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m.thylGenotyper:Accurate Estim.tion of SNP Genotypes and Genetic Relatedness from.DNA m.thylation Data

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Genom.cs, Proteom.cs & Bioinform.tics 2024年第3期22卷 43-54页

作者： Yi Jiang m.nghan Qu m.nghui Jiang Xuan Jiang Shane Fernandez Tenielle Porter Sim.n m.Laws colin L.m.sters Huan Guo Shanshan Cheng Chaolong Wang m.nistry of Education Key Laboratory of Environm.nt and Health School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China Departm.nt of Epidem.ology and Biostatistics School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China Centre for Precision Health Edith Cowan UniversityPerthWA 6027Australia Collaborative Genom.cs and Translation Group School of Medical and Health SciencesEdith Cowan UniversityPerthWA 6027Australia Curtin m.dical School BentleyWA 6102Australia The Florey Institute of Neuroscience and m.ntal Health University of MelbourneMelbourneVIC 3052Australia Departm.nt of Occupational and Environm.ntal Health School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China

Epigenom.-wide association studies(EWAS)are susceptible to widespread confounding caused by population structure and genetic ***,kinship estim.tion is challenging in EWAS without genotyping ***,we proposed m.thylGenotyper,a m.thod that for the first tim. enables accurate genotyping at thousands of single nucleotide polym.rphism.(SNPs)directly from.com.ercial DNA m.thylation *** m.deled the intensities of m.thylation probes near SNPs with a m.xture of three beta distributions corresponding to different genotypes and estim.ted param.ters with an expectation-m.xim.zation *** conducted extensive sim.lations to dem.nstrate the perform.nce of the *** applying m.thylGenotyper to the Infinium.EPIC array data of 4662 Chinese sam.les,we obtained genotypes at 4319 SNPs with a concordance rate of 98.26%,enabling the identification of 255 pairs of close ***,we showed that m.thylGenotyper allows for the estim.tion of both population structure and cryptic relatedness am.ng 702 Australians of diverse *** also im.lem.nted m.thylGenotyper in a publicly available R package(https://***/Yi-Jiang/m.thylGenotyper)to facilitate future large-scale EWAS.

关键词： DNA m.thylation Genotype calling Genetic relatedness Population structure Epigenom.-wide association study

The Influence of Variable (m.nsoon) Rainfall on Sedim.ntation in the Roaches Grit and Other Upper Carboniferous Delta Sequences in the UK Pennine Basin

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International Journal of Geosciences 2024年第8期15卷 632-666页

作者： colin m.chael Jones Retired Cambridge UK

The Roaches Grit in the UK Pennine Basin was a com.lex deep water deltaic sequence deposited during the Late Carboniferous glacial period. The channels of the upper part of the Roaches Grit, deposited towards the end of the cyclothem.after the eustatic m.nim.m. contain evidence for very high seasonal discharges related to strong m.nsoon rainfall in the catchm.nt areas. In som. channels, intense turbulence near the delta front, led to knick point recession and deep incision. These channels were filled with sedim.nts during reduced discharge, including very large sets of cross-bedding up to 16 m.thick. Channels were short-lived with frequent avulsions. Over tim. slightly lower discharges form.d laterally m.grating channels dom.nated by bar form.. Different discharge-controlled processes operated on the reactivated delta slope. Incised channels generated turbidity currents during floods which transported sedim.nts directly into the basin far from.the delta. m.grating channels built m.uth bars;resedim.ntation during floods form.d density currents which then deposited sedim.nt on the lower parts of the slope.

关键词： Carboniferous Delta Clim.te m.nsoon Rainfall ITCZ Precession

CD8+T cell m.tabolic flexibility elicited by CD28-ARS2 axisdriven alternative splicing of PKm.supports antitum.r im.unity

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Cellular & m.lecular Im.unology 2024年第3期21卷 260-274页

作者： G.Aaron Holling colin A.Chavel Anand P.Sharda m.ckenzie m.Lieberm.n Caitlin m.Jam.s Shivana m.Lightm.n Jason H.Tong Guanxi Qiao Tiffany R.Em.ons Thejaswini Giridharan Shengqi Hou Andrew m.Intlekofer Richard m.Higashi Teresa W.m.Fan Andrew N.Lane Kevin H.Eng Brahm.H.Segal Elizabeth A.Repasky Kelvin P.Lee Scott H.Olejniczak Departm.nt of Im.unology Roswell Park Comprehensive Cancer CenterBuffaloNY 14263USA Departm.nt of m.dicine Roswell Park Comprehensive Cancer CenterBuffaloNY 14263USA Hum.n Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer CenterNew YorkNY 10065USA Center for Environm.ntal System. Biochem.stry Department of Toxicology and Cancer Biology and Markey Cancer CenterLexingtonKY 40536USA Departm.nt of Cancer Genetics and Genom.cs Roswell Park Comprehensive Cancer CenterBuffaloNY 14263USA Present address:University of Colorado Boulder BoulderCO 80309USA Present address:Dana Farber Cancer Institute BostonMA 02215USA Present address:m.ssachusetts Institute of Technology BostonMA 02139USA Present address:m.lvin and Bren Sim.n Com.rehensive Cancer Center Indiana University School of MedicineIndianapolisIN 46202USA

m.tabolic flexibility has em.rged as a critical determ.nant of CD8+T-cell antitum.r activity,yet the m.chanism. driving the m.tabolic flexibility of T cells have not been *** this study,we investigated the influence of the nuclear cap-binding com.lex(CBC)adaptor protein ARS2 on m.ture T *** doing so,we discovered a novel signaling axis that endows activated CD8+T cells with flexibility of glucose ***2 upregulation driven by CD28 signaling reinforced splicing factor recruitm.nt to pre-m.NAs and affected approxim.tely one-third of T-cell activation-induced alternative splicing *** these effects,the CD28-ARS2 axis suppressed the expression of the m. isoform.of pyruvate kinase in favor of PKm.,a key determ.nant of CD8+T-cell glucose utilization,interferon gam.a production,and antitum.r effector ***,PKm.alternative splicing occurred independently of CD28-driven PI3K pathway activation,revealing a novel m.ans by which costim.lation reprogram. glucose m.tabolism.in CD8+T cells.

关键词： Im.unom.tabolism m.NA splicing CD8 T cells ARS2 PKm.

Bravo capsule system.optim.zes intragastric pH m.nitoring over prolonged tim.:Effects of ghrelin on gastric acid and horm.ne secretion in the rat

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World Journal of Gastroenterology 2008年第40期14卷 6180-6187页

作者： Tobias Rudholm.Per m.kael Hellstrm.Elvar Theodorsson colin Allan campbell Peter Geoffrey m.Lean Erik Nslund Departm.nt of m.dicine Solna Karolinska Institutet Departm.nt of Neurochem.stry Linkping University Hospital Neurology and GI CEDD GlaxoSmithKlineHarlowUKEssex CM19 5AWUnited Kingdom Division of Surgery Department of Clinical SciencesDanderyd HospitalKarolinska Institutet

AIm. To evaluate m.asurem.nts of intragastric pH with the Bravo capsule system.over a prolonged ***: A Bravo capsule was placed inside the rat gastric body and pH was studied for periods up to five consecutive *** com.arison,a gastric fistula m.del was *** of ghrelin and esom.prazole,with or without pentagastrin,on gastric pH were *** addition,effects of esom.prazole on plasm. ghrelin,gastrin and som.tostatin were ***: All rats recovered after *** average 24-h pH during free feeding was 2.3 ± 0.1 (n = 20) with a variation of 18% ± 6% over 5 ***,2400 pm.l/kg,*** pH from.1.7 ± 0.1 to 3.1 ± 0.3 (P m.prazole (1 m./kg,3 m./kg and 5 m./kg) there was a dose-dependent pH increase of m.xim.lly 3.4 ± 0.1,with day-to-day variation over the entire period of 8% ± 3%.The fistula and pH studies generated sim.lar *** inhibition with esom.prazole increased plasm. ghrelin from.10 ± 2 pm.l/L to 65 ± 26 pm.l/L (P m.tostatin from.10 ± 2 pm.l/L to 67 ± 18 pm.l/L (P m.asurem.nts with the Bravo capsule are reliable,and com.arable to those of the gastric fistula *** Bravo system.optim.zes accurate intragastric pH m.nitoring over prolonged periods and allows both short-and long-term.evaluation of effects of drugs and horm.nes.

关键词： Gastric acid Bravo system Intragastric pH, Ghrelin Som.tostatin

Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis

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m.lecular Plant 2009年第5期2卷 1015-1024页

作者： m.rek m.twil colin Ruprecht Federico m. Giorgi m.rtin Bringm.nn Bjorn Usadel Staffan Persson m.x-Planck-lnstitute for m.lecular Plant Physiology Am Muhlenberg 1 14476 Potsdam Germany

Transcriptional coordination, or co-expression, of genes m.y signify functional relatedness of the corresponding proteins. For exam.le, several genes involved in secondary cell wall cellulose biosynthesis are co-expressed with genes engaged in the synthesis of xylan, which is a m.jor com.onent of the secondary cell wall. To extend these types of analyses, we investigated the co-expression relationships of all Carbohydrate-Active enZYm.s （CAZy）-related genes for Arabidopsis thaliana. Thus, the intention was to transcriptionally link different cell wall-related processes to each other, and also to other biological functions. To facilitate easy m.nual inspection, we have displayed these interactions as networks and m.trices, and created a web-based interface （http：***） containing downloadable files for all the transcriptional associations.

关键词： Cell walls bioinform.tics Arabidopsis co-expression.

Targeted therapy for capillary-venous m.lform.tions

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Signal Transduction and Targeted Therapy 2024年第7期9卷 3024-3039页

作者： Lola Zerbib Sophia Ladraa Antoine Fraissenon Charles Bayard m.rina Firpion Quitterie Venot Sanela Protic Clém.nt Hoguin Am.ndine Thom.s Sylvie Fraitag Jean-Paul Duong Sophie Kaltenbach Estelle Balducci coline Lefevre Patrick Villarese Vahid Asnafi Christine Broissand Nicolas Goudin Ivan Nem.zanyy Gwennhael Autret Bertrand Tavitian Christophe Legendre Nadia Arzouk Veronique m.nard-colin Caroline Chopinet m.chael Dussiot Denise m.dam. Tristan m.rault Laurent Guibaud Paul Isenring Guillaum. Canaud UniversitéParis Cité ParisFrance INSERm.U1151 Institut Necker-Enfants MaladesParisFrance Service d’Im.gerie Pédiatrique Hôpital Femme-Mère-EnfantHCLBronFrance CREATIS Um. 5220 Villeurbanne 69100France Service de Radiologie m.re-Enfant Hôpital NordSaint EtienneFrance Service d’Anatom.e pathologique Hôpital Necker-Enfants MaladesAP-HPParisFrance Laboratoire d’Oncohém.tologie Hôpital Necker-Enfants MaladesAP-HPParisFrance Pharm.cie Hôpital Necker-Enfants MaladesAP-HPParisFrance Necker Bio-Im.ge Analysis INSERM US24/CNRS UMS 3633ParisFrance Platform.for m.tabolic Analyses Structure Fédérative de Recherche NeckerINSERM US24/CNRS UMS 3633ParisFrance Plateform. Im.geries du Vivant Universitéde ParisPARCCINSERMParisFrance Service de Néphrologie Transplantation AdultesHôpital Necker-Enfants MaladesAP-HPParisFrance Service de Transplantation Hôpital La PitiéSalpétrièreAP-HPParisFrance Departm.nt of Pediatric and Adolescent Oncology INSERM 1015Gustave RoussyUniversitéParis-SaclayVillejuifFrance Service de Physiologie&Explorations Fonctionnelles Cardiovasculaires CHU de LilleLille 59000France INSERm.U1163 Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutic ImplicationsLaboratoire d’Excellence GR-ExParisFrance Division of Oncology Comprehensive Vascular Anomalies ProgramChildren’s Hospital of PhiladelphiaPhiladelphiaPAUSA Service de m.decine Vasculaire hôpital Européen Georges-PompidouParisFrance Nephrology Research Group L’Hôtel-Dieu de Québec Research CenterDepartment of MedicineFaculty of MedicineLaval UniversityQuebecQC G1R2J6Canada Unitéde m.decine translationnelle et thérapies ciblées Hôpital Necker-Enfants MaladesAP-HPParisFrance CNRS Um.8253 Institut Necker-Enfants MaladesParisFrance

Sporadic venous m.lform.tions are genetic conditions prim.rily caused by som.tic gain-of-function m.tation of PIK3CA or TEK,an endothelial transm.m.rane receptor signaling through *** m.lform.tions are associated with pain,bleedings,throm.osis,pulm.nary em.olism.esthetic deform.ties and,in severe cases,life-threatening *** authorized m.dical treatm.nt exists for patients with venous ***,we created a genetic m.use m.del of PIK3CA-related capillary venous m.lform.tions that replicates patient *** showed that these m.lform.tions only partially signal through AKT *** com.ared the efficacy of different drugs,including rapam.cin,a m.ORC1 inhibitor,m.ransertib,an AKT inhibitor and alpelisib,a PI3Kαinhibitor at im.roving the lesions seen in the m.use *** dem.nstrated the effectiveness of alpelisib in preventing vascular m.lform.tions’occurrence,im.roving the already established ones,and prolonging *** these findings,we were authorized to treat 25 patients with alpelisib,including 7 children displaying PIK3CA(n=16)or TEK(n=9)-related capillary venous m.lform.tions resistant to usual therapies including sirolim.s,debulking surgical procedures or percutaneous *** assessed the volum. of vascular m.lform.tions using m.gnetic resonance im.ging(m.I)for each *** dem.nstrated im.rovem.nt in all 25 *** m.lform.tions previously considered intractable were reduced and clinical sym.tom. were *** showed a decrease of 33.4%and 27.8%in the m.dian volum. of PIK3CA and TEK m.lform.tions respectively,over 6 m.nths on *** conclusion,this study supports PI3Kαinhibition as a prom.sing therapeutic strategy in patients with PIK3CA or TEK-related capillary venous m.lform.tions.

关键词： PIK3CA m.lform.tions venous

Integrating beneficiaries into assessm.nt of ecosystem.services from.m.naged forests at the Hubbard Brook Experim.ntal Forest,USA

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Forest Ecosystem. 2016年第4期3卷 243-257页

作者： Jesse Caputo colin m.Beier Valerie A.Luzadis Peter m.Groffm.n SUNY College of Environm.ntal Science and Forestry Department of Forest and Natural Resources Management Syracuse NY 13210 USA Cary Institute of Ecosystem.Studies Millbrook 12545 NY USA

Background：Forests contribute to hum.n wellbeing through the provision of im.ortant ecosystem.***：In this study,we investigated how the perceived im.ortance of ecosystem.services m.y im.act the overall benefit provided by m.naged watersheds at the Hubbard Brook Experim.ntal Forest over a 45-year period,using standardized m.asures of service capacity weighted by service im.ortance weights derived from.a survey of ***：The capacity of watersheds to regulate water flow and quality was high in all watersheds throughout the study period,whereas cultural services such as scenic beauty declined after *** on greenhouse gas regulation depended on the efficiency with which harvested biom.ss was *** revealed that stakeholders placed high value on all ecosystem.services,with regulating and cultural services seen as m.re im.ortant than provisioning *** service m.trics were weighted by survey responses and aggregated into a single m.asure,total service provision followed the sam. overall trend as greenhouse gas *** biom.ss use was less efficient in term. of greenhouse gas em.ssions,harvesting resulted in an overall ＂ecosystem.service debt＂;where use was m.re efficient,this ＂ecosystem.service debt＂ was ***＇ educational backgrounds significantly affected overall assessm.nt of service *** with college or university degrees incurred sm.ller ＂ecosystem.service debts＂ and were less negatively affected by harvesting ***：This study highlights the im.ortance of including em.irical m.asures of beneficiary preference when attem.ting to quantify overall provision of ecosystem.services to hum.n beneficiaries over tim..

关键词： Ecosystem.services Forests Long-term.ecological research Hubbard Brook Experim.ntal Forest Regulating services

Participation in cooperative prey capture and the benefits gained from.it are associated with individual personality

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Current Zoology 2017年第5期63卷 561-567页

作者： Jam.s L.L. LICHTENSTEIN colin m. WRIGHT Lauren P. LUSCUSKIE Graham.A. m.NTGOm.RY PINTER-WOLLm.N Jonathan N. PRUITT Departm.nt of Biological Sciences University of Pittsburgh Pittsburgh PA 15260 USA Departm.nt of Ecology and Evolutionary Biology University of California Los Angeles CA 90095 USA Departm.nt of Ecology Evolution and Marine Biology University of California Santa Barbara Santa Barbara CA 93106 USA

In anim.l societies, behavioral idiosyncrasies of the individuals often guide which tasks theyshould perform. Such personality-specific task participation can increase individual task efficiency,thereby im.roving group perform.nce. While several recent studies have docum.nted group-levelbenefits of within-group behavioral （i.e., personality） diversity, how these benefits are realized atthe individual level is unclear. Here we probe the individual-level benefits of personality-driven taskparticipation in the social spider Stegodyphus dum.cola. In S. dum.cola, the presence of at leastone highly bold individual catalyzes foraging behavior in shy colony m.m.ers, and all group con-stituents heavily com.ete for prey. We assessed boldness by exam.ning how quickly spidersresum.d norm.l m.vem.nt after a sim.lated predator attack. We test here whether （1） participantsin collective foraging gain m.re m.ss from.prey item. and （2） whether bold individuals are less re-sistant to starvation than shy spiders, which would m.tivate the bold individuals to forage ***, we assem.led colonies of shy spiders with and without a bold individual, added one preyitem. and then tracked the m.ss gain of each individual spider after this single feeding event. Wefound that spiders that participated in prey capture （whether bold or shy） gained m.re m.ss thannonparticipators, and colonies containing a single bold spider gained m.re total m.ss than purelyshy colonies. We also found that bold spiders participated in m.re collective foraging events andwere m.re susceptible to starvation than shy spiders, suggesting that the aggressive foraging ofbold individuals m.y represent a strategy to offset starvation risk. These findings add to the bodyof evidence that anim.l personality can shape social organization, individual perform.nce, andgroup success.

关键词： anim.l personality, keystone individuals, social behaviour, task allocation.

Population increase and changes in behavior and m.rphology in the Critically Endangered Redonda ground lizard(Pholidoscelis atratus)following the successful rem.val of alien rats and goats

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Integrative Zoology 2021年第3期16卷 379-389页

作者： colin m.DONIHUE Jennifer C.DALTRY Shanna CHALLENGER Anthony HERREL Um. 7179 C.N.R.S/m.N.H.N. Département Adaptations du VivantParisFrance Departm.nt of Biology Washington University in St.LouisSt.LouisMissouriUSA Fauna&Flora International David Attenborough BuildingPembroke StreetCambridgeUK Departm.nt of Environm.nt St.John’sAntigua Environm.ntal Awareness Group St.John’sAntigua

Redonda is a sm.ll volcanic Caribbean island that is hom. to at least 4 endem.c lizard species,including the Critically Endangered ground lizard(Pholidoscelis atratus).Black rats(Rattus rattus)and dom.stic goats(Capra hircus)were introduced to the island at som. tim. after its discovery by Europeans in the late *** had a devastating effect on the island,resulting in the loss of nearly all trees and m.st of the ground *** count surveys of *** in 2012 indicated low densities,and the invasive rats were observed hunting and preying on the *** populations of rats and goats were successfully rem.ved in 2017 as part of an ecological restoration program.and native vegetation and invertebrate populations have increased rapidly *** surveys in 2017,2018,and 2019 show the lizard population has increased by m.re than *** 2017,as rats and goats were being rem.ved,we evaluated the m.rphology and escape behavior of this species and repeated these m.asurem.nts 1 year *** observed that *** had becom. bolder,with a reduced flight *** also detected changes in lim. m.rphology related to locom.tion and suggest possible explanations that will need to be further investigated in the *** results show how the rem.val of invasive species can rapidly affect lizard population recovery and behavior,potentially restoring island ecosystem. to their pre-hum.n interference dynam.cs.

关键词： Antigua and Barbuda Caribbean conservation endangered species invasive alien species island biology Lesser Antilles pest rem.val