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Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume

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

作者： Sergio Alan Cervantes-Pérez Sandra Thibivilliers Carole Laffont andrew d.farmer Florian Frugier Marc Libault department 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

Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named *** symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria,as well as the initiation of nodule primordia from root cortical,endodermal,and pericycle cells,leading to the development of a new root organ,the nodule,where bacteria fix and assimilate the atmospheric dinitrogen 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 deeper understanding of early responses to rhizobial infection in Medicago roots.A gene expression map of the Medicago root was generated,comprising 25 clusters,which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes.A focus on root hair,cortex,endodermis,and pericycle cell types,showing the strongest differential regulation in response to a short-term(48 h)rhizobium inoculation,revealed not only known genes and functional pathways,validating 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： Medicago root single-cell transcriptomic rhizobium nodule initiation root hair cells cortical cells

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Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume

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Molecular Plant 2023年第2期16卷 481-483页

作者： Sergio Alan Cervantes-Perez Sandra 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 differing areas of the two side-by-side UMAPs,were misaligned in the *** corrected Figure 1,in which the red circles indicate areas of differing density 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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Effectiveness of Wastewater-Based Epidemiology as an Early Warning Tool to detect SARS-CoV-2 (COVId-19)

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Health 2024年第7期16卷 635-656页

作者： Rakib Ahmed Chowdhury daniel E. Meeroff Sumaiya Sharmin Alamgir Kabir Sara Hollenbeck Valerie dalencourt Thu Nguyen Zack farmer Frederick Bloetscher Waseem Asghar Stacey Volnick College of Engineering and Computer Science Florida Atlantic University Boca Raton FL USA

Medical diagnostic tests to detect Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) for individuals in the United States were initially limited to people who were traveling or symptomatic to track disease incidence due to the cost of providing testing for all people in a community on a routine basis. As an alternative to randomly sampling large groups of people to track disease incidence at significant cost, wastewater-based epidemiology (WBE) is a well-established and cost-effective technique to passively measure the prevalence of disease in communities without requiring invasive testing. WBE can also be used as a forecasting tool since the virus is shed in individuals prior to developing symptoms that might otherwise prompt testing. This study applied the WBE approach to understand 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 including dormitories, academic buildings, and athletic facilities. The WBE analysis was conducted by sampling from building-specific lift stations and enumerating target viral copies using RT-qPCR analysis. The WBE results were compared with the 7-day rolling averages of confirmed infected individuals for the following week after the wastewater sample analysis. In most cases, changes in the WBE outcomes were followed by similar trends in the clinical data. The positive predictive value of the applied WBE approach was 86% for the following week of the sample collection. In contrast, positive correlations between the two data 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 identified on the next day of the sampling events. The P value of 0.007 for dorm A suggests high significance, while moderate significance was observed for the other dormitories (B, C, and d). The outcomes of this in

关键词： SARS-CoV-2 Wastewater detection Wastewater-Based Epidemiology (WBE)

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

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

作者： dake Hao Jonathan Lin Ruiwu Liu Christopher Pivetti Kaeli Yamashiro Linda M.Schutzman Junichiro Sageshima Mimmie Kwong Nataliya Bahatyrevich diana L.farmer Misty d.Humphries Kit S.Lam Alyssa Panitch Aijun Wang department of Surgery School of MedicineUniversity of California DavisSacramentoCA95817United States Institute for Pediatric Regenerative Medicine Shriners Hospitals for ChildrenSacramentoCA95817United States department of Biochemistry and Molecular Medicine School of MedicineUniversity of California DavisSacramentoCA95817United States Wallace H.Coulter department of Biomedical Engineering Georgia Institute of Technology and Emory UniversityAtlant1GA30332United States department of Biomedical Engineering University of California DavisDavisCA95616United States

Implantable vascular devices are widely used in clinical treatments for various vascular diseases. However, current approved clinical implantable vascular devices generally have high failure rates primarily due to their surface lacking inherent functional endothelium. Here, inspired by the pathological mechanisms of vascular device failure and physiological functions of native endothelium, we developed a new generation of bioactive parylene (poly(p-xylylene))-based conformal coating to address these challenges of the vascular devices. This coating used a polyethylene glycol (PEG) linker to introduce an endothelial progenitor cell (EPC) specific binding ligand LXW7 (cGRGddvc) onto the vascular devices for preventing platelet adhesion and selectively capturing endogenous EPCs. Also, we confirmed the long-term stability and function of this coating in human serum. Using two vascular disease-related large animal models, a porcine carotid artery interposition model and a porcine carotid artery-jugular vein arteriovenous graft model, we demonstrated that this coating enabled rapid generation of self-renewable “living” endothelium on the blood contacting surface of the expanded 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 devices for long-lasting performance in the clinical settings.

关键词： Parylene coating Integrin ligand Thrombosis Intimal hyperplasia Implantable vascular devices

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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： Himabindu Kudapa 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 dutta deepak K. Gupta Archana Singh Kishor Gaikwad Tilak R. Sharma Gregory d. May Nagendra 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 department of Agriculture-Agricultural Research Service (USdA-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 department 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 developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, 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 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were predicted 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 validated, 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 breeding applications in pigeonpea.

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

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Early gestation chorionic villi-derived 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 Volodymyr Ryzhuk Connor Long diana farmer Aijun Wang department of Surgery University of California Davis Health System Sacramento CA 95817 United States

AIM: To investigate the potential for early gestation placenta-derived 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 donor 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. delivery vehicle compatibility of PMSCs was determined using three common scaffold systems: fibrin glue, collagen hydrogel, and biodegradable nanofibrous scaffolds made from a combination of polylactic acid(PLA) and poly(lactic-co-glycolic acid)(PLGA). Viral transduction of PMSCs was performed using a Luciferase-GFPcontaining lentiviral vector and efficiency of transduction was tested by fluorescent microscopy and flow cytometry ***: We determined 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), indicating that therapeutic numbers of cells can be rapidly expanded from very limited masses of tissue. Immunophenotyping by flow cytometry demonstrated that PMSCs were positive for MSC markers Cd105, Cd90, Cd73, Cd44, and Cd29, and were negative for hematopoietic and endothelial markers Cd45, Cd34, and Cd31. PMSCs displayed trilineage differentiation capability, and were found to express developmental 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 detected 34 factors with spot density values exceeding 103. detected factors had widely div

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. delfii)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 dÌnCsoy 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/da)的K_2SO_4肥(50%K_2O)和3种HA施用量(0、20和40kgHA/da)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/da)的K_2SO_4肥(50%K_2O)和3种HA施用量(0、20和40kgHA/da)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： Adam d.farmer Sahar d Mohammed George E dukes S Mark Scott Anthony R Hobson Centre for digestive diseases 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 development durham County NC 27709-3398United States Functional Gut Clinic London W1G 6NBUnited Kingdom

AIM:To ascertain whether caecal pH is different in patients with irritable bowel syndrome(IBS),whose primary symptoms are bloating and distension,to healthy ***:Motility and pH data were reviewed from16 patients with RomeⅢdefined IBS and 16 healthy controls,who had undergone a wireless motility capsule(WMC)study using a standardized *** measures were anchored around known anatomical landmarks as identified by compartmental pH ***-minute epochs were used to quantify antral,duodenal,ileal,caecal and distal colonic *** maximum and minimum pH was measured either side of the ileo-caecal ***:No differences 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 distension have a lower caecal pH compared to *** measurement of caecal pH using the WMC provides a quantifiable biomarker of fermentation potentially identifying those patients that may preferentially benefit from antibiotic or dietary interventions.

关键词： Caecal pH Caecoparesis Bloating Colonic microbiota

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South Asian dairy smallholders: A scoping review of practices and zoonoses

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Asian Pacific Journal of Tropical Medicine 2023年第10期16卷 446-452页

作者： Emily Schembri Angus J d Campbell Juan Pablo Villanueva-Cabezas Melbourne School of Population and Global Health The University of MelbourneVictoriaAustralia The Nossal Institute for Global Health The University of MelbourneVictoriaAustralia The Peter doherty Institute for Infection and Immunity The University of Melbourne and the Royal Melbourne HospitalVictoriaAustralia

Objective: To identify and discuss on-farm management practices linked to bacterial zoonosis risk in smallholder dairy farmers in South Asia. Methods: This scoping review was conducted as per the PRISMA-ScR guidelines. Five hundred and two publications were retrieved from five online databases using a comprehensive search strategy. Studies were selected if they discussed a farm management practice which impacted human health within a South Asian country. Results: Twenty-two studies were included. Seven management practices relevant to farmers, livestock and their shared environment were identified including raw milk consumption, farm hygiene management, personal protective equipment uses, animal vaccination, cleaning udders, hand washing and disposal of afterbirth materials. Preventive practices were found to be utilized at lower frequencies compared to risk increasing practices. Awareness of bacterial zoonoses is particularly low within the region. Conclusions: Based on the results of this review, it was determined that improving farmer awareness of bacterial zoonotic diseases may favor several of the presented leverage points within the South Asian smallholder dairy system. Relying on formal school education to improve this awareness may not solve this problem, instead, more focus on accessible and affordable zoonoses education and farming programs is required.

关键词： Management practices Zoonoses dairy Smallholder system

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High efficiency, high power 808nm laser array and stacked arrays optimized for elevated temperature operation

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光机电信息 2004年第6期21卷 1-11页

作者： Crump P A Crum T R deVito M farmer J Grimshaw M Huang Z Igl S A Macomber S Thiagarajan P Wise d nLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USAnLight Photonics Corporation 5408 NE 88th Street Building E Vancouver WA 98665 USA

Operation of 808-nm laser diode pumping at elevated temperature is crucial to many applications. Reliable operation at high power is limited by high thermal load and low catastrophic optical mirror damage (COMd) threshold at elevated temperature range. We demonstrated high efficiency and high power operation at elevated temperature with high COMd power. These results were achieved through device design optimization such as growth conditions, doping profile, and materials composition of the quantum-well and other layers. Electrical-to-optical efficiency as high as 62% was obtained through lowered threshold current, lowered series resistance and increased slope efficiency. The performance of single broad-area laser diodes scales to that of high power single bars on water-cooled copper micro-channel heatsinks or conductively-cooled CS heatsinks. No reduction in bar performance or significant spectral broadening is seen when these micro-channel coolers are assembled into 6-bar and 18-bar CW stacks for the highest power levels.

关键词：激光技术高功率激光激光二极管单发射器 COMd

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