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Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project

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Journal of Genetics and genomics 2011年第1期38卷 47-53页

作者： Tae-Ho Park Beom-Seok Park Jin-A Kim Joon Ki Hong Mina Jin Young-Joo Seol Jeong-Hwan Mun genomics and Functional Bio-Material Division National Academy of Agricultural ScienceRural Development Administration The department of Horticultural Science Daegu University

As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.

关键词： Brassica rapa Chinese cabbage Fosmid library Genome sequencing Physical contig

Antiapoptotic activity of 30 kDa lipoproteins family from fat body tissue of silkworm, Bombyx moil

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Insect Science 2015年第5期22卷 629-638页

作者： Britto Cathrin Pakkianathan Nitin Kumar Singh Simone Konig Muthukalingan Krishnan department of Environmental Biotechnology Bharathidasan University Tiruchirappalli India and Integrated Functional genomics Interdisciplinary Center for Clinical Research University of MEmster Germany

The family of 30kDa lipoproteins （LP1-5） is abundant in silkworm pupa fat body （FB） and hemolymph. One of its members, the 29 kDa protein decreased in concentration from peripheral （PP） FB tissue but was sustained in perivisceral （PV） FB tissue at the time of apoptosis. This study investigated the correlation of the 30kDa proteins with FB apoptosis. Two protein fractions were purified, a 29 and a 30/31 kDa protein fraction, and they were used to test for activity against actinomycin D-induced apoptosis in the FB tissues. Concentrations as little as 50/zg/mL of the 29 kDa protein fraction efficiently inhibited apoptosis. Less antiapoptotie activity was detected for the higher MW fraction; DNA fragmentation was observed in FB tissue treated with 50 #g/mL of the 30/31 kDa fraction. The viability of the cells in the 29 kDa protein-supplemented culture was 40% higher than in the 31 kDa protein-supplemented culture. However, the 30 kDa lipoproteins were not able to prevent scheduled FB degeneration during silkworm metamorphosis. Thus, it is hypothesized that the antiapoptotic 29 kDa protein needs to be proteolytically degraded by a regulatory mechanism to allow programmed cell death of FB tissue.

关键词： actinomycin D apoptosis Bombyx mori fat body tissue 30 kDa proteins

Blood F_2-isoprostanes are significantly associated with abnormalities of lipid status in rats with steatosis

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World Journal of Gastroenterology 2008年第29期14卷 4677-4683页

作者： Man-Jie Zhu Li-Juan Sun Yue-Qin Liu Yan-Ling Feng Hai-Tao Tong Ying-He Hu Zheng Zhao Laboratory of Pharmacology Institute of Brain Functional Genomics East China Normal University Key Laboratory of Brain Functional Genomics MOE & STCSM Shanghai 200062 China department of Pathology Shanghai Public Health Clinical Center Fudan University Shanghai 201508 China

AIM: To investigate oxidative stress and lipid peroxi-dation in hepatic steatosis and the underlying implica-tions in pathological mechanisms of non-alcoholic fatty liver disease (NAFLD). METHODS: F_2-isoprostanes (iPF2α-) in blood and liver samples from steatotic (n = 9) and control (n = 7) rats were measured as in vivo marker of lipid peroxida-tion by a mass spectrometric approach. The lipid pro-fi le and endogenous antioxidant status (SOD and CAT) in the rats were also analyzed. RESULTS: Signifi cantly higher levels of iPF2α-(mean 3.47 vs 2.40 pmol/mg tissue, P = 0.004) and lower activities of SOD (mean 1.26 U vs 1.40 U, P < 0.001) and CAT (mean 1026.36 U/mg vs 1149.68 U/mg pro-tein, without signifi cance) were observed in the livers of steatotic rats. Plasma total iPF2α-was signifi cantly correlated with the abnormalities of blood lipids as well as alanine aminotransferase (ALT) levels in the rats with simple steatosis, whereas no similar tendencies were observed in the control rats. CONCLUSION: Enhancement of hepatic oxidative imbalance occurring at the steatotic stage of NAFLD suggests a possibility that manifestation of the local ⅢⅢⅢoxidative damage precedes that of systemic oxidative imbalance. Predominant metabolic features of the in-creased lipid peroxidation further suggest a close asso-ciation of the oxidative imbalance and the dyslipidemia with functional deterioration of the steatotic liver. The fi ndings need to be further evaluated, especially in hu-man studies.

关键词： Isoprostanes Oxidative stress Lipid per-oxidation Steatosis Non-alcoholic fatty liver disease

The BPP program for species tree estimation and species delimitation

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Current Zoology 2015年第5期61卷 854-865页

作者： Ziheng YANG Center for Computational genomics Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China department of Genetics Evolution and Environment University College London Darwin Building Gower Street London WC1E 6BT England

This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny （A00）, species tree estimation when the assignment and species delimitation are fixed （A01）, species delimitation using a fixed guide tree （A10）, and joint species delimitation and species-tree estimation or unguided species delimitation （A11）. For the joint analysis （A11）, two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis [Current Zoology 61 （5）： 854-865, 2015].

关键词： BPP MCMC Multispecies coalescent Species delimitation Species tree

Quantitative trait loci controlling Phytophthora cactorum resistance in the cultivated octoploid strawberry(Fragaria×ananassa)

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Horticulture Research 2019年第1期6卷 965-978页

作者： Charlotte F.Nellist Robert J.Vickerstaff Maria K.Sobczyk César Marina-Montes Fiona M.Wilson David W.Simpson Adam B.Whitehouse Richard J.Harrison department of Genetics Genomics and BreedingNIAB EMRNew RoadEast Malling ME196BJUK

The cultivated strawberry,Fragaria×ananassa(Fragaria spp.)is the most economically important global soft *** cactorum,a water-borne oomycete causes economic losses in strawberry production globally.A biparental cross of octoploid cultivated strawberry segregating for resistance to ***,the causative agent of crown rot disease,was screened using artificial *** putative resistance quantitative trait loci(QTL)were identified and *** major effect QTL(FaRPc6C,FaRPc6D and FaRPc7D)explained 37%of the variation *** were no epistatic interactions detected between the three major *** a subset of the mapping population progeny against a range of *** isolates revealed no significant interaction(p=0.0593).However,some lines showed higher susceptibility than predicted,indicating that additional undetected factors may affect the expression of some quantitative resistance *** historic crown rot disease score data from strawberry accessions,a preliminary genome-wide association study(GWAS)of 114 individuals revealed an additional locus associated with resistance to *** of the Fragaria vesca Hawaii 4 v1.1 genome revealed candidate resistance genes in the QTL regions.

关键词： straw Fragaria

Dependence of Generation of Hippocampal CAI Slow Oscillations on Electrical Synapses

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Neuroscience Bulletin 2020年第1期36卷 39-48页

作者： Yuan Xu Feng-Yan Shen Yu-Zhang Liu Lidan Wang Ying-Wei Wang Zhiru Wang Institute and Key Laboratory of Brain Functional genomics of The Chinese Ministry of Education Shanghai Key Laboratory of Brain Functional GenomicsSchool of Life SciencesEast China Normal UniversityShanghai 200062China department of Anesthesiology Huashan HospitalFudan UniversityShanghai 200040China

Neuronal oscillations in the hippocampus are critical for many brain functions including learning and *** underlying mechanism of oscillation generation has been extensively investigated in terms of chemical synapses and ion ***,electrical synapses have also been indicated to play important roles,as reported in various brain areas in vivo and in brain ***,this issue remains to be further clarified,including in hippocampal ***,using the completely isolated hippocampus,we investigated in vitro the effect of electrical synapses on slow CA1 oscillations(0.5 Hz-1.5 Hz)generated intrinsically by the *** found that these oscillations were totally abolished by bath application of a general blocker of gap junctions(carbenoxolone)or a specific blocker of electrical synapses(mefloquine),as determined by whole-cell recordings in both CA1 pyramidal cells and fast-spiking *** findings indicate that electrical synapses are required for the hippocampal generation of slow CA1 oscillations.

关键词： Electrical synapse Hippocampus Oscillation CA1 Mefloquine Carbenoxolone Introduction

HBx-induced reactive oxygen species activates hepatocellular carcinogenesis via dysregulation of PTEN/Akt pathway

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World Journal of Gastroenterology 2010年第39期16卷 4932-4937页

作者： Hye-Lin Ha Dae-Yeul Yu Disease Model Research Laboratory Aging Research CenterKorea Research Institute of Bioscience and Biotechnology department of Functional genomics University of Science and Technology

AIM:To investigate the role of hepatitis B virus X-protein(HBx)-induced reactive oxygen species(ROS)on liver carcinogenesis in HBx transgenic mice and HepG2-HBx ***:Cell growth rate was analyzed,and through western blotting,mitogenic signaling was *** ROS from wild and HBx transgenic mice and HepG2-Mock and HBx cells were assayed by *** of oxidized and reduced phosphatase and tensin homolog(PTEN)was analyzed through N-ethylmaleimide alkylation,nonreducing ***:We observed that the cell-proliferation-related phosphoinositide 3-kinase/Akt pathway is activated by HBx in vivo and in *** ROS were detected by *** suppressor PTEN,via dephosphorylation of Akt,was oxidized and inactivated by increased *** oxidized PTEN activated the mitogenic pathway through over-activated ***,treatment with ROS scavenger N-acetyl cysteine can reverse PTEN to a reduced *** produced ROS also stimulated HBx ***:HBx induced ROS promoted Akt pathways via oxidized inactive *** and ROS maintained a positive regulatory loop,which aggravated carcinogenesis.

关键词： Hepatitis B virus X protein Hepatocellular carcinoma Akt Reactive oxygen species Phosphatase and tensin homolog

The Role of Dopamine in Associative Learning in Drosophila: An Updated Unified Model

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Neuroscience Bulletin 2021年第6期37卷 831-852页

作者： Mohamed Adel Leslie C.Griffith department of Biology Volen National Center for Complex Systems and National Center for Behavioral GenomicsBrandeis UniversityWalthamMA 02454-9110USA

Learning to associate a positive or negative experience with an unrelated cue after the presentation of a reward or a punishment defines associative *** ability to form associative memories has been reported in animal species as complex as humans and as simple as insects and sea *** memory has even been reported in tardigrades[1],species that diverged from other animal phyla 500 million years *** the mechanisms of memory formation is a fundamental goal of neuroscience *** this article,we work on resolving the current contradictions between different Drosophila associative memory circuit models and propose an updated version of the circuit model that predicts known memory behaviors that current models do ***,we propose a model for how dopamine may function as a reward prediction error signal in Drosophila,a dopamine function that is well-established in mammals but not in insects[2,3].

关键词： associative contradiction function

Screening analysis of candidate gene mutations in a kindred with polycystic liver disease

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World Journal of Gastroenterology 2015年第8期21卷 2343-2351页

作者： Song Jin Kai Cui Zi-Qiang Sun Yang-Yang Shen Pang Li Zhen-Dan Wang Fei-Fei Li Ke-Nan Gong Sheng Li department of Hepatobiliary and Vascular Surgery Affiliated Hospital of Jining Medical College department of Hepatobiliary Surgery Shandong Cancer Hospital Laboratory of Disease genomics and Individualized Medicine Beijing Institute of Genomics Chinese Academy of Sciences Shandong Provincial Collaborative Innovation Center for Neurodegenerative Disorders Qingdao University

AIM:To find potential mutable sites by detecting mutations of the candidate gene in a kindred with polycystic liver disease(PCLD).METHODS:First,we chose a kindred with PCLD and obtained five venous blood samples of this kindred after the family members signed the informed consent *** the kindred two cases were diagnosed with PCLD,and the left three cases were normal *** the blood samples were preserved at-85?℃.Second,we extracted the genomic DNA from the venous blood samples of the kindred using a QIAamp DNA Mini Kit and then performed long-range polymerase chain reaction(PCR)with different *** exons of PKD1 were all sequenced with the forward and reverse primers to ensure the accuracy of the ***,we purified the PCR products and directly sequenced them using Big Dye Terminator Chemistry version *** sequencing reaction was conducted with Biomek FX(Beckman).Finally,we analyzed the ***:A total of 42 normal exons were identified in detecting mutations of the PKD1 gene.A synonymous mutation occurred in exon *** mutation was a homozygous T in the proband and was C in the reference *** mutation was located in the third codon and did not change the amino acid encoded by the *** mutations occurred in exons 11 and *** mutations were located in the second codon;they changed the amino acid sequence and existed in the db SNP library.A nonsense mutation occurred in exon *** mutation was a heterozygous CT in the proband and was C in the *** mutation was located in the first codon and resulted in a termination *** mutation had an obvious influence on the encoded protein and changed the length of the protein from 4303 to 2246amino *** was a new mutation that was not present in the db SNP ***:The nonsense mutation of exon 15existed in the proband and in the third ***,the proband was heterozygous for this mutation,so the mutable site was a

关键词： Gene mutation Polycystic liver disease Kindred