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Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids

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National Science Review 2021年第5期8卷 23-37页

作者： Ying Wu Fan Lin Yao Zhou Jie wang Shuai Sun Bin wang Zhibin Zhang Guo Li Xiuyun Lin Xutong wang Yue Sun Qianli Dong Chunming Xu Lei Gong jonathan F.Wendel Zhiwu Zhang Bao Liu Key Laboratory of Molecular Epigenetics of the Ministry of Education Northeast Normal University Department of Crop & Soil Sciences Washington State University Brightseed Inc. Department of Ecology Evolution& Organismal BiologyIowa State University

Allopolyploidy is an important process in plant speciation, yet newly formed allopolyploid species typically suffer from extreme genetic bottlenecks. One escape from this impasse might be homoeologous meiotic pairing, during which homoeologous exchanges(HEs) generate phenotypically variable progeny. However,the immediate genome-wide patterns and resulting phenotypic diversity generated by HEs remain largely unknown. Here, we analyzed the genome composition of 202 phenotyped euploid segmental allopolyploid individuals from the fourth selfed generation following chromosomal doubling of reciprocal F1 hybrids of crosses between rice subspecies, using whole-genome sequencing. We describe rampant occurrence of HEs that, by overcoming incompatibility or conferring superiority of hetero-cytonuclear interactions, generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration in tetraploids affects known-function genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level following a single initial hybridization. Our results illuminate the immediate genomic landscapes possible in a tetraploid genomic environment, and underscore HE as an important mechanism that fuels rapid phenotypic diversification accompanying the initial stages of allopolyploid evolution.

关键词： nascent allopolyploidy homoeologous recombination phenotypic diversity plant evolution GWAS dosage effects epistasis

Chronic Cholestatic Liver Injury Attributable to Vedolizumab

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Journal of Clinical and Translational Hepatology 2016年第3期4卷 277-280页

作者： jonathan G.Stine Jennifer wang Brian W.Behm Division of Gastroenterology & Hepatology Department of Medicine University of Virginia Charlottesville VA USA Department of Medicine University of Virginia Charlottesville VA USA

Drug-induced liver injury is a rare but clinically important *** is an α4β7 integrin inhibitor recently approved for use in patients with moderate-to-severe inflammatory bowel *** of hepatoxicity due to vedolizumab in the pre-marketing stage were rare,and all cases resolved upon drug *** present here the first reported case of hepatotoxicity attributable to vedolizumab,which despite drug cessation persisted with chronic cholestatic liver injury.

关键词： Hepatotoxicity Integrin inhibitor Primary sclerosing cholangitis Inflammatory bowel disease

COVID-19 and atherosclerosis: looking beyond the acute crisis

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Emergency and Critical Care Medicine 2022年第1期2卷 1-4页

作者： Zhang Shi Yuanliang Jiang jonathan Weir-McCall Ximing wang Zhongzhao Teng Department of Radiology Zhongshan HospitalFudan UniversityShanghaiChina Department of Radiology University of CambridgeCambridgeUK Department of Radiology General Hospital of Central Theater of the PLAWuhanChina Department of Radiology Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina Nanjing Jingsan Medical Science and Technology Ltd.NanjingChina

The novel coronavirus disease 2019(COVID-19)was firstly reported in Wuhan,China,and eventually identified on December 31,2019 and remains as an ongoing worldwide *** acute respiratory syndrome coronavirus 2(SARS-CoV-2)invades human alveolar epithelial cells in the nose and throat mainly through angiotensin-converting enzyme 2(ACE2),[1]inducing innate inflammation in the lungs largely mediated by pro-inflammatory macrophages and granulocytes.

关键词： acute inflammation respiratory

Neonatal Dubin-Johnson Syndrome and its Differentiation from Biliary Atresia

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Journal of Clinical and Translational Hepatology 2023年第1期11卷 163-173页

作者： Teng Liu Jing Zhao Jia-Yan Feng Yi Lu jonathan A.Sheps Ren-Xue wang Jun Han Victor Ling Jian-She wang The Center for Pediatric Liver Diseases Children’s Hospital of Fudan UniversityShanghaiChina The Department of Pathology Children’s Hospital of Fudan UniversityShanghaiChina BC Cancer Agency VancouverBritish ColumbiaV5Z 1L3Canada University of Victoria-Genome BC Proteomics Center University of VictoriaVictoriaBritish ColumbiaV8Z 7X8Canada Shanghai Key Laboratory of Birth Defects ShanghaiChina

Background and Aims:The aim was to determine if liver biochemistry indices can be used as biomarkers to help differentiate patients with neonatal Dubin–Johnson syndrome(nDJS)from those with biliary atresia(BA).Methods:Patients with genetically-confirmed nDJS or cholangiographically confirmed BA were retrospectively enrolled and randomly assigned to discovery or verification *** liver chemistries,measured during the neonatal period,were *** values were calculated by receiver operating characteristic curve ***:A cohort of 53 nDJS patients was recruited,of whom 13 presented with acholic stools,and 14 underwent diagnostic cholangiography or needle liver biopsy to differentiate from ***-five patients in the cohort,with complete biochemical information measured during the neonatal period,were compared with 133 infants with cholangiographically confirmed *** and direct bilirubin,alanine aminotransferase(ALT),aspartate aminotransferase(AST),total bile acids,alkaline phosphatase,and gamma-glutamyl transferase were significantly lower in nDJS than in *** the discovery cohort,the areas under the curve for ALT and AST were 0.908 and 0.943,*** the validation cohort,13/15 patients in the nDJS group were classified as nDJS,and 10/53 in the BA control group were positive(p<0.00001)with an ALT biomarker cutoff value of 75 IU/*** of 15 patients were classified as nDJS and none were classified positive in the BA group(13/15 vs.0/53,p<0.00001)with an AST cutoff of 87 IU/***:Having assembled and investigated the largest cohort of nDJS patients reported to date,we found that nDJS patients could be distinguished from BA patients using the serum AST level as a *** finding may be clinically useful to spare cholestatic nDJS patients unnecessary invasive procedures.

关键词： Jaundice ABCC2 Cholestasis MRP2 Acholic stools

Insight into the effects of electrochemical factors on host-guest interaction induced signature events in a biological nanopore

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纳米技术与精密工程（英文） 2020年第1期3卷 2-8页

作者： XiaojunWei Zehui Zhang Xiaoqinwang Brian Lenhart Roberto Gambarini jonathan Gray Chang Liu Biomedical Engineering Program University of South CarolinaColumbiaSC 29208USA Department of Chemical Engineering University of South CarolinaColumbiaSC 29208USA

The signature events caused by host-guest interactions in the nanopore system can be used as a novel and characteristic signal in quantitative detection and analysis of various ***,the effect of several electrochemical factors on the host-guest interactions in nanopore still remains ***,we systematically studied host-guest interactions,especially oscillation of DNA-azide adamantane@cucurbit[6]inα-Hemolysin nanopore under varying pH,concentration of electrolytes and counterions(Li+,Na+,K+).Our results indicate correlations between the change of pH and the duration of the oscillation *** addition,the asymmetric electrolyte concentration and the charge of the counterions affects the frequency of signature events in oscillation signals,and even the integrity of the protein *** study provides insight into the design of a future biosensing platform based on signature oscillation signals of the host-guest interaction within a nanopore.

关键词： Nanopore Host-guest interaction Biosensors Electrochemistry

Green manure rotation and application increase rice yield and soil carbon in the Yangtze River valley of China

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Pedosphere 2023年第4期33卷 589-599页

作者： Qian YUE Jianfei SUN jonathan HILLIER Jing SHENG Zhi GUO Puping ZHU Kun CHENG Genxing PAN Yunpeng LI Xin wang Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment Jiangsu Academy of Agricultural SciencesNanjing 210014(China) Nanjing Institute of Environmental Sciences Ministry of Ecology and EnvironmentNanjing 210042(China) Global Academy of Agriculture and Food Security The Royal(Dick)School of Veterinary Studies and The Roslin InstituteThe University of EdinburghEaster Bush CampusMidlothian EH259RG(UK) Institute of Resource Ecosystem and Environment of AgricultureNanjing Agricultural UniversityNanjing 210095(China)

The addition of organic matter via green manure rotation with rice is considered a smart agricultural practice to maintain soil productivity and support environmental ***,few studies have quantitatively assessed the impact of green manure rotation and application on the interactions between agronomic management practice,soil fertility,and crop *** this study,800 pairs of data from 108 studies conducted in the agricultural region of the Yangtze River,China were assessed,and random forest(RF)modeling was performed to evaluate the effect of green manure rotation and application on rice yield and soil *** to a winter fallow system,rotation and application of green manure significantly increased rice yield and soil organic carbon(SOC)by 8.1%and 8.4%,*** to the RF models,rice type,green manure application rate and duration,mineral and organic nitrogen application rates,and initial SOC content and soil pH were identified as the main drivers for rice yield and SOC *** benefit analysis revealed that green manure application rates for early rice in double cropping system and the rice in single cropping system were approximately 20 and 26 t ha-1(fresh weight),***,the optimum green manure application rate was approximately 25 t ha-1(fresh weight)for carbon ***,it should be noted that green manure application to soils with high SOC level might result in the soils becoming a net carbon *** study contributed scientific and quantitative indicators for achieving the greatest benefits in rice yield and increasing SOC upon application of green manure.

关键词： carbon sequestration crop production random forest model soil fertility soil organic carbon

United States-based practice patterns and resource utilization in advanced neuroendocrine tumor treatment

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World Journal of Gastroenterology 2013年第15期19卷 2348-2354页

作者： jonathan Strosberg Roman Casciano Lee Stern Rohan Parikh Maruit Chulikavit Jacob Willet Zhimei Liu Xufang wang Krzysztof J Grzegorzewski H Lee Moffitt Cancer Center and Research Institute Gastrointestinal Tumor DepartmentTampaFL 33612United States LA-SER Analytica New YorkNY 10018United States Novartis Oncology Florham Park Novartis Oncology Florham ParkNJ 07932United States

AIM: To assess advanced neuroendocrine tumor (NET) treatment patterns and resource utilization by tumor progression stage and tumor site in the United States. METHODS: United States Physicians meeting eligibility criteria were provided with online data extraction forms to collect patient chart data on recent NET patients. Resource utilization and treatment pattern data were collected over a baseline period (after diagnosis and before tumor progression), as well as initial and secondary progression periods, with progression defined according to measureable radiographic evidence of tumor progression. Resource categories used in the analysis include: Treatments (e.g. , surgery, chemotherapy, radiotherapy, targeted therapies), hospitalizations and physician visits, diagnostic tests (biomarkers, imaging, laboratory tests). Comparisons between categories of resource utilization and tumor progression status were examined using univariate (by tumor site) and multivariate analyses (across all tumor sites). RESULTS: Fifty-five physicians were included in the study and completed online data extraction forms using the charts of 110 patients. The physician sample showed a relatively even distribution for those affiliated with academic versus community hospitals (46% vs 55%). Forty (36.3%) patients were reported to have pancreatic NET (pNET), while 70 (63.6%) patients had gastrointestinal tract (GI)/Lung as the primary NET site. Univariate analysis showed the proportion of patients hospitalized increased from 32.7% during baseline to 42.1% in the progression stages. While surgeries were performed at similar proportions overall at baseline and progression, pNET patients, were more likely than GI/Lung NET patients to have undergone surgery during the baseline (33.3% vs 25.0%) and any progression periods (26.7% vs 23.4%). While peptide-receptor radionuclide and targeted therapy utilization was low across NET types and tumor stages, GI/Lung types exhibited greater utilization of thes

关键词： Gastrointestinal cancers Neuroendocrine tumors Resource utilization Health economics Clinical practice patterns

Tunable nonlinear refractive index of two-dimensional MoS2, WS2, and MoSe2 nanosheet dispersions [Invited]

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Photonics Research 2015年第2期3卷 51-55页

作者： Gaozhong wang Saifeng Zhang Xiaoyan Zhang Long Zhang Ya Cheng Daniel Fox Hongzhou Zhang jonathan N.Coleman Werner J.Blau Jun wang Key Laboratory of Materials for High-Power Laser Shanghai Institute of Optics and Fine MechanicsChinese Academy of Sciences School of Physics and the Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN) Trinity College Dublin State Key Laboratory of High Field Laser Physics Shanghai Institute of Optics and Fine MechanicsChinese Academy of Sciences

Liquid-phase-exfoliation technology was utilized to prepare layered MoS2, WS2, and MoSe2 nanosheets in cyclohexylpyrrolidone. The nonlinear optical response of these nanosheets in dispersions was investigated by observing spatial self-phase modulation（SSPM） using a 488 nm continuous wave laser beam. The diffraction ring patterns of SSPM were found to be distorted along the vertical direction right after the laser traversing the nanosheet dispersions. The nonlinear refractive index of the three transition metal dichalcogenides dispersions n2 was measured to be 10-7cm2W-1, and the third-order nonlinear susceptibility χ（3）10-9 esu. The relative change of effective nonlinear refractive index Δn2e∕n（2e） of the MoS2, WS2, and MoSe2 dispersions can be modulated 0.012–0.240, 0.029–0.154, and 0.091–0.304, respectively, by changing the incident intensities. Our experimental results imply novel potential application of two-dimensional transition metal dichalcogenides in nonlinear phase modulation devices.

关键词： Mo show exp Tunable nonlinear refractive index of two-dimensional MoS2 WS2

Straw biochar strengthens the life strategies and network of rhizosphere fungi in manure fertilized soils

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Soil Ecology Letters 2019年第1期1卷 72-84页

作者： Dandan wang Na Zhang Haoqi Tang jonathan M.Adams Bo Sun Yuting Liang State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China School of Environmental and Safety Engineering Changzhou UniversityChangzhou 213164China University of the Chinese Academy of Sciences No.19A Yuquan RoadBeijing 100049China

Soil fungi have many important ecological functions,however,their life strategies and interactions in manure fertilized soils are not well *** aim of this study was to investigate the effects of biochar amendment on the fungal life strategies and species interactions in ryegrass(Lolium perenne L.)rhizosphere soil by high-throughput *** soil treatments were evaluated:soil and pig manure mixture without planting ryegrass and biochar application(bulk soil),mixture with ryegrass planting(rhizosphere soil(RS)),and addition of 2%(w/w)biochar with ryegrass(RS+biochar).Our results indicated that temporal turnover,defined as the slope of linear regression between community similarity and time,was significantly higher in the biochar amendment(slope=-0.2689,p<0.0001)relative to the rhizosphere *** biochar addition,the percentage of species employing slow acclimation ecological strategies decreased(from 27% to 17%)and the percentage of sensitive species increased(from 40% to 50%)in comparison to the rhizosphere *** analysis indicated that fungal communities in the biochar amendment enhanced positive correlations compared to the rhizosphere soil and bulk *** equation model indicated that soil pH was the most important factor in altering fungal life strategies and interactions in manure fertilized soils.

关键词： Rhizosphere Biochar Fungal community Life strategies Network analysis