez, Itzamná Baqueiro-Peña, Jorge Verdín
Rhizospheric microbiomes of Capsicum annuum L. cultivated either conventionally or amended with a synthetic microbial consortium or a root exudate inductor, were characterized by 16S/internal transcribed spacer 2 (ITS2) rRNA amplicon metagenome sequencing. The most abundant taxa found, although differently represented in each treatment, were Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, and Bacilli, as well as Chytridiomycetes and Mortierellomycotina.
July 27, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28749477/mapping-the-genomic-landscape-of-inherited-retinal-disease-genes-prioritizes-genes-prone-to-coding-and-noncoding-copy-number-variations
#4
Kristof Van Schil, Sarah Naessens, Stijn Van de Sompele, Marjolein Carron, Alexander Aslanidis, Caroline Van Cauwenbergh, Anja Kathrin Mayer, Mattias Van Heetvelde, Miriam Bauwens, Hannah Verdin, Frauke Coppieters, Michael E Greenberg, Marty G Yang, Marcus Karlstetter, Thomas Langmann, Katleen De Preter, Susanne Kohl, Timothy J Cherry, Bart P Leroy, Elfride De Baere
PurposePart of the hidden genetic variation in heterogeneous genetic conditions such as inherited retinal diseases (IRDs) can be explained by copy-number variations (CNVs). Here, we explored the genomic landscape of IRD genes listed in RetNet to identify and prioritize those genes susceptible to CNV formation.MethodsRetNet genes underwent an assessment of genomic features and of CNV occurrence in the Database of Genomic Variants and literature. CNVs identified in an IRD cohort were characterized using targeted locus amplification (TLA) on extracted genomic DNA...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28724936/an-engineered-protein-antagonist-of-k-ras-b-raf-interaction
#5
Monique J Kauke, Michael W Traxlmayr, Jillian A Parker, Jonathan D Kiefer, Ryan Knihtila, John McGee, Greg Verdine, Carla Mattos, K Dane Wittrup
Ras is at the hub of signal transduction pathways controlling cell proliferation and survival. Its mutants, present in about 30% of human cancers, are major drivers of oncogenesis and render tumors unresponsive to standard therapies. Here we report the engineering of a protein scaffold for preferential binding to K-Ras G12D. This is the first reported inhibitor to achieve nanomolar affinity while exhibiting specificity for mutant over wild type (WT) K-Ras. Crystal structures of the protein R11.1.6 in complex with K-Ras WT and K-Ras G12D offer insight into the structural basis for specificity, highlighting differences in the switch I conformation as the major defining element in the higher affinity interaction...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28669763/new-species-in-the-papaya-ringspot-virus-cluster-insights-into-the-evolution-of-the-prsv-lineage
#6
C Desbiez, C Wipf-Scheibel, P Millot, E Verdin, G Dafalla, H Lecoq
The "Papaya ringspot virus (PRSV) cluster" of cucurbit-infecting potyviruses contains five acknowledged species that have similar biological, serological and molecular properties. Additional data suggest there are other uncharacterized species from various locations in the world that likely belong to the PRSV cluster including a new PRSV-like virus reported from Sudan in 2003. Molecular and biological data indicated that the virus from Sudan belongs to a new species, tentatively named wild melon vein banding virus (WMVBV)...
June 29, 2017: Virus Research
https://www.readbyqxmd.com/read/28648414/prognostic-role-of-ki-67-score-in-localized-prostate-cancer-a-systematic-review-and-meta-analysis
#7
REVIEW
Alejandro Berlin, Julio F Castro-Mesta, Laura Rodriguez-Romo, David Hernandez-Barajas, Juan F González-Guerrero, Iván A Rodríguez-Fernández, Galileo González-Conchas, Adrian Verdines-Perez, Francisco E Vera-Badillo
BACKGROUND: Ki-67 for quantifying tumor proliferation is widely used. In localized prostate cancer (PCa), despite a suggested predictive role of Ki-67 for outcomes after therapies, it has not been incorporated into clinical practice. Herein, we conduct a systematic review and meta-analysis of the literature reporting the association of Ki-67 and disease outcomes in PCa treated radically. METHODS: Medline and EMBASE databases were searched without date or language restrictions, using "KI67" and "prostate cancer" MeSH terms...
June 22, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28603085/kaempferol-increases-levels-of-coenzyme-q-in-kidney-cells-and-serves-as-a-biosynthetic-ring-precursor
#8
Lucía Fernández-Del-Río, Anish Nag, Elena Gutiérrez Casado, Julia Ariza, Agape M Awad, Akil I Joseph, Ohyun Kwon, Eric Verdin, Rafael de Cabo, Claus Schneider, Jorge Z Torres, María I Burón, Catherine F Clarke, José M Villalba
Coenzyme Q (Q) is a lipid-soluble antioxidant essential in cellular physiology. Patients with Q deficiencies, with few exceptions, seldom respond to treatment. Current therapies rely on dietary supplementation with Q10, but due to its highly lipophilic nature, Q10 is difficult to absorb by tissues and cells. Plant polyphenols, present in the human diet, are redox active and modulate numerous cellular pathways. In the present study, we tested whether treatment with polyphenols affected the content or biosynthesis of Q...
September 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28576697/sequencing-viral-sirnas-to-identify-previously-undescribed-viruses-and-viroids-in-a-panel-of-ornamental-plant-samples-structured-as-a-matrix-of-pools
#9
REVIEW
Eric Verdin, Catherine Wipf-Scheibel, Patrick Gognalons, François Aller, Mireille Jacquemond, Mark Tepfer
Ornamental plants constitute a largely unknown and potentially important source of pathogens affecting not only ornamental plants, but also major crop species. We have carried out studies using high-throughput sequencing of 21-24 nt RNAs from potentially virus-infected ornamental plants, followed by assembly of sequence scaffolds, to identify the virus and viroid genomes present in a panel of 67 plant samples representing 46 species belonging to the main sectors of the ornamental plant industry (cut flowers, pot plants, bulbs)...
May 30, 2017: Virus Research
https://www.readbyqxmd.com/read/28572504/a-pet-imaging-strategy-to-visualize-activated-t-cells-in-acute-graft-versus-host-disease-elicited-by-allogenic-hematopoietic-cell-transplant
#10
John A Ronald, Byung-Su Kim, Gayatri Gowrishankar, Mohammad Namavari, Israt S Alam, Aloma D'Souza, Hidekazu Nishikii, Hui-Yen Chuang, Ohad Ilovich, Chih-Feng Lin, Robert Reeves, Adam Shuhendler, Aileen Hoehne, Carmel T Chan, Jeanette Baker, Shahriar S Yaghoubi, Henry F VanBrocklin, Randall Hawkins, Benjamin L Franc, Salma Jivan, James B Slater, Emily F Verdin, Kenneth T Gao, Jonathan Benjamin, Robert Negrin, Sanjiv Sam Gambhir
A major barrier to successful use of allogeneic hematopoietic cell transplantation is acute graft-versus-host disease (aGVHD), a devastating condition that arises when donor T cells attack host tissues. With current technologies, aGVHD diagnosis is typically made after end-organ injury and often requires invasive tests and tissue biopsies. This affects patient prognosis as treatments are dramatically less effective at late disease stages. Here, we show that a novel PET radiotracer, 2'-deoxy-2'-[18F]fluoro-9-β-D-arabinofuranosylguanine ([18F]F-AraG), targeted toward two salvage kinase pathways preferentially accumulates in activated primary T cells...
June 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/28547390/mono-substitution-effects-on-antimicrobial-activity-of-stapled-heptapeptides
#11
Huy X Luong, Do-Hee Kim, Ngoan T Mai, Bong-Jin Lee, Young-Woo Kim
We previously reported a de novo design of antimicrobial heptapeptide helices using Verdine's all-hydrocarbon peptide stapling system. One of the important structure-activity relationships we found from these previous studies was that extending of the hydrophobic face by replacing of alanine with leucine in positon 5 increases antimicrobial activity. In this study, to further improve the activity profile of this peptide series, we investigated the substitution effects of position 5 on conformational and proteolytic stability as well as antimicrobial and hemolytic activity...
May 25, 2017: Archives of Pharmacal Research
https://www.readbyqxmd.com/read/28538176/tonic-lat-hdac7-signals-sustain-nur77-and-irf4-expression-to-tune-naive-cd4%C3%A2-t-cells
#12
Darienne R Myers, Tannia Lau, Evan Markegard, Hyung W Lim, Herbert Kasler, Minghua Zhu, Andrea Barczak, John P Huizar, Julie Zikherman, David J Erle, Weiguo Zhang, Eric Verdin, Jeroen P Roose
CD4(+) T cells differentiate into T helper cell subsets in feedforward manners with synergistic signals from the T cell receptor (TCR), cytokines, and lineage-specific transcription factors. Naive CD4(+) T cells avoid spontaneous engagement of feedforward mechanisms but retain a prepared state. T cells lacking the adaptor molecule LAT demonstrate impaired TCR-induced signals yet cause a spontaneous lymphoproliferative T helper 2 (TH2) cell syndrome in mice. Thus, LAT constitutes an unexplained maintenance cue...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28448128/total-chemical-synthesis-and-folding-of-all-l-and-all-d-variants-of-oncogenic-kras-g12v
#13
Adam M Levinson, John H McGee, Andrew G Roberts, Gardner S Creech, Ting Wang, Michael T Peterson, Ronald C Hendrickson, Gregory L Verdine, Samuel J Danishefsky
The Ras proteins are essential GTPases involved in the regulation of cell proliferation and survival. Mutated oncogenic forms of Ras alter effector binding and innate GTPase activity, leading to deregulation of downstream signal transduction. Mutated forms of Ras are involved in approximately 30% of human cancers. Despite decades of effort to develop direct Ras inhibitors, Ras has long been considered "undruggable" due to its high affinity for GTP and its lack of hydrophobic binding pockets. Herein, we report a total chemical synthesis of all-l- and all-d-amino acid biotinylated variants of oncogenic mutant KRas(G12V)...
June 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28447069/long-term-calorie-restriction-in-humans-is-not-associated-with-indices-of-delayed-immunologic-aging-a-descriptive-study
#14
A Janet Tomiyama, Jeffrey M Milush, Jue Lin, James M Flynn, Pankaj Kapahi, Eric Verdin, Elizabeth Sinclair, Simon Melov, Elissa S Epel
BACKGROUND: Delayed immunologic aging is purported to be a major mechanism through which calorie restriction (CR) exerts its anti-aging effects in non-human species. However, in non-obese humans, the effect of CR on the immune system has been understudied relative to its effects on the cardiometabolic system. OBJECTIVE: To examine whether CR is associated with delayed immunologic aging in non-obese humans. METHODS: We tested whether long-term CR practitioners (average 10.03 years of CR) evidenced decreased expression of T cell immunosenescence markers and longer immune cell telomeres compared to gender-, race/ethnicity-, age-, and education-matched "healthy" Body Mass Index (BMI) and "overweight"/"obese" BMI groups...
March 31, 2017: Nutrition and Healthy Aging
https://www.readbyqxmd.com/read/28408723/nucleic-acid-detection-with-crispr-cas13a-c2c2
#15
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 clustered regularly interspaced short palindromic repeats (CRISPR) effector Cas13a (previously known as C2c2) exhibits a "collateral effect" of promiscuous ribonuclease 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 28, 2017: Science
https://www.readbyqxmd.com/read/28376236/inland-waters-and-their-role-in-the-carbon-cycle-of-alaska
#16
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 data sets 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...
July 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
#17
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
#18
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
#19
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
#20
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
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