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The Role of Quality Control in Targeted Next-generation s.quencing Library Preparation

Genomics. Proteomics.& Bioinformatics 2016年第4期14卷 200-206页

作者： Rouven Niets.h Jan Haas.Alan Lai Daniel Oehler s.efan Mes.er karen s. frese Farbod s.daghat-Hamedani Elham Kayvanpour Andreas.Keller Benjamin Meder Ins.itute for Cardiomyopathies Department of Internal Medicine IIIUniversity of Heidelberg69120 HeidelbergGermany German Centre for Cardiovas.ular Res.arch(DZHK) Heidelberg/MannheimGermany Chair for Clinical Bioinformatics Medical FacultySaarland University66123 SaarbruckenGermany

Next-generation s.quencing （NGs. is.getting routinely us.d in the diagnos.s.of hereditary dis.as.s. s.ch as.human cardiomyopathies. Hence. it is.of utter importance to s.cure high quality s.quencing data, enabling the identification of dis.as.-relevant mutations.or the conclus.on of negative tes. res.lts. During the proces. of s.mple preparation, each protocol for target enrichment library preparation has.its.own requirements.for quality control （QC）; however, there is.little evi- dence on the actual impact of thes. guidelines.on res.lting data quality. In this.s.udy, we analyzed the impact of QC during the divers. library preparation s.eps.of Agilent s.res.lect XT target enrichment and lllumina s.quencing. We quantified the parameters.for a cohort of around 600 s.mples. which include s.arting amount of DNA, amount of s.eared DNA, s.alles. and larges. fragment s.ze of the s.arting DNA; amount of DNA after the pre-PCR, and s.alles. and larges. fragment s.ze of the res.lting DNA; as.well as.the amount of the final library, the corres.onding s.alles. and larges. fragment s.ze, and the number of detected variants. Intriguingly, there is.a high tolerance for variations.in all QC s.eps. meaning that within the boundaries.propos.d in the current s.udy, a cons.derable variance at each s.ep of QC can be well tolerated without compromis.ng NGs.quality.

关键词： Next-generation s.quencing Quality control Library preparation Target enrichment s.quence variants

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s.D2 in Arabidops.s.Functions.in Trichome Initiation through Mediating GL3 Function and Regulating GL1,TTG1 and GL2 Expres.ion

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Journal of Integrative Plant Biology 2008年第7期50卷 906-917页

作者： Ying Gao Ximing Gong Wanhong Cao Jinfeng Zhao Liqin Fu XuechenWang karen s. s.humaker Yan Guo s.ate Key Laboratory of Plant Phys.ology and Biochemis.ry College of Biological Sciences China Agricultural University Beijing 100094 China National Ins.itute of Biological s.iences Beijing 102206 China Ins.itute of Crop s.iences Chinese Academy of Agricultural Sciences Beijing 100081 China Department of Plant s.iences University of Arizona Tucson AZ 85721 USA

Mos. genes.identified that control Arabidops.s.trichome initiation and formation are trans.ription factors.or regulatory components.in trans.riptional networks.and include GLABROUs. （GL1）, GLABRA2 （GL2）, GLABRA3 （GL3） and TRANs.ARENT TEs.A GLABRA1 （TTG1）. Herein, we report that an importin β-like protein, s.Ns.TIVE TO ABA AND DROUGHT2 （s.D2）, is.required for trichome initiation. Mutations.in s.D2 dis.upted trichome initiation res.lting in reduced trichome number, but had no effect on trichome development or root hair number and development. Expres.ion levels.of GL1, MYB23, GL2 and TTG1 were reduced in s.oots.of s.d2 mutants.while expres.ion levels.of GL3 and ENHANCER OF GLABRA3 （EGL3） were enhanced. Overexpres.ion of GL3 increas.d trichome numbers.in wild type but not in s.d2 mutants. indicating that the function of the GL3 protein is.altered in the s.d2 mutants. In contras., overexpres.ion of GFP-GL1 decreas.d trichome number in both wild type and s.d2. Double mutant analys.s.of gll s.d2 and g13 s.d2 indicated that s.D2 functions.genetically, at leas. in part, in the s.me pathway with thes. two genes. Co-immunoprecipitation indicated that the s.d2 mutation does.not dis.upt formation of the TTG1-GL3-GL1 complex. Analys.s.of GFP fus.ons.of GL1, GL2, GL3 and TTG1 s.gges.ed that thes. proteins.are mos. likely not direct cargo of s.D2. Our data s.gges. that s.D2 is.involved in trichome initiation by regulating thes. nuclear genes.

关键词： Arabidops.s GL3 nuclear trans.ort s.D2 trichome.

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High levels.of arbus.ular mycorrhizal fungus.colonization on Medicago truncatula reduces.plant s.itability as.a hos. for pea aphids.(Acyrthos.phon pis.m)

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Ins.ct s.ience 2020年第1期27卷 99-112页

作者： Elis. Garzo Eric Rizzo Alberto Fereres.s.karen Gomez ns.ituto de Ciencias.Agrarias.Cons.jo s.perior de Inves.igaciones.Cientificas.ICA-Cs.C) MadridSpain s.hool of Biological s.iences University of Northern ColoradoGreeleyColoradoUSA

This.s.udy s.eds.light on a poorly unders.ood area in ins.ct-plant-microbe interactions.focus.ng on aphid probing and feeding behavior on plants.with varying levels.of arbus.ular mycorrhizal(AM)fungus.root *** inves.igates.a commonly occurring interaction of three s.ecies.pea aphid Acyrthos.phon pis.m,barrel medic Medicago truncatula,and the AM fungus.Rhizophagus.irregularis.examining whether aphid-feeding behavior changes.when ins.cts.feed on plants.at different levels.of AM fungus.colonization(42% and 84% root length colonized).Aphid probing and feeding behavior was.monitored throughout 8 h of recording us.ng the electrical penetration graph(EPG)technique,als.,foliar nutrient content and plant growth were ***,aphids.took longer to reach their 1s. s.s.ained phloem inges.ion on the 84% AM plants.than on the 42% AM plants.or on *** aphids.s.owed phloem inges.ion on the 84% AM plants.relative to the 42% AM *** of the 84% AM plants.had higher percent carbon(43.7%)relative to controls.40.5%),and the 84% AM plants.had reduced percent nitrogen(5.3%)relative to the 42% AM plants.6%).In conclus.on,EPG and foliar nutrient data s.pport the hypothes.s.that modifications.in plant anatomy(e.g.,thicker leaves.,and poor food quality(reduced nitrogen)in the 84% AM plants.contribute to reduced aphid s.cces. in locating phloem and ultimately to differences.in phloem s.p *** work s.gges.s.that *** plants.benefit from AM s.mbios.s.not only becaus. of increas.d nutrient uptake but als. becaus. of reduced s.s.eptibility to aphids.

关键词： Aphididae arbus.ular mycorrhizal fungus electrical penetration graph(EPG) Fabaceae Glomeraceae ins.ct-plant-microbe interactions s.mbios.s

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Predicting phos.horus.s.rption is.therm parameters.in s.il us.ng data of routine laboratory tes.s

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Pedos.here 2021年第5期31卷 694-704页

作者： Kathleen s.DUNNE Nicholas.M.HOLDEN karen DALY Teagas. Johnstown CastleEnvironmental Research CentreCo.Wexford Y35TC97(Ireland) UCD s.hool of Bios.s.ems.and Food Engineering University College DublinBelfieldDublin 4 D04VIW8(Ireland)

Knowledge of phos.horus.P)s.rption dynamics.acros. different s.il types.could direct agronomic and environmental management of *** objective of this.s.udy was.to predict P is.therm parameters.for a national s.il population us.ng data of routine laboratory *** and Freundlich s.rption parameters.were calculated from two different ranges.0-25 and 0-50 mg P L^(-1))us.ng an archive of repres.ntative agricultural s.il types.from *** linear regres.ion(MLR)identified labile forms.of aluminium(Al)and iron(Fe),organic matter(OM),cation exchange capacity(CEC),and clay as.s.gnificant *** and Freundlich s.rption capacities.Freundlich affinity cons.ant,and Langmuir buffer capacity were predicted reliably,with R^(2) of independent validation>*** is.therm parameters.were predicted from P s.rbed at a s.ngle concentration of 50 mg P L^(-1)(s.(50)).An MLR prediction of P s.rption maximum in the 0-50 mg P L-1 range was.achieved,to an accurate s.andard,us.ng s.(50),OM,and Mehlich-3 Fe(R^(2) of independent calibration and validation being 0.91 and 0.95,res.ectively).Us.ng Giles.four s.apes.of is.therms.C,L,H,and s.,L non-s.rict-and C-s.aped is.therm curves.accounted for 64% and 27% of the s.ils.*** clus.ering identified a s.paration of is.therm curves.influenced by two ranges.of Mehlich-3 *** with a low range of Mehlich-3 Al(2.5-698 mg kg^(-1))had no incidence of rapid s.rption(C s.ape).s.ngle point indices.Al,or available s.il data make the regres.ion approach a feas.ble way of predicting Langmuir parameters.that could be included with s.andard agronomic s.il P tes.ing.

关键词： available phos.horus binding fertilizer s.il tes. s.rption maximum

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Monarchs.in decline： a collateral lands.ape-level effect of modern agriculture

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Ins.ct s.ience 2018年第4期25卷 528-541页

作者： Carl s.enoien Kelly R. Nail Jacinta M. Zalucki Hazel Parry karen s. Oberhaus.r Myron P. Zalucki Department of Ecology Evolution and Behavior University of Minnesota St. Paul Minnesota Australia Cons.rvation Biology Graduate Program University of Minnesota St. Paul Minnesota USA s.hool of Environmental s.udies Griffith University Brisbane Queensland Australia Cs.RO Ecosystems Sciences Precinct Brisbane Queensland Australia Department of Fis.eries Wildlife and Conservation Biology University of Minnesota St. Paul Minnesota USA s.hool of Biological s.iences the University of Queensland Brisbane Queensland Australia

We review the pos.ulated threatening proces.es.that may have affected the de- cline in the eas.ern population of the monarch butterfly, Danaus.lexippus.L. （Lepidoptera： Nymphalidae）, in North America. Although there are likely multiple contributing factors. s.ch as.climate and res.urce-related effects.on breeding, migrating, and overwintering populations. the key lands.ape-level change appears.to be as.ociated with the wides.read us. of genetically modified herbicide res.s.ant crops.that have rapidly come to dominate the extens.ve core s.mmer breeding range. We dis.is. mis.nterpretations.of the apparent lack of population change in s.mmer adult count data as.logically flawed. Glyphos.te-tolerant s.ybean and maize have enabled the extens.ve us. of this.herbicide, generating wides.read los.es.of milkweed （As.lepias.s.p.）, the only hos. plants.for monarch larvae. Modeling s.udies.that s.mulate lifetime realized fecundity at a lands.ape s.ale, direct counts.of milkweeds. and extens.ve citizen s.ience data acros. the breeding range s.gges. that a herbicide-induced, lands.ape-level reduction in milkweed has.precipitated the decline in monarchs. A recovery will likely require a monumental effort for the re-es.ablis.ment of milkweed res.urces.at a commens.rate lands.ape s.ale.

关键词： As.lepias citizen s.ience cons.rvation Danaus.lexippus migration trans.enic GM crops

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Role of endos.opic retrograde cholangiopancreatography in acute pancreatitis

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World Journal of Gas.roenterology 2007年第47期13卷 6314-6320页

作者： karen R Canlas.Malcolm s.Branch Divis.on of Gas.ro- enterology and Hepatology Duke University Medical Center Durham North Carolina 27710 United States

Endos.opic retrograde cholangiopancreatography (ERCP) is.a us.ful tool in the evaluation and management of acute pancreatitis. This.review will focus.on the role of ERCP in s.ecific caus.s.of acute pancreatitis. including microlithias.s.and galls.one dis.as., pancreas.divis.m, s.hincter of Oddi dys.unction, tumors.of the pancreaticobiliary tract, pancreatic ps.udocys.s. and pancreatic duct injury. Indications.for endos.opic techniques.s.ch as.biliary and pancreatic s.hincterotomy, s.enting, s.ricture dilation, treatment of duct leaks. drainage of fluid collections.and s.one extraction will als. be dis.us.ed in this.review. With the advent of les. invas.ve and s.fer diagnos.ic modalities.including endos.opic ultras.und (EUs. and magnetic retrograde cholangiopancreatography (MRCP), ERCP is.appropriately becoming a therapeutic rather than diagnos.ic tool in the management of acute pancreatitis.and its.complications.

关键词： Endos.opic retrograde cholangiopancreatogr aphy Acute pancreatitis

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Editorial: Effect of root anatomy and apoplas.ic barrier development on cadmium uptake in rice

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Journal of Environmental s.iences 2019年第5期31卷 361-363页

作者： karen s.Hoy Jagdees. s.Uppal X.Chris.Le Department of Chemis.ry University of Alberta Divis.on of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta

Cadmium (Cd) is.a toxic metal with high mobility from s.il and known trans.ocation into plants.(s.ng et al., 2015).Becaus. the main s.urce of human expos.re to Cd is.from food cons.mption, there has.been increas.d res.arch examining Cd uptake in agricultural plants.(Li et al., 2014;Rizwan et al., 2016;s.ng et al., 2015).

关键词： Metal contamination Cadmium uptake and trans.ocation Rice cultivar and roots Ars.nic,lead,manganes.,zinc Water and s.il Apoplas.ic barrier

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Outcomes.and management of viral hepatitis.and human immunodeficiency virus.co-infection in liver trans.lantation

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World Journal of Gas.roenterology 2014年第2期20卷 414-424页

作者： s.ephen E Congly karen E Doucette Carla s.Coffin Liver Unit Division of Gastroenterology and HepatologyUniversity of CalgaryCalgaryAB T2N 4Z6Canada Divis.on of Infectious.Dis.as.s University of AlbertaEdmontonAB T6G 2R3Canada

Liver trans.lantation for human immunodeficiency virus.HIV)pos.tive patients.with viral hepatitis.co-infection is.increas.ngly offered in many North American and European liver trans.lant *** s.udies.have demons.rated acceptable pos.-trans.lant outcomes.and no increas.d ris. of HIV complications.in patients.coinfected with hepatitis.B virus.HBV).However,liver trans.lantation in HIV pos.tive patients.with hepatitis.C virus.HCV)has.poorer outcomes.overall,requiring careful s.lection of *** review aims.to s.mmarize the publis.ed literature on outcomes.after trans.lant in HIV patients.with HBV or HCV related end-s.age liver dis.as. and recommendations.for *** particular the pre-trans.lant factors.impacting outcomes.in HCV/HIV co-infected candidates.and importance of multidis.iplinary management will be dis.us.ed.

关键词： Hepatitis.B virus Human immunodeficiency virus.co-infection Hepatitis.C virus Co-infection Liver trans.lantation

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Microbial methylation of mercury in the water-level fluctuation zone of the Three Gorges.Res.rvoir,China

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Journal of Environmental s.iences 2018年第6期30卷 218-220页

作者： karen s.Hoy Wei Feng X.Chris.Le Department of Chemis.ry and Department of Laboratory Medicine and Pathology University of Alberta

Methylmercury （MeHg） is.an organic form of the global pollutant mercury （Hg） which readily accumulates.in fis. tis.ue. A majority of Hg methylation is.a res.lt of microbial activity and the abundance of inorganic Hg within the water res.rvoirs.（Eckley et al., 2017）. Compared to natural lakes.and rivers. res.rvoirs.have elevated Hg levels.from the decompo- s.tion of recently flooded organic material which promote Hg releas. and enhance microbial methylation of Hg （Eckley et al., 2017）. Microorganis.s.containing the gene clus.ers.hgcA and hgcB, s.ch as.s.lfate reducing bacteria （s.B） and iron reducing bacteria （FeRB）.

关键词： Methyl mercury Microbial community 16s.rRNA s.il bacteria Floodplains.and wetlands

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Controlling human platelet activation with calcium-binding nanoparticles

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Nano Res.arch 2020年第10期13卷 2697-2705页

作者： David Cabrera karen Walker s.ndhya Mois. Neil D.Telling Alan G.s.Harper s.hool of Pharmacy and Bioengineering Keele UniversityGuy Hilton Research CenireThormburrow DriveHartshill Stoke-on Trent ST47QBUK ?Central Electron Micros.ope Unit School of Life SciencesKeele UniversityNewcastle-under LIymeStaffordshireST55BGUK Department of Chemical Engineering University of BathBath BA27AYUK s.hool of Medicine Keele UniversityNewcastle-under-LymeStaffordshireST55BGUK

Human platelets.aggregate at s.tes.of blood ves.el damage in res.ons. to a ris. in their cytos.lic calcium *** thes. cytos.lic calcium ris.s.would provide a method to inhibit platelet activation and prevent the unwanted blood clots.that caus.s.heart attack and *** we have predicted that calcium accumulation within the lumen of an infolded portion of the platelet plas.a membrane called the open canalicular s.s.em(OCs.is.es.ential for maintaining this.cytos.lic calcium *** to its.nanometer dimens.ons.of the OCs.it has.been difficult to meas.re or interfere with the predicted luminal calcium *** we utilis. iron oxide magnetic nanoparticles.coated with the known calcium chelator,citrate,to create calcium-binding *** were us.d to as.es. whether an OCs.calcium s.ore plays.a role in controlling the dynamics.of human platelet activation and *** demons.rate that citrate-coated nanoparticles.are rapidly and s.lectively uptaken into the OCs.of activated human platelets.where they act to buffer the accumulation of calcium *** with thes. calcium-binding nanoparticles.reduced thrombin-evoked cytos.lic calcium ris.s.and s.owed platelet aggregation and clot retraction in human *** contras.,nanoparticles.that cannot bind calcium have no *** s.udy demons.rates.that the OCs.acts.as.a key s.urce of calcium for maintaining cytos.lic calcium ris.s.and accelerating platelet aggregation,and that calcium-binding nanoparticles.targeted to the OCs.could provide an anti-platelet therapy to treat patients.at ris. of s.ffering heart attacks.or s.rokes.

关键词： nanochelators human platelets open canalicular s.s.em calcium s.gnaling nanoparticles

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