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Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans

Science China(Life Sciences) 2019年第4期62卷 579-593页

作者： Wenyu Zhang Yuanxiao Gao Manyuan Long Bairong Shen Institutes for Systems genetics West China Hospital Sichuan University Department of Ecology and Evolution the University of Chicago Department of Evolutionary genetics Max-Planck Institute for Evolutionary Biology Department of Evolutionary Theory Max-Planck Institute for Evolutionary Biology committee on genetics the University of Chicago

Orphan genes that lack detectable homologues in other lineages could contribute to a variety of biological functions. However,their origination and function mechanisms remain largely unknown. Herein, through a comprehensive and systematic computational pipeline, we identified 893 orphan genes in the lineage of C. elegans, of which only a low fraction(0.9%) were derived from transposon elements. Six new protein-coding genes that de novo originated from non-coding DNA sequences in the genome of C. elegans were also identified. The authenticity and functionality of these orphan genes and de novo genes are supported by three lines of evidences, consisting of transcriptional data, and in silico proteomic data, and the fixation status data in wild populations. Orphan genes and de novo genes exhibited simple gene structures, such as, short in protein length, of fewer exons,and are frequently X-linked. RNA-seq data analysis showed these orphan genes are enriched with expression in embryo development and gonad, and their potential function in early development was further supported by gene ontology enrichment analysis results. Meanwhile, de novo genes were found to be with significant expression in gonad, and functional enrichment analysis of the co-expression genes of these de novo genes suggested they may be functionally involved in signaling transduction pathway and metabolism process. Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes.

关键词： Caenorhabditis elegans,orphan genes de novo genes

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PI3K/AKT signaling pathway as a critical regulator of Cisplatin response in tumor cells

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Oncology Research 2021年第4期29卷 235-250页

作者： ZAHRA NASRPOUR NAVAEI GHAZALEH KHALILI-TANHA AMIR SADRA ZANGOUEI MOHAMMAD REZA ABBASZADEGAN MEYSAM MOGHBELI Department of Medical genetics and Molecular Medicine School of MedicineMashhad University of Medical SciencesMashhadIran Student Research committee Faculty of MedicineMashhad University of Medical SciencesMashhadIran Medical genetics Research Center Mashhad University of Medical SciencesMashhadIran

Chemotherapy is one of the main therapeutic modalities for cancer ***(CDDP),as one of theﬁrst-line drugs,is of great importance in the chemotherapy of various ***,a signiﬁcant percentage of cancer patients are resistant to CDDP *** to the CDDP side effects on normal tissues,the diagnosis of CDDP resistance is required to suggest the most efﬁcient therapeutic strategies for cancer *** molecular mechanisms and signaling pathways are associated with CDDP *** PI3K/AKT signaling pathway has a pivotal role in the transmission of extracellular signals into the cells to regulate various pathophysiological processes such as cell proliferation,migration,and drug *** the present review,we summarized all of the studies which have been reported on the role of PI3K/AKT pathway in regulation of CDDP *** was shown that the PI3K/AKT pathway is mainly involved in CDDP response in lung,ovarian,and gastrointestinal *** was also observed that the non-coding RNAs have a key role in CDDP response by regulation of PI3K/AKT *** review paves the way for suggesting a PI3K/AKT-related panel marker for the prediction of CDDP response in different cancer patients.

关键词： PI3K/AKT Cancer Chemoresistance Cisplatin Chemotherapy

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Isolation and characterization of an ERF-B3 gene associated with flower abnormalities in non-heading Chinese cabbage

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Journal of Integrative Agriculture 2016年第3期15卷 528-536页

作者： XU Yu-chao HOU Xi-lin XU Wei-wei SHEN Lu-lu Lü Shan-wu ZHANG Shi-lin HU Chun-mei State Key Laboratory of Crop genetics and Germplasm Enhancement Ministry of Science and Technology/College of Horticulture Nanjing Agricultural University Nanjing 210095 P.R. China Agriculture committee of Feixi County Hefei 230001 P.R. China

BrcERF-B3 gene, a member of ethylene-responsive factor family, was screened from a mutant plant in non-heading Chinese cabbage（Brassica rapa ssp. chinensis） by cDNA-AFLP technology. We got full length cDNA of two BrcERF-B3 genes by homology-based cloning from two materials and found that their nucleotide sequences were the same by sequencing. The BrcERF-B3 protein, belonging to the B3 subgroup of the ERF subfamily, shared a close relationship with B. rapa. RT-PCR result showed that BrcERF-B3 expressed only in mutant stamen rather than maintainer stamen. qRT-PCR results indicated that BrcERF-B3 expressed highly during reproductive growth development and in the early of mutant buds, suggesting BrcERF-B3 might be involved in the formation of abnormal flower in mutant. What＇s more, the expression of BrcERF-B3 was more significant to ABA, Me JA and cold stresses in mutant than in maintainer and was down-regulated in NaCl treatment in two lines, implying BrcERF-B3 might be different roles in biotic and abiotic stresses.

关键词： non-heading Chinese cabbage stamen-petalody ethylene-responsive factor gene expression

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Kaempferol and docetaxel diminish side population and down-regulate some cancer stem cell markers in breast cancer cell line MCF-7

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BIOCELL 2017年第2期41卷 33-40页

作者： SARA SOLTANIAN HELIA RIAHIRAD ATHAREH PABARJA MOHAMMAD REZA KARIMZADEH KOLSOUM SAEIDI Department of Biology Faculty of ScienceShahid Bahonar University of KermanKermanIran Department of Medical genetics Afzalipour School of MedicineKerman University of Medical SciencesKermanIran Student Research committee Kerman University of Medical SciencesKermanIran Department of Medical genetics Kerman University of Medical SciencesKermanIran

Cancer stem cells(CSCs)are a small subpopulation of cancer cells whose resistance to chemotherapy and radiotherapy plays a pivotal role in treatment failure,tumor recurrence and ***,the ability of many phytochemicals in targeting of CSCs has been *** is a plant phytoestrogen that was recognized as a useful agent for targeting cancer cells by apoptosis induction,cell cycle arrest and inhibition of angiogenesis,migration,and invasion of cancer *** this study,we compared the effect of docetaxel as a common breast cancer chemotherapy drug and kaempferol on MCF-7 breast *** showed that both docetaxel and kaempferol caused a dose-dependent reduction in cell *** 123 dye staining and flow cytometry analysis revealed that after docetaxel and kaempferol treatment,SP cells proportion of MCF-7 decreased to 11.83±2.2% and 3±0.25% respectively relative to proportion of untreated control cells(23±3.2%).Moreover,real time PCR results showed that kaempferol treatment of MCF-7 was more effective than docetaxel in down-regulating the CSC-associated markers(***4,nanog,abcb1 and aldh1a1).Taken together,these results indicate that kaempferol is an effective anti-CSCs agent,therefore it may be a therapeutic strategy for eradicating breast cancer through the elimination of CSCs.

关键词： Breast cancer Cancer stem like cells Kaempferol Docetaxel

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ESTABLISHMENT OF A HUMAN/CHINESE HAMSTER HYBRID CLONE PANEL

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Science in China,Ser.B 1987年第6期30卷 630-637页

作者：徐芸邱信芳薛京伦周洁民徐一玲 Institute of genetics Fudan University Shanghai

Combined with the chromosome G-banding, followed by Ciemsa-11 techniques and chromosomalmarker isozyme analysis, 6 out of 200 subclones have been analyzed in detail. A primary hybrid clonepanel has been established, which can be used to map genes on chromosomes 4, 5, 8, 12, 20 and *** the panel contains deleted chromosomes 4, 5, 8 and 12, genes on these chromosomes can be map-ped regionally.

关键词： ESTABLISHMENT OF A HUMAN/CHINESE HAMSTER HYBRID CLONE PANEL

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Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows

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National Science Review 2020年第1期7卷 113-127页

作者： Yanhua Qu Chunhai Chen Ying Xiong Huishang She Yong E Zhang Yalin Cheng Shane Du Bay Dongming Li Per G P Ericson Yan Hao Hongyuan Wang Hongfeng Zhao Gang Song Hailin Zhang Ting Yang Chi Zhang Liping Liang Tianyu Wu Jinyang Zhao Qiang Gao Weiwei Zhai Fumin Lei Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences BGI Genomics BGI-Shenzhen University of Chinese Academy of Sciences Center for Excellence in Animal Evolution and genetics Chinese Academy of Sciences committee on Evolutionary Biology University of Chicago Life Sciences Section Integrative Research Center Field Museum of Natural History Key Laboratory of Animal Physiology Biochemistry and Molecular Biology of Hebei Province College of Life Sciences Hebei Normal University Department of Bioinformatics and genetics Swedish Museum of Natural History College of Life Sciences Shaanxi Normal University China National Gene Bank BGI-Shenzhen Human genetics Genome Institute of Singapore Agency for Science Technology and Research

Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet Plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.

关键词： denovo genome early stage adaptation high elevation muscle phenotypes polygenic adaptation regulatory evolution

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Whole-exome sequencing identified a novel mutation of MLH1 in an extended family with lynch syndrome

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Genes & Diseases 2020年第4期7卷 614-619页

作者： Hamid Ghaedi Samira Molaei Ramsheh Maryam Erfanian Omidvar Afsaneh Labbaf Elham Alehabib Sanaz Akbari Fatemeh Pourfatemi Hossein Darvish Department of Medical genetics School of MedicineShahid Beheshti University of Medical SciencesTehranIran Department of Medical Laboratory Technology School of Allied Medical SciencesShahid Beheshti University of Medical SciencesTehranIran Student Research committee Department of Medical GeneticsSchool of MedicineShahid Beheshti University of Medical SciencesTehranIran Nourdanesh Institute MeymehIsfahanIran Deputy for Prevention Affairs of State Welfare Organization of Mazandaran SariIran Cancer Research Center Semnan University of Medical SciencesSemnanIran Department of Medical genetics School of MedicineSemnan University of Medical SciencesSemnanIran

Hereditary nonpolyposis colorectal cancer or Lynch syndrome is autosomal dominant cancer predisposition syndrome characterized by early onset of colorectal cancer and neoplasia in other *** condition typically caused by germline mutations in the mismatch repair genes MLH1,MSH2,MSH6,and *** date,a considerable number of MLH1 gene mutations have been found to be associated with Lynch *** were aimed at identifying a genetic mutation in an extended Iranian family affected by Lynch syndromerelated ***,we applied whole-exome sequencing to identifying mutation in the ***,we applied Sanger sequencing to validate the candidate *** found a heterozygous novel single nucleotide deletion(c.206delG)in the exon two of the MLH1 gene in the ***,Sanger sequencing analysis showed that this mutation has segregated in all affected family *** mutation(c.206delG:p.R69fs)may create a premature stop codon followed by the formation of a truncated(p.R69fs)Mlh1 *** findings expand the mutational spectra of MLH1 gene related Lynch syndrome which is vital for screening and genetic diagnosis of the disease.

关键词： Colorectal cancer Lung cancer Mismatch repair MLH1

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Genetic variation of Laminaria japonica (Phaeophyta) populations in China as revealed by RAPD markers

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Acta Oceanologica Sinica 2011年第2期30卷 103-112页

作者： BI Yanhui HU Yuanjie ZHOU Zhigang Key Laboratory of Genetic Resources and Ecology in Aquaculture Aquaculture E-Institute ofShanghai Municipal Education Committee Shanghai Ocean University Shanghai 201306 China

For the population genetics analysis of the naturally grown brown seaweed Laminaria japonica （Laminariales,Phaeophyta） sampled from Dalian,Yantai,Weihai,Rongcheng and Qingdao in China,ten primers were employed to produce 88 bands as revealed by randomly amplified polymorphic DNA （RAPD） markers,and all these bands were *** to these band patterns,there were 94 distinct phenotypes occurred in 100 samples indicating the high heterozygosity of this *** population samples showed the highest percentage of polymorphism （71.67%）,and also the higher diversity estimated on the basis of the Shannon’s index （8.498）,suggesting that this population could be chosen as the best resource for genetic *** highest diversity of Yantai population possibly resulted from the introduction of *** used for interspecific cross breeding with *** cultivated in *** Dalian southwards to Qingdao,the genetic variation of the five populations became less with a decrease in latitude,possibly due to the natural selection especially of high *** genetic distance （Φ ST values） of the five populations was a little significantly correlated with the geographical distance （r=0.496） at P =0.05 by Mantel’s ***,Rongcheng and Yantai populations were closely grouped genetically together by Neighbor-joining cluster analysis probably in that the dispersal of the kelp by propagules more easily occurring in the range of relatively short *** analysis of molecular variance （AMOVA） also demonstrated that the relatively higher variation occurred among populations （71.49%） at an extremely significant level （P 0.000 1）.All these evidence showed that there was a relatively distinct genetic differentiation among the sampled kelp populations,and *** grown in China was also rather heterozygous in heredity.

关键词： AMOVA brown seaweed Laminaria japonica Aresch. population genetics RAPD genetic variation

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Effects of Nitrogen Application Levels on Ammonia Volatilization and Nitrogen Utilization during Rice Growing Season

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Rice science 2012年第2期19卷 125-134页

作者： LIN Zhong-cheng DAI Qi-gen YE Shi-chao WU Fu-guan JIA Yu-shu CHEN Jing-dou XU Lu-sheng ZHANG Hong-cheng Huo Zhong-yang Xu Ke WEt Hai-yan Key Laboratory of Crop genetics and Physiology of Jiangsu Province / Innovation Center of Rice Cultivation Technology in Yangtze Valley Ministry of Agriculture Yangzhou University Yangzhou 225009 China Agriculture committee of Wujiang County Jiangsu Province Wujiang 215200 China Agriculture Bureau of Guannan County Jiangsu Province Guannan 222500 China

We conducted field trials of rice grown in sandy soil and clay soil to determine the effects of nitrogen application levels on the concentration of NH4＋-N in surface water, loss of ammonia through volatilization from paddy fields, rice production, nitrogen-use efficiency, and nitrogen content in the soil profile. The concentration of NH4＋-N in surface water and the amount of ammonia lost through volatilization increased with increasing nitrogen application level, and peaked at 1-3 d after nitrogen application. Less ammonia was lost via volatilization from clay soil than from sandy soil. The amounts of ammonia lost via volatilization after nitrogen application differed depending on the stage when it was applied, from the highest loss to the lowest： N application to promote tillering 〉 the first N topdressing to promote panicle initiation （applied at the last 4-leaf stage）〉 basal fertilizer 〉 the second N topdressing to promote panicle initiation （applied at the last 2-leaf stage）. The total loss of ammonia via volatilization from clay soil was 10.49-87.06 kg/hm2, equivalent to 10.92%-21.76% of the nitrogen applied. The total loss of ammonia via volatilization from sandy soil was 11.32-102.43 kg/hm2, equivalent to 11.32%-25.61 % of the nitrogen applied. The amount of ammonia lost via volatilization and the concentration of NH4＋-N in surface water peaked simultaneously after nitrogen application; both showed maxima at the tillering stage with the ratio between them ranging from 23.76% to 33.65%. With the increase in nitrogen application level, rice production and nitrogen accumulation in plants increased, but nitrogen-use efficiency decreased. Rice production and nitrogen accumulation in plants were slightly higher in clay soil than in sandy soil. In the soil, the nitrogen content was the lowest at a depth of 40-50 cm. In any specific soil layer, the soil nitrogen content increased with increasing nitrogen application level, and the soil nitrogen content was higher in

关键词： ammonia volatilization nitrogen application level soil type nitrogen-use efficiency rice

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Synthesis of betanin by expression of the core betalain biosynthetic pathway in carrot

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Horticultural Plant Journal 2024年第3期10卷 732-742页

作者： Bo Wang Yahui Wang Yuanjie Deng Quanhong Yao Aisheng Xiong State Key Laboratory of Crop genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjingJiangsu 210095China Shanghai Key Laboratory of Agricultural genetics and Breeding Biotechnology Research Institute of Shanghai Academy of Agricultural ScienceShanghai 201106China

Betalain has received increased attention because of its high nutritional value and crucial physiological *** on the elucidation of its core biosynthetic pathway,betalain can be produced in additional plants by metabolic *** of betalain in carrot(Daucus carota L.)can improve its nutritional quality and economic value by extracting betalain from the fleshy root,non-edible part,and processing residue of *** this study,two different constructs,namely,pYB:mCD(AomelOS,BvCYP76AD1S,and BvDODA1S)and p YB:CDD(BvCYP76AD1S,BvDODA1S,and MjcDOPA5GTS),were introduced into carrot for betanin synthesis by Agrobacterium-mediated *** can be synthetized in both transgenic calli,and p YB:m CD-transgenic callus can be used to produce betacyanin by suspension ***,pYB:mCD-transgenic seedlings can synthetize betanin only by tyrosine *** p YB:CDD-transgenic lines can synthetize betanin in whole *** betanin content in fleshy root of pYB:CDD-transgenic carrot was(63.4±9)μg·g^(-1)fresh weight according to quantitative *** betanin-producing carrot plant materials can be used to synthesize betanin for industrial application or consumption as dietary sources.

关键词： Daucus carota L. Betanin Biosynthesis Metabolic engineering Biofortification

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