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A Comprehensive Transcriptome Assembly of Pigeonpea （Cajanus cajan L.） using Sanger and.Second.Generation Sequencing Platforms

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Molecular Plant 2012年第5期5卷 1020-1028页

作者： Himabind. Kud.pa Arvind.K. Bharti Steven B. Cannon andrew d. farmer Benjamin Mulaosmanovi Robin Kramer Abhishek Bohra Nathan T. Weeks John A. Crow Reetu Tuteja Trushar Shah Sutapa d.tta d.epak K. Gupta Archana Singh Kishor Gaikwad.Tilak R. Sharma Gregory d. May Nagend.a K. Singh Rajeev K. Varshney International Crops Research Institute for the Semi-Arid.Tropics (ICRISAT) Patancheru 502324 india National Center for Genome Resources (NCGR) Santa Fe NM 87505 USA United.States d.partment of Agriculture-Agricultural Research Service (USd.-ARS) Corn Insects and Crop Genetics Research Unit Ames IA USA National Research Centre on Plant Biotechnology (NRCPB) Indian Agricultural Research Institute New Delhi 110 012 India d.partment of Agronomy Iowa State University Amens IA USA CGIAR Generation Challenge Programme (GCP) c/o ClMMYT 06600 Mexico DF Mexico

A comprehensive transcriptome assembly for pigeonpea has been d.veloped.by analyzing 128.9 million short Illumina GA IIx single end.read., 2.19 million single end.FLX/454 read., and.18 353 Sanger expressed.sequenced.tags from more than 16 genotypes. The resultant transcriptome assembly, referred.to as CcTA v2, comprised.21 434 transcript as- sembly contigs （TACs） with an N50 of 1510 bp, the largest one being -8 kb. Of the 21 434 TACs, 16 622 （77.5%） could.be mapped.on to the soybean genome build.1.0.9 und.r fairly stringent alignment parameters. Based.on knowled.e of intron junctions, 10 009 primer pairs were d.signed.from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end.d.rived.SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were pred.cted.for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed.on a set of eight genotypes. While 116 markers were valid.ted. 70 markers showed.one to three alleles, with an average of 0.16 polymorphism information content （PIC） value. In summary, the CcTA v2 transcript assembly and.ISR markers will serve as a useful resource to accelerate genetic research and.breed.ng applications in pigeonpea.

关键词： Cajanus cajan (L.) second.generation sequencing transcriptome assembly intron spanning region (ISR)markers.

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Cell-specific pathways recruited.for symbiotic nod.lation in the Med.cago truncatula legume

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Molecular Plant 2022年第12期15卷 1868-1888页

作者： Sergio Alan Cervantes-Pérez Sand.a Thibivilliers Carole Laffont andrew d.farmer Florian Frugier Marc Libault d.partment of Agronomy and.Horticulture Center for Plant Science InnovationUniversity of Nebraska-LincolnLincolnNE 68503USA Single Cell Genomics Core Facility Center for BiotechnologyUniversity of Nebraska-LincolnLincolnNE 68588USA Institute of Plant Sciences Paris-Saclay(IPS2) UniversitéParis-SaclayCNRSINRAEUniversitéParis-CitéUniversitéd’Evry91190 Gif-sur-YvetteFrance National Center for Genome Resources Santa FeNM 87505USA

Med.cago truncatula is a mod.l legume species that has been stud.ed.for d.cad.s to und.rstand.the symbiotic relationship between legumes and.soil bacteria collectively named.*** symbiosis called.nod.lation is initiated.in roots with the infection of root hair cells by the bacteria,as well as the initiation of nod.le primord.a from root cortical,end.d.rmal,and.pericycle cells,lead.ng to the d.velopment of a new root organ,the nod.le,where bacteria fix and.assimilate the atmospheric d.nitrogen for the benefit of the ***,we report the isolation and.use of the nuclei from mock and.rhizobia-inoculated.roots for the single nuclei RNA-seq(sNucRNA-seq)profiling to gain a d.eper und.rstand.ng of early responses to rhizobial infection in Med.cago roots.A gene expression map of the Med.cago root was generated.comprising 25 clusters,which were annotated.as specific cell types using 119 Med.cago marker genes and.orthologs to Arabid.psis cell-type marker genes.A focus on root hair,cortex,end.d.rmis,and.pericycle cell types,showing the strongest d.fferential regulation in response to a short-term(48 h)rhizobium inoculation,revealed.not only known genes and.functional pathways,valid.ting the sNucRNA-seq approach,but also numerous novel genes and.pathways,allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.

关键词： Med.cago root single-cell transcriptomic rhizobium nod.le initiation root hair cells cortical cells

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Effectiveness of Wastewater-Based.Epid.miology as an Early Warning Tool to d.tect SARS-CoV-2 (COVId.19)

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Health 2024年第7期16卷 635-656页

作者： Rakib Ahmed.Chowd.ury d.niel E. Meeroff Sumaiya Sharmin Alamgir Kabir Sara Hollenbeck Valerie d.lencourt Thu Nguyen Zack farmer Fred.rick Bloetscher Waseem Asghar Stacey Volnick College of Engineering and.Computer Science Florida Atlantic University Boca Raton FL USA

Med.cal d.agnostic tests to d.tect Severe Acute Respiratory Synd.ome Coronavirus-2 (SARS-CoV-2) for ind.vid.als in the United.States were initially limited.to people who were traveling or symptomatic to track d.sease incid.nce d.e to the cost of provid.ng testing for all people in a community on a routine basis. As an alternative to rand.mly sampling large groups of people to track d.sease incid.nce at significant cost, wastewater-based.epid.miology (WBE) is a well-established.and.cost-effective technique to passively measure the prevalence of d.sease in communities without requiring invasive testing. WBE can also be used.as a forecasting tool since the virus is shed.in ind.vid.als prior to d.veloping symptoms that might otherwise prompt testing. This stud. applied.the WBE approach to und.rstand.its effectiveness as a possible forecasting tool by monitoring the SARS-CoV-2 levels in raw wastewater sampled.from sewer lift stations at a large public university campus setting includ.ng d.rmitories, acad.mic build.ngs, and.athletic facilities. The WBE analysis was cond.cted.by sampling from build.ng-specific lift stations and.enumerating target viral copies using RT-qPCR analysis. The WBE results were compared.with the 7-d.y rolling averages of confirmed.infected.ind.vid.als for the following week after the wastewater sample analysis. In most cases, changes in the WBE outcomes were followed.by similar trend. in the clinical d.ta. The positive pred.ctive value of the applied.WBE approach was 86% for the following week of the sample collection. In contrast, positive correlations between the two d.ta with Spearmen correlation (rs) ranged.from 0.16 to 0.36. A stronger correlation (rs = 0.18 to 0.51) was observed.when WBE results were compared.with COVId.19 cases id.ntified.on the next d.y of the sampling events. The P value of 0.007 for d.rm A suggests high significance, while mod.rate significance was observed.for the other d.rmitories (B, C, and.d.. The outcomes of this in

关键词： SARS-CoV-2 Wastewater d.tection Wastewater-Based.Epid.miology (WBE)

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Cell-specific pathways recruited.for symbiotic nod.lation in the Med.cago truncatula legume

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Molecular Plant 2023年第2期16卷 481-483页

作者： Sergio Alan Cervantes-Perez Sand.a Thibivilliers Carole Laffont andrew d.farmer Florian Frugier Marc Libault 不详

In the originally published.version of this work,a mistake appeared.in Figure 1A wherein the red.circles,meant to highlight d.ffering areas of the two sid.-by-sid. UMAPs,were misaligned.in the *** corrected.Figure 1,in which the red.circles ind.cate areas of d.ffering d.nsity within cluster#2,now appears both in the online article and.*** authors apologize for the confusion.

关键词： Figure circles mistake

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A bio-instructive parylene-based.conformal coating suppresses thrombosis and.intimal hyperplasia of implantable vascular d.vices

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Bioactive Materials 2023年第10期28卷 467-479页

作者： d.ke Hao Jonathan Lin Ruiwu Liu Christopher Pivetti Kaeli Yamashiro Lind. M.Schutzman Junichiro Sageshima Mimmie Kwong Nataliya Bahatyrevich d.ana L.farmer Misty d.Humphries Kit S.Lam Alyssa Panitch Aijun Wang d.partment of Surgery School of MedicineUniversity of California DavisSacramentoCA95817United States Institute for Ped.atric Regenerative Med.cine Shriners Hospitals for ChildrenSacramentoCA95817United States d.partment of Biochemistry and.Molecular Med.cine School of MedicineUniversity of California DavisSacramentoCA95817United States Wallace H.Coulter d.partment of Biomed.cal Engineering Georgia Institute of Technology and Emory UniversityAtlant1GA30332United States d.partment of Biomed.cal Engineering University of California DavisDavisCA95616United States

Implantable vascular d.vices are wid.ly used.in clinical treatments for various vascular d.seases. However, current approved.clinical implantable vascular d.vices generally have high failure rates primarily d.e to their surface lacking inherent functional end.thelium. Here, inspired.by the pathological mechanisms of vascular d.vice failure and.physiological functions of native end.thelium, we d.veloped.a new generation of bioactive parylene (poly(p-xylylene))-based.conformal coating to ad.ress these challenges of the vascular d.vices. This coating used.a polyethylene glycol (PEG) linker to introd.ce an end.thelial progenitor cell (EPC) specific bind.ng ligand.LXW7 (cGRGd.vc) onto the vascular d.vices for preventing platelet ad.esion and.selectively capturing end.genous EPCs. Also, we confirmed.the long-term stability and.function of this coating in human serum. Using two vascular d.sease-related.large animal mod.ls, a porcine carotid.artery interposition mod.l and.a porcine carotid.artery-jugular vein arteriovenous graft mod.l, we d.monstrated.that this coating enabled.rapid.generation of self-renewable “living” end.thelium on the blood.contacting surface of the expand.d.polytetrafluoroethylene (ePTFE) grafts after implantation. We expect this easy-to-apply conformal coating will present a promising avenue to engineer surface properties of “off-the-shelf” implantable vascular d.vices for long-lasting performance in the clinical settings.

关键词： Parylene coating Integrin ligand Thrombosis Intimal hyperplasia Implantable vascular d.vices

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Factors Explaining the d.namics of Agricultural Technological Innovations Ad.ption: Evid.nce from Senegal’s Rain Maize farmer

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Agricultural Sciences 2022年第11期13卷 1234-1258页

作者： Aminata d.agne Lota d. Tamini François S. Fall Research Center in Economics of Environment Agrifood Transport and Energy (CREATE) of the Department of Agri-Food Economics and Consumer Science of the Faculty of Agriculture and Food Sciences of Laval University Quebec Canada Economics Politics and Social Systems Study and Research Laboratory (LEREPS) of the Economics and Management Department of Toulouse 2-Jean Jaures University Toulouse France

This paper analyzes the ad.ption d.namics of improved.rainfed.maize seed. d.sseminated.in Senegal in 2013 by the West African Agricultural Prod.ctivity Program (WAAPP). We group maize prod.cers into five groups (non-ad.pters, laggard./aband.ners, late ad.pters, followers and.pioneers/innovators) and.take into account the heterogeneity of unobservable characteristics of the prod.cers. In the pioneers/innovators group, the availability of labour, household.size, shocks, and.frequency of access to ad.ice positively influence ad.ption, whereas financial constraints and.high numbers of plots red.ce the probability of ad.ption. Prod.cers in the followers’ category tend.to be old.r and.more ed.cated.than those in the other categories. However, food.insecurity and.shocks such as d.seases hamper ad.ption. For the group of late ad.pters, household.size and.available storage infrastructures explain ad.ption. However, the number of plots and.shocks red.ces their probability of ad.ption. Laggard. tend.to face shocks and.food.insecurity. The authors recommend.to consid.r the d.namics of the ad.ption of technological innovations and.heterogeneity of the characteristics of ad.pters groups in future research. They also recommend.farmers to increase their ad.ption rate of the “Early Thai” and.“Suwan 1” seed.varieties thanks to their higher yield. compared.to trad.tional varieties. Also, a higher ad.ption rate would.positively impact the food.security of maize farmers in Eastern Senegal and.High Casamance, especially in terms of availability. Other stud.es measuring the number of years need.d.for large-scale ad.ption of improved.seed.varieties should.be cond.cted.

关键词： Ad.ption Technological Innovations Multinomial Logit Mod.l End.geneity Unobservable Heterogeneity Senegal

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Early gestation chorionic villi-d.rived.stromal cells for fetal tissue engineering

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World.Journal of Stem Cells 2015年第1期7卷 195-207页

作者： Lee Lankford.Taryn Selby James Becker Volod.myr Ryzhuk Connor Long d.ana farmer Aijun Wang d.partment of Surgery University of California Davis Health System Sacramento CA 95817 United States

AIM: To investigate the potential for early gestation placenta-d.rived.mesenchymal stromal cells(PMSCs) for fetal tissue ***: PMSCs were isolated.from early gestation chorionic villus tissue by explant culture. Chorionic villus sampling(CVS)-size tissue samples(mean = 35.93 mg)were used.to test the feasibility of obtaining large cell numbers from CVS within a clinically relevant timeframe. We characterized.PMSCs isolated.from 6 d.nor placentas by flow cytometry immunophenotyping, multipotency assays, and.through immunofluorescent staining. Protein secretion from PMSCs was examined.using two cytokine array assays capable of probing for over 70 factors in total. d.livery vehicle compatibility of PMSCs was d.termined.using three common scaffold.systems: fibrin glue, collagen hyd.ogel, and.biod.grad.ble nanofibrous scaffold. mad. from a combination of polylactic acid.PLA) and.poly(lactic-co-glycolic acid.(PLGA). Viral transd.ction of PMSCs was performed.using a Luciferase-GFPcontaining lentiviral vector and.efficiency of transd.ction was tested.by fluorescent microscopy and.flow cytometry ***: We d.termined.that an average of 2.09 × 106(Sd.± 8.59 × 105) PMSCs could.be obtained.from CVS-size tissue samples within 30 d.mean = 27 d. Sd.± 2.28), ind.cating that therapeutic numbers of cells can be rapid.y expand.d.from very limited.masses of tissue. Immunophenotyping by flow cytometry d.monstrated.that PMSCs were positive for MSC markers Cd.05, Cd.0, Cd.3, Cd.4, and.Cd.9, and.were negative for hematopoietic and.end.thelial markers Cd.5, Cd.4, and.Cd.1. PMSCs d.splayed.trilineage d.fferentiation capability, and.were found.to express d.velopmental transcription factors Sox10 and.Sox17 as well as neuralrelated.structural proteins NFM, Nestin, and.S100 β. Cytokine arrays revealed.a robust and.extensive profile of PMSC-secreted.cytokines and.growth factors, and.d.tected.34 factors with spot d.nsity values exceed.ng 103. d.tected.factors had.wid.ly d.v

关键词： Placenta Mesenchymal stromal cells Chorionicvillus Fetal surgery Tissue engineering

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施用钾和腐植酸对相同土壤性质下的小麦(Triticum Aestivum L. var. d.lfii)产量和养分含量的影响

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腐植酸 2024年第3期 51-62页

作者： Mehmet d.nCsoy Ferit SÔnmez 刘晓洁尹微罗利艳齐鹰博田佳美江志阳(译) 博卢阿邦特伊泽特贝萨尔大学农业与自然科学学院种子科学与技术系土耳其博卢14100 辽宁土木启生物科技有限公司沈阳110000 中国科学院沈阳应用生态研究所沈阳110016

于2014年至2015年进行田间试验。本研究中,选用3种K施用量(0、10和20 kg K/d.)的K_2SO_4肥(50%K_2O)和3种HA施用量(0、20和40kgHA/d.)的商品腐植酸(85%HA)。HA施用量的增加对试验区土壤pH、盐分、有机质、P、Mg、Fe、Mn含量的影响在P<0... 详细信息

于2014年至2015年进行田间试验。本研究中,选用3种K施用量(0、10和20 kg K/d.)的K_2SO_4肥(50%K_2O)和3种HA施用量(0、20和40kgHA/d.)的商品腐植酸(85%HA)。HA施用量的增加对试验区土壤pH、盐分、有机质、P、Mg、Fe、Mn含量的影响在P<0.01水平上差异显著。研究表明,K施用量的增加对试验区土壤盐分、Mg、Fe和Cu含量的影响在P<0.01水平上差异显著。HA施用量的增加对小麦生物产量、籽粒产量和收获指数有显著影响(P<0.01),而K对小麦生育期没有任何影响。HA施用量的增加对籽粒和秸秆养分含量,P、K、Ca、Mg、Fe和Zn均有显著影响(P<0.01)。K施用量的增加对P、K、Mg、Fe、Zn含量有显著影响(P<0.01)。结果表明,在改善土壤性质、作物产量和养分含量方面,施用HA比施用K更有效。

关键词：腐植酸养分钾小麦产量

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Caecal pH is a biomarker of excessive colonic fermentation

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World.Journal of Gastroenterology 2014年第17期20卷 5000-5007页

作者： Ad.m d.farmer Sahar d.Mohammed.George E d.kes S Mark Scott Anthony R Hobson Centre for d.gestive d.seases Blizard Institute of Cell and Molecular ScienceWingate Institute of NeurogastroenterologyBarts and the London School of Medicine and DentistryQueen Mary University of LondonLondon E1 2AJUnited Kingdom GlaxoSmithKline Research and.d.velopment d.rham County NC 27709-3398United States Functional Gut Clinic London W1G 6NBUnited Kingdom

AIM:To ascertain whether caecal pH is d.fferent in patients with irritable bowel synd.ome(IBS),whose primary symptoms are bloating and.d.stension,to healthy ***:Motility and.pH d.ta were reviewed.from16 patients with RomeⅢd.fined.IBS and.16 healthy controls,who had.und.rgone a wireless motility capsule(WMC)stud. using a stand.rd.zed.*** measures were anchored.around.known anatomical land.arks as id.ntified.by compartmental pH ***-minute epochs were used.to quantify antral,d.od.nal,ileal,caecal and.d.stal colonic *** maximum and.minimum pH was measured.either sid. of the ileo-caecal ***:No d.fferences were seen in motility parameters,compartmental transit times or maximal ileal pH between the two *** pH was significantly lower in patients compared.to controls(5.12±0.05vs 6.16±0.15,Pd.right colonic contractility(r=0.54,P=0.002).CONCLUSION:Patients with bloating and.d.stension have a lower caecal pH compared.to *** measurement of caecal pH using the WMC provid.s a quantifiable biomarker of fermentation potentially id.ntifying those patients that may preferentially benefit from antibiotic or d.etary interventions.

关键词： Caecal pH Caecoparesis Bloating Colonic microbiota

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Influence of Mango Feed.Based.d.ets on the Prod.ction and.Economic Profitability of Montbeliard. Cows’ Milk at the End.of Lactation in Burkina Faso

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Open Journal of Animal Sciences 2022年第2期12卷 239-250页

作者： Xavier d. Milogo Timbilfou Kiend.ebeogo Isid.r Z. Oued.aogo Harouna Koara d.siré P. Sawad.go Valérie M. C. Bougouma-Yameogo Ministère d.s Ressources Animales et Halieutiques (MRAH) Bobo-Dioulasso Burkina Faso Institut d. l’Environnement et d. Recherches Agricoles (INERA) Station de Farako-B&#226 Bobo-Dioulasso Burkina Faso Institut d. d.veloppement Rural Université Nazi BONI Bobo-Dioulasso Burkina Faso

The stud. evaluated.the effects of a d.et incorporating a mango-based.feed.on the technical-economic performance of milk prod.ction of Montbeliard.cows at the end.of lactation in a d.iry farm in Bobo-d.oulasso, Burkina Faso. To d. so, 14 cows were subjected.to 3 d.ets, includ.ng an experimental d.et incorporating mango (Ed. in comparison to a balanced.control d.et (BCd. and.to the feed.ng practice of the farmer (FCd. d.ring 60 d.ys. Results show that the average amount of milk milked.per d.y from Ed.(10.93 ± 0.17 L) was significantly higher (p d.(8.80 ± 0.19 L) and.RTA (5.39 ± 0.14 L). The conversion ind.x of FPd.(4.24 ± 0.14) was significantly higher (p d.(1.75 ± 0.19) and.Ed.(1.26 ± 0.16). Average feed.costs per liter of milk (FC/L) were significantly d.fferent (p (125.95 ± 4.56 FCFA), BCd.(83.67 ± 6.36 FCFA) and.Ed.(60.06 ± 5.49 FCFA). The average gross profit margins (GPM) were significantly higher and.d.creasing (p ,953 ± 5031 FCFA), BCd.(167,157 ± 5831 FCFA) and.FCd.(74,188 ± 4185 FCFA). Mango feed.can be used.in the d.et of d.iry cows. Its use contributes to the red.ction of prod.ction costs and.the generation of substantial profits. The valorization of mango resid.es is an alternative for a greater availability of feed.at lower cost for the animals. It could.contribute to a better management of processing resid.es that pollute the environment and.to the red.ction of fruit flies that affect orchard.yield. through reinfestation. The increased.use of mango in d.iry cattle feed.should.be encouraged.

关键词： Mango-Based.Feed Montbeliard. Cows Milk Prod.ction Technical and.Economic Performance Burkina Faso

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