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Simultaneously quantifying hundreds of acylcarnitines in multiple biological matrices within ten minutes using ultrahigh-performance liquid-chromatography and tandem mass spectrometry

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Journal of Pharmaceutical Analysis 2024年第1期14卷 140-148页

作者： Jingxian Zhang Qinsheng Chen Lianglong Zhang Biru Shi Men Yu Qingxia Huang Huiru Tang State Key Laboratory of Genetic Engineering School of Life SciencesHuman Phenome InstituteZhangjiang Fudan International Innovation CenterMetabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular PhenomicsZhongshan HospitalFudan UniversityShanghai200032China Wuhan Laboratory for Shanghai Metabolome Institute(SMI)Ltd. Wuhan430000China

Acylcarnitines are metabolic intermediates of fatty acids and branched-chain amino acids having vital biofunctions and pathophysiological significances. Here, we developed a high-throughput method for quantifying hundreds of acylcarnitines in one run using ultrahigh performance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS). This enabled simultaneous quantification of 1136 acylcarnitines (C0–C26) within 10-min with good sensitivity (limit of detection 0.992), accuracy (relative error 0.998) for predicting retention time (tR) of acylcarnitines with no standards and built a database of their multiple reaction monitoring parameters (tR, ion-pairs, and collision energy). Furthermore, we quantified 514 acylcarnitines in human plasma and urine, mouse kidney, liver, heart, lung, and muscle. This provides a rapid method for quantifying acylcarnitines in multiple biological matrices.

关键词： Acylcarnitine UPLC-MS/MS Quantitative structure-retention relationship molecular phenotype

molecular phenotypes reveal heterogeneous engraftments of patient-derived hepatocellular carcinoma xenografts

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Chinese Journal of Cancer Research 2021年第4期33卷 470-479页

作者： Jianyong Zhuo Di Lu Jianguo Wang Zhengxing Lian Jiali Zhang Huihui Li Beini Cen Xuyong Wei Qiang Wei Haiyang Xie Xiao Xu Department of Hepatobiliary and Pancreatic Surgery The Center for Integrated Oncology and Precision MedicineAffiliated Hangzhou First People’s HospitalZhejiang University School of MedicineHangzhou 310003China Department of Hepatobiliary and Pancreatic Surgery the First Affiliated HospitalZhejiang University School of MedicineHangzhou 310003China National Health Commission Key Laboratory of Combined Multi-organ Transplantation Institute of Organ TransplantationZhejiang UniversityHangzhou 310003China

Objective:Patient-derived xenograft(PDX)models provide a promising preclinical platform for hepatocellular carcinoma(HCC).However,the molecular features associated with successful engraftment of PDX models have not been ***:HCC tumor samples from 76 patients were implanted in immunodeficient *** molecular expression was evaluated by *** and tumor characteristics as well as tumor molecular expressions were compared for PDX engraftment using the Chi-square *** independent prediction parameters were identified by logistic regression ***:The engraftment rate for PDX models from patients with HCC was 39.47%(30/76).Tumors from younger patients and patients with elevated preoperative alpha-fetoprotein level had higher engraftment *** with poor differentiation and vascular invasion were related to engraftment *** positive expression of CK19,CD133,glypican-3(GPC3),and Ki67 in tumor samples was associated with engraftment *** regression analyses indicated that GPC3 and Ki67 were two of the strongest predictors of PDX *** with GPC3/Ki67 phenotypes showed heterogeneous engraftment rates,with 71.9%in GPC3^(+)/Ki67^(+)tumors,30.8%in GPC3^(-)/Ki67^(+)tumors,15.0%in GPC3^(+)/Ki67^(-)tumors,and 0 in GPC3^(-)/Ki67^(-)***:Successful engraftment of HCC PDXs was significantly related to molecular *** with the GPC3+/Ki67+phenotype were the most likely to successfully establish HCC PDXs.

关键词： Hepatocellular carcinoma patient-derived xenografts heterogeneous establishment molecular phenotype

Proteomic analysis of F_(1)hybrids and intermediate variants in a Littorina saxatilis hybrid zone

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Current Zoology 2022年第3期68卷 351-359页

作者： Angel P.DIZ Mónica R.ROMERO Juan GALINDO María SAURA David O.F.SKIBINSKI Emilio ROLÁN-ALVAREZ Centro de Investigación Mariña(CIM-UVIGO) Universidade de VigoVigo 36310Spain Departamento de Mejora Genética Animal INIAMadrid 28040Spain Institute of Life Science Swansea University Medical SchoolSwansea SA28PPUK

Proteomic analysis was carried out on the Crab(upper-shore)and Wave(lower-shore)ecotypes of Littorina saxatilis from a hybrid zone at Silleiro Cape,*** profiles of individual snails were *** expression in F_(1)hybrid snails bred in the laboratory and snails with intermediate shell phenotypes collected from the mid-shore were compared with Crab and Wave ecotypes using analytical approaches used to study *** analysis over many protein spots showed that the F_(1)snails are distinct from both ecotypes but closer to the Wave *** intermediate snails are highly variable,some closer to the Crab and others to the Wave *** on a protein by protein basis,some proteins are significantly closer in expression to the Crab and others to the Wave ecotype for both F_(1)and intermediate ***,a significant majority of proteins were closer in expression to the Wave ecotype for the F_(1),consistent with the multivariate *** such significant majority toward either the Crab or Wave ecotype was observed for the intermediate *** closer similarity of F_(1)and Wave ecotype expression patterns could be the result of similar selective pressures in the similar mid-shore and low-shore *** a significantly larger number of proteins,intermediate snails were closer in expression to the ecotype having the lower expression,for both Crab and Wave *** is somewhat unexpected as lower expression might be expected to be an indication of impairment of function and lower *** analysis could be important for the identification of candidate proteins useful for gaining improved understanding of adaptation and barriers to gene flow in hybrid zones.

关键词： F_(1)hybrids gene expression marine invertebrates molecular phenotype reproductive isolation speciation

Application of molecular phenotypes detected with new available SCAR markers to distinguish different commercial strains of Lentinula edodes in China

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Application of molecular phenotypes detected with new availa...

Analyses of functional conservation and divergence reveal requirement of b HLH010/089/091 for pollen development at elevated temperature in Arabidopsis

第二届全国食用菌中青年专家学术交流会

作者： Haibo Li~(a,b,*),Xueqian Wu~(a,b,c,*),Lizhong Fu~(a,b,c),Hailong Wei~(a,b,c),Qingqi Wu~(a,b,c),Huazheng Peng~(a,b),Liang He~(a,b), Junwen Cheng~(a,b),and Qunying Jin~(a,b) a Zhejiang Forestry Academy,Hangzhou 310023,China b Zhejiang Provincial Key Laboratory of Biological and Chemical Utilization of Forest Resource,Hangzhou 310023,China c Zhejiang Essence Fungi Development Company,Lishui 323000,China

＜正＞Lentinula edodes is an important edible and medical mushroom and is widely cultivated in some Asian countries,especially in China,Korea,and *** than 100 strains of *** are cultivated on a commercial scale in *** differences on mature period,yield and quality traits of its fruitbody exsit among different strains and it is difficult to distinguish them accurately through morphological and physiological features.A simple, reliable and effective method to distinguish these commercial strains is very important for the Lentinula *** the present study,23 commercial strains of *** cultivated in large areas in China at present were collected and analyzed with randomly amplified polymorphic DNA（RAPD） and sequence-related amplified polymorphism （SRAP） *** informative dominant sequence characterized amplified region（SCAR） markers were developed by designing ten pairs of specific SCAR primers from ten sequenced differential RAPD and SRAP bands, *** on these SCAR markers,eleven SCAR phenotypes were detected among the 23 studied commercial *** differences in SCAR phenotypes between different strains made these SCAR phenotypes potentially useful to characterize six strains and distinguish them from other seventeen ***,based on SCAR phenotypes,the other seventeen strains were divided into four groups which could also be distinguished between each *** our knowledge,this study is the first to use jointly many SCAR markers for distinguishing different commercial strains of *** in China.

关键词： Lentinula edodes Edible mushroom Commercial strain SCAR marker molecular phenotype

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Journal of Genetics and Genomics 2020年第8期47卷 477-492页

作者： Ying Fu Mengyu Li Shiting Zhang Qi Yang Engao Zhu Chenjiang You Ji Qi Hong Ma Fang Chang State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity SciencesInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China Department of Biology The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA

The Arabidopsis b HLH010/089/091(basic helix-loop-helix)genes are functionally redundant and are required for both anther development and normal expression of DYT1-activated anther-related *** three genes are conserved in Brassicaceae,suggesting that each of them is under selection pressure;however,little is known about the possible functional differences among these b HLH genes and between the b HLH and DYT1 ***,we compared novel anther transcriptomic data sets from b HLH010/089/091 single and double mutants,with an anther transcriptomic data set from the wild type(WT)and a previously obtained anther transcriptomic data set from the bhlh010 bhlh089 bhlh091 triple *** results revealed molecular phenotypes that support the functional redundancy and divergence of b HLH010,b HLH089,and b HLH091,as well as the functional overlap and difference between them and ***-binding analyses revealed that DYT1 and b HLH089 specifically recognize the TCATGTGC box to activate the expression of target genes,including ATA20,EXL4,and *** addition,among genes whose expression was affected in the bhlh010 bhlh089 double and bhlh010 bhlh089 bhlh091 triple mutants,genes that are involved in the stress response and cell signaling were enriched,which included256 genes whose expression was preferentially induced by heat during early flower ***,the bhlh double mutants exhibited defective pollen development when the plants were grown under elevated temperature,suggesting that b HLH genes are important for anther gene expression under such *** results are consistent with the observation that the heat-induced expression of several genes is less in the bhlh mutants than that in the ***,our results provide important insights into the molecular mechanism underlying the activation of direct targets by DYT1-b HLH089 heterodimers and demonstrate the protective roles of b HLH010/089/091 in maintaining fertility upon heat stress.

关键词： DYT1 bHLH010/089/091 Male fertility molecular phenotype Transcriptional activation Heat response

Factors affecting the prognosis of children with medulloblastoma: A single institution retrospective analysis of 40 cases

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Translational Neuroscience and Clinics 2017年第1期3卷 16-27页

作者： Jianzhong Yu We Shi Hao Li Department of Neurosurgery Children's Hospital of Fudan University

Few studies have investigated the factors associated with the prognosis of children with medulloblastoma. This retrospective observational study evaluated the association of molecular subtype, clinical characteristics, and pathological types with the outcomes of children with medulloblastoma. This study included 40 patients with medulloblastoma who underwent surgical resection at the Affiliated Children's Hospital of Fudan University between January 2004 and June 2014. The primary outcome was overall survival(OS). Risk factors associated with survival, disease progression, and recurrence were analyzed by univariate Cox regression analysis; the identified significant risk factors were further analyzed by Kaplan-Meier survival curves. Immunohistochemistry analysis of Yes-associated protein 1(YAP1) and GRB2-associated protein 1(GAB1) was used for medulloblastoma subtype identification; 20% of tumors were the WNT subtype, and 32.5% were the SHH subtype, with the remainder being non-SHH/*** associated with OS included M stage, calcification, cerebrospinal fluid fistula,postoperative treatment(radiotherapy, chemotherapy, or both), postoperative Karnofsky Performance Scale score, and molecular subtype(P molecular subtyping of medulloblastoma was more predictive of survival than histopathology in patients undergoing adjuvant therapy.

关键词： child medulloblastoma clinical factors molecular phenotype overall survival time prognosis