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Integrating Genomic and Transcriptomic Data to Reveal Genetic mechanisms Underlying Piao Chicken Rumpless Trait

Genomics, Proteomics & Bioinformatics 2021年第5期19卷 787-799页

作者： Yun-mei Wang Saber Khederzadeh Shi-Rong Li Newton Otieno Otecko david m.irwin mukesh Thakur Xiao-Die Ren ming-Shan Wang Dong-Dong Wu Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Kunming College of Life Science University of the Chinese Academy of SciencesKunming 650223China Center for Neurobiology and Brain Restoration Skolkovo Institute of Science and TechnologyMoscow 143026Russia Department of Laboratory medicine and Pathobiology University of TorontoToronto M5S 1A8Canada Zoological Survey of India Kolkata 700053India

Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail *** far,the molecular mechanisms underlying tail absence in this breed remain *** this study,we comprehensively employed comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in Piao *** results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this *** regions contain candidate genes associated with rumplessness,including Irx4,Il18,Hspb2,and *** of quantitative trait loci(QTL)and gene functions implies that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao *** hypothesize that strong selection pressures on regulatory elements might lead to changes in gene activity in mesenchymal stem cells of the tail *** ectopic activity could eventually result in tail truncation by impeding differentiation and proliferation of the stem *** study provides fundamental insights into early initiation and genetic basis of the rumpless phenotype in Piao chicken.

关键词： Comparative transcriptomics Population genomics Rumplessness Vertebra development Artificial selection

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Establishment of an optimized CTC detection model consisting of EpCAm,mUC1 and WT1 in epithelial ovarian cancer and its correlation with clinical characteristics

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Chinese Journal of Cancer Research 2022年第2期34卷 95-108页

作者： Tongxia Wang Yan Gao Xi Wang Junrui Tian Yuan Li Bo Yu Cuiyu Huang Hui Li Huamao Liang david m.irwin Huanran Tan Hongyan Guo Department of Obstetrics and Gynecology Peking University Third HospitalBeijing 100191China Department of Pharmacology School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China Department of Laboratory medicine and Pathobiology University of TorontoToronto M5S1A8Canada

Objective:Emerging studies have demonstrated the promising clinical value of circulating tumor cells(CTCs)for diagnosis,disease assessment,treatment monitoring and prognosis in epithelial ovarian ***,the clinical application of CTC remains restricted due to diverse detection techniques with variable sensitivity and specificity and a lack of common ***:We enrolled 160 patients with epithelial ovarian cancer as the experimental group,and 90 patients including 50 patients with benign ovarian tumor and 40 healthy females as the control *** enriched CTCs with immunomagnetic beads targeting two epithelial cell surface antigens(EpCAm and mUC1),and used multiple reverse transcription-polymerase chain reaction(RT-PCR)detecting three markers(EpCAm,mUC1 and WT1)for *** then we used a binary logistic regression analysis and focused on EpCAm,mUC1 and WT1 to establish an optimized CTC detection ***:The sensitivity and specificity of the optimized model is 79.4%and 92.2%,*** specificity of the CTC detection model is significantly higher than CA125(92.2%vs.82.2%,P=0.044),and the detection rate of CTCs was higher than the positive rate of CA125(74.5%vs.58.2%,P=0.069)in early-stage patients(stage I and II).The detection rate of CTCs was significantly higher in patients with ascitic volume≥500 mL,suboptimal cytoreductive surgery and elevated serum CA125 level after 2 courses of chemotherapy(Pmo-resistant patients(26.3%vs.11.9%;26.4%vs.13.4%,Pmedian progression-free survival time for CTC;patients trended to be longer than CTC;patients,and overall survival was shorter in CTC;patients(P=0.043).Conclusions:Our study presents an optimized detection model for CTCs,which consists of the expression levels of three markers(EpCAm,mUC1 and WT1).In comparison with CA125,our model has high specificity and demonstrates better diagnostic values,especi

关键词： Circulating tumor cells epithelial ovarian cancer optimized detection model diagnosis and prognosis

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Hologenomic insights into mammalian adaptations to myrmecophagy

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National Science Review 2023年第4期10卷 24-36页

作者： Shao-Chen Cheng Chun-Bing Liu Xue-Qin Yao Jing-Yang Hu Ting-Ting Yin Burton K.Lim Wu Chen Guo-Dong Wang Cheng-Lin Zhang david m.irwin Zhi-Gang Zhang Ya-Ping Zhang Li Yu State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Department of Natural History Royal Ontario Museum Guangzhou Zoo Center for Excellence in Animal Evolution and Genetics Kunming Institute of ZoologyChinese Academy of Sciences Beijing Zoo Department of Laboratory medicine and Pathobiology University of Toronto

Highly specialized myrmecophagy(ant-and termite-eating) has independently evolved multiple times in species of various mammalian orders and represents a textbook example of phenotypic evolutionary convergence. We explored the mechanisms involved in this unique dietary adaptation and convergence through multi-omic analyses, including analyses of host genomes and transcriptomes, as well as gut metagenomes, in combination with validating assays of key enzymes’ activities, in the species of three mammalian orders(anteaters, echidnas and pangolins of the orders Xenarthra, monotremata and Pholidota, respectively) and their relatives. We demonstrate the complex and diverse interactions between hosts and their symbiotic microbiota that have provided adaptive solutions for nutritional and detoxification challenges associated with high levels of protein and lipid metabolisms, trehalose degradation, and toxic substance detoxification. Interestingly, we also reveal their spatially complementary cooperation involved in degradation of ants’ and termites’ chitin exoskeletons. This study contributes new insights into the dietary evolution of mammals and the mechanisms involved in the coordination of physiological functions by animal hosts and their gut commensals.

关键词： myrmecophagy adaptive evolution hologenome genomics metagenomics convergent evolution

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Single-cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-genesis in Pigs

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 423-436页

作者： Jianbo Li Ligang Wang Dawei Yu Junfeng Hao Longchao Zhang Adeniyi C.Adeola Bingyu mao Yun Gao Shifang Wu Chunling Zhu Yongqing Zhang Jilong Ren Changgai mu david m.irwin Lixian Wang Tang Hai Haibing Xie Yaping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Core Facility for Protein Research Institute of BiophysicsChinese Academy of SciencesBeijing 100101China State Key Laboratory for molecular and Developmental Biology CAS Center for Excellence in Brain Science and Intelligence TechnologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650223China Department of Laboratory medicine and Pathobiology University of TorontoTorontoOntario M5S1A8Canada Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Development of thoracolumbar vertebra(TLV)and rib primordium(RP)is a common evolutionary feature across vertebrates,although whole-organism analysis of the expression dynamics of TLV-and RP-related genes has been ***,we investigated the single-cell transcriptome landscape of thoracic vertebra(TV),lumbar vertebra(LV),and RP cells from a pig embryo at 27 days post-fertilization(dpf)and identified six cell types with distinct gene expression ***-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP *** analysis of cell type-specific and strand-specific expression uncovered the extremely high level of HOXA103′-UTR sequence specific to osteoblasts of LV cells,which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV ***,this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell type-specific resolution,which serves as a comprehensive view on the transcriptional profile of animal embryo development.

关键词： scRNA-seq Thoracolumbar vertebra transition Rib-genesis Osteogenesis Angiogenesis

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Comparative population genomics reveals genetic basis underlying body size of domestic chickens

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Journal of molecular Cell Biology 2016年第6期8卷 542-552页

作者： ming-Shan Wang Yong-Xia Huo Yan Li Newton OOtecko Ling-Yan Su Hai-Bo Xu Shi-Fang Wu min-Sheng Peng He-Qun Liu Lin Zeng david m.irwin Yong-Gang Yao Dong-Dong Wu Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204China College of Life Science Anhui UniversityHefei 230601China Laboratory for Conservation and Utilization of Bio-Resource Yunnan UniversityKunming 650091China Key Laboratory of Animal models and Human Disease mechanisms of the Chinese Academy of Sciences&Yunnan Province Kunming Institute of ZoologyKunming 650223China Department of Laboratory medicine and Pathobiology University of TorontoTorontoOntario M5S 1A8Canada Banting and Best Diabetes Centre University of TorontoTorontoOntario M5G 2C4Canada

Body size is the most important economic trait for animal production and *** hundreds of loci have been reported to be associated with growth trait and body weight in *** loci are mapped to large genomic regions due to the low density and limited number of genetic markers in previous ***,we employed comparative population genomics to identify genetic basis underlying the small body size of Yuanbao chicken(a famous ornamental chicken)based on 89 whole *** most significant signal was mapped to the BmP10 gene,whose expression was upregulated in the Yuanbao *** of BmP10 induced a significant decrease in body length by inhibiting angiogenic vessel development in *** addition,three other loci on chromosomes 1,2,and 24 were also identified to be potentially involved in the development of body *** results provide a paradigm shift in identification of novel loci controlling body size variation,availing a fast and efficient *** loci,particularly BmP10,add insights into ongoing research of the evolution of body size under artificial selection and have important implications for future chicken breeding.

关键词： body size artificial selection comparative population genomics domestication

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c-Cbl介导了hSef的泛素化和降解(英文)

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生物化学与生物物理进展 2008年第1期35卷 43-49页

作者：任永明荣知立李智勇程龙李颖华王银银任芳丽 david m.irwin 常智杰清华大学医学院清华大学生物科学与技术系生物膜与膜生物技术国家重点实验室北京100084 Department of Laboratory medicine and Pathobiology University of Toronto TorontoOntCanada

Sef(similar expression to fgf genes)作为FGF信号通路中可诱导的拮抗分子相继在斑马鱼,小鼠,和人类中被鉴定出来,并进行了相应的功能研究.目前对于Sef蛋白本身稳定性的研究还未见报道.对c-Cbl对Sef稳定性的影响进行了研究.免疫荧光实... 详细信息

Sef(similar expression to fgf genes)作为FGF信号通路中可诱导的拮抗分子相继在斑马鱼,小鼠,和人类中被鉴定出来,并进行了相应的功能研究.目前对于Sef蛋白本身稳定性的研究还未见报道.对c-Cbl对Sef稳定性的影响进行了研究.免疫荧光实验表明Sef能够和c-Cbl蛋白在细胞中发生共定位,随后的免疫共沉淀实验证明Sef能够和c-Cbl发生相互作用.体内泛素化实验表明c-Cbl能够使Sef发生明显的泛素化作用.这种泛素化最终导致了Sef本身的剂量依赖性的降解.针对c-Cbl的siRNA表达也使Sef稳定细胞系的表达水平得到恢复.结果表明,c-Cbl对Sef的泛素化及降解可能作为一种调控拮抗因子的蛋白质水平从而最终调节信号通路的一种机制.

关键词： hSef c-Cbl 泛素化降解

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人类基因组中保守二级结构的纯净化选择及其在转录调控网络中的作用

人类基因组中保守二级结构的纯净化选择及其在转录调控网络中的作...

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中国遗传学会第八次代表大会暨学术讨论会

作者：谢海兵 david m.irwin 张亚平中国科学院昆明动物研究所云南大学生物资源保护与利用实验室 Department of Laboratory medicine and Pathobiology University of Toronto100 College StreetTorontoOnt.Canada M5G 1L5

保守基因组序列是一些在远源物种基因组间仍保持着高度相似性的 DNA 序列。因为与人类遗传疾病有着紧密的联系,对保守基因组序列的研究是近年来比较基因组学的一个热点。保守二级结构是一类自身能折叠形成二级结构的特殊的保守基因组序... 详细信息

保守基因组序列是一些在远源物种基因组间仍保持着高度相似性的 DNA 序列。因为与人类遗传疾病有着紧密的联系,对保守基因组序列的研究是近年来比较基因组学的一个热点。保守二级结构是一类自身能折叠形成二级结构的特殊的保守基因组序列。本文结合 Hapmap 计划提供的现代人群 SNP 信息,分析了保守二级结构上的 SNP 的分布特征,发现这些保守二级结构上的 SNP 密度显著地低于其侧翼序列上的 SNP 密度。将 SNP 位点划分为祖先型等位基因 (ancestral allele)和新生型等位基因(derived allele),我们发现相对于侧翼序列, 有更高比例的保守二级结构 SNP 具有低的新生型等位基因频率(derived allele frequency, DAF),说明保守二级结构在现代人群中受到了纯净化选择的作用。将保守二级结构的序列划分为茎区位点和环区(包含泡区)位点时,茎区位点比环区位点具有更低的 SNP 密度,并且有更高比例的茎区 SNP 具有低的 DAF,说明保守二级结构的茎区比环区受到更强的纯净化选择作用。比较基因间保守二级结构与已知的转录因子结合位点发现,有很多保守二级结构可能是作为转录因子在基因组内的结合位点发挥作用。基因间保守二级结构倾向于聚集于转录因子编码基因附近,提示这些保守二级结构可能作为顺式作用元件,通过结合转录因子完成对邻近转录因子编码基因表达的调控,因而可能在转录调控网络中发挥着重要的作用。

关键词：保守二级结构 SNP DAF 纯净化选择转录调控网络

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The role of N-glycosylation in cancer

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Acta Pharmaceutica Sinica B 2024年第3期14卷 1098-1110页

作者： Yu Lin david m.Lubman Department of Surgery University of Michigan Medical CenterAnn ArborMI 48109USA

Despite advances in understanding the development and progression of cancer in recent years,there remains a lack of comprehensive characterization of the cancer *** play an important role in medicine and are involved in various human disease conditions including ***-moieties participate in fundamental cancer processes like cell signaling,invasion,angiogenesis,and *** N-glycosylation significantly impacts cancer processes and targeted therapies in ***,understanding N-glycosylation in a tumor is essential for comprehending disease progression and discovering anti-cancer targets and biomarkers for therapy monitoring and *** review presents the fundamental process of protein N-glycosylation and summarizes glycosylation changes in tumor cells,including increased terminal sialylation,N-glycan branching,and ***,the role of N-glycosylation in tumor signaling pathways,migration,and metabolism are *** and glycopeptides as potential biomarkers for early detection of cancer based on site specificity have been ***,understanding and exploring the cancer glycoproteome,along with its role in medicine,implication in cancer and other human diseases,highlights the significance of N-glycosylation in tumor processes,necessitating further research for potential anticancer targets and biomarkers.

关键词： N-Glycosylated proteins Cancer signaling Cancer angiogenesis Cancer metabolism Cancer biomarkers

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东亚地区家犬群体背景下的松狮起源研究

东亚地区家犬群体背景下的松狮起源研究

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2015中国遗传学会大会

作者：杨贺川王国栋王猛马娅萍尹婷婷樊若溪吴宏钟丽 david m.irwin 翟巍巍张亚平中国科学技术大学生命科学学院中国科学院昆明动物研究所遗传资源与进化国家重点实验室新加坡基因组研究所云南大学生物资源保护与利用重点实验室中国科学院大学中国科学院大学昆明生命科学学院加拿大多伦多大学药物与病理学实验室

东亚地区的品种犬是家犬被驯化后在这一地区品种化所产生。这些品种犬中有许多群体在系统发育树上形成相对古老的分支。其中,松狮犬的品种形成历史久远,而且具有许多独特的表型,例如结实的体形,双层被毛,以及蓝黑色的舌头。在本工作中,... 详细信息

东亚地区的品种犬是家犬被驯化后在这一地区品种化所产生。这些品种犬中有许多群体在系统发育树上形成相对古老的分支。其中,松狮犬的品种形成历史久远,而且具有许多独特的表型,例如结实的体形,双层被毛,以及蓝黑色的舌头。在本工作中,我们采用基于限制性酶切位点相关DNA测序(RAD-seq)的方法,对采自中国地区的9只松狮犬的全基因组DNA进行了简化测序。将这一数据与他人已发表的包括4只灰狼,33只家犬的全基因组测序数据,以及包含1191只犬科动物的全基因组SNP芯片数据相结合,通过主成分分析,群体结构分析以及Treemix等分析,我们发现松狮与沙皮犬、秋田犬等东亚的品种犬同属于东亚地区的一个古老的分支。与其他家犬群体相比较,松狮与中国土狗关系最为密切。我们通过采用G-PhoCS对松狮犬与中国土狗的分歧时间进行了估计,发现这两个群体的分歧时间在10000年前左右。我们同时通过PBS和SweepFinder两种方法对松狮基因组中可能受到选择的位点进行了检测,发现松狮基因组中与消化和代谢相关的基因,以及与肌肉形成和心脏发育相关的基因受到了正选择的作用。我们这一工作是对东亚地区的品种犬起源问题进行研究的早期工作,为未来这一方向的研究提供了重要参照。

关键词：家犬驯化松狮东亚品种犬群体历史人工选择

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Evaluation of hand infections in the emergency department using point-of-care ultrasound

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World Journal of Emergency medicine 2024年第4期15卷 283-288页

作者： david Ahmad Haidar david mintz Brandon m Wubben Omar Rizvi Srikar Adhikari Department of Emergency medicine Michigan MedicineAnn Arbor 48109-1382USA University of Arizona College of medicine Tucson 85724USA Department of Emergency medicine University of IowaIowa City 52242-1009USA Department of Surgery University of Arizona College of MedicineTucson 85724USA Department of Emergency medicine University of Arizona College of MedicineTucson 85724USA

BACKGROUND:We aimed to evaluate the utility of point-of-care ultrasound(POCUS)in the assessment of hand infections that present to the emergency department(ED)and its impact on medical decision making and patient ***:We conducted a retrospective review of patients who presented to two urban academic EDs with clinical presentations concerning for skin and soft tissue infections(SSTI)of the hand between December 2015 and December *** trained POCUS fellowship physicians reviewed an ED POCUS database for POCUS examinations of the *** then reviewed patients’electronic health records(EHR)for demographic characteristics,history,physical examination findings,ED course,additional imaging studies,consultations,impact of POCUS on patient care and final ***:We included a total of 50 cases(28 male,22 female)in the final *** most common presenting symptoms and exam findings were pain(100%),swelling(90%),and erythema(74%).The most common sonographic findings were edema(76%),soft tissue swelling(78%),and fluid surrounding the tendon(57%).POCUS was used in medical decision making 68%of the time(n=34),with the use of POCUS leading to changes in management 38%of the time(n=19).POCUS use led to early antibiotic use(11/19),early consultation(10/19),and led to the performance of a required procedure(8/19).The POCUS diagnosis was consistent with the discharge diagnosis of flexor tenosynovitis 8/12 times,abscess 12/16 times,and cellulitis 14/20 ***:POCUS is beneficial for evaluating of hand infections that present to the ED and can be used as an important part of medical decision making to expedite patient care.

关键词： Ultrasound Point-of-care ultrasound Cellulitis Abscess Flexor tenosynovitis

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