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Journal of Genetics and genomics 2025年第1期52卷 66-77页

作者： Yingying Hu Zhou Luo Meiwen Wang Zekai Wu Yunxing Liu Zhenchao Cheng Yuhan Sun Jing-Wei Xiong Xiangjun Tong Zuoyan Zhu Bo Zhang Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education College of Life SciencesPeking UniversityBeijing 100871China Laboratory of Chemical genomics School of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhen University TownShenzhenGuangdong 518055China College of Biological sciences China Agricultural UniversityBeijing 100193China Institute of Molecular Medicine College of Future TechnologyPeking UniversityBeijing 100871China

The liver is a key endoderm-derived multifunctional organ within the digestive *** homeobox 1(Prox1)is an essential transcription factor for liver development,but its specific function is not well ***,we show that hepatic development,including the formation of intrahepatic biliary and vascular networks,is severely disrupted in prox1a mutant *** find that Prox1a is essential for liver growth and proper differentiation but not required for early hepatic cell fate ***,prox1a depletion leads to ectopic initiation of a Cdx1b-mediated intestinal program and the formation of intestinal lumen-like structures within the *** knockdown of cdx1b alleviates liver defects in the prox1a mutant ***,chromatin immunoprecipitation analysis reveals that Prox1a binds directly to the promoter region of cdx1b,thereby repressing its ***,our findings indicate that Prox1a is required to promote and protect hepatic development by repression of Cdx1b-mediated intestinal cell fate in zebrafish.

关键词： Zebrafish Liver development prox1a cdx1b Cell fate transition

Impact of residual antibiotics on microbial decomposition of livestock manures in Eutric Regosol:Implications for sustainable nutrient recycling and soil carbon sequestration

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Journal of Environmental sciences 2025年第1期147卷 498-511页

作者： Linfa Fang Prakash Lakshmanan Xiaoxuan Su Yujia Shi Zheng Chen Yu Zhang Wei Sun Junxi Wu Ran Xiao Xinping Chen Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin College of Resources and EnvironmentSouthwest UniversityChongqing 400715China Key Laboratory of Sugarcane biotechnology and Genetic Improvement(Guangxi) Ministry of Agriculture and Rural AffairsGuangxi Key Laboratory of Sugarcane Genetic ImprovementSugarcane Research InstituteGuangxi Academy of Agricultural SciencesNanning 530007China Queensland Alliance for Agriculture and Food Innovation University of QueenslandSt Lucia 4067QLDAustralia Key Laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and National Resources ResearchChinese Academy of SciencesBeijing 100101China

The land application of livestock manure has been widely acknowledged as a beneficial approach for nutrient recycling and environmental ***,the impact of residual antibiotics,a common contaminant of manure,on the degradation of organic compounds and nutrient release in Eutric Regosol is not well ***,we studied,how oxytetracycline(OTC)and ciprofloxacin(CIP)affect the decomposition,microbial community structure,extracellular enzyme activities and nutrient release from cattle and pig manure using litterbag incubation *** showed that OTC and CIP greatly inhibited livestock manure decomposition,causing a decreased rate of carbon(28%-87%),nitrogen(15%-44%)and phosphorus(26%-43%)*** relative abundance of gramnegative(G-)bacteria was reduced by 4.0%-13%while fungi increased by 7.0%-71%during a 28-day incubation ***-occurrence network analysis showed that antibiotic exposure disrupted microbial interactions,particularly among G-bacteria,G+bacteria,and *** changes in microbial community structure and function resulted in decreased activity of urease,β-1,4-N-acetyl-glucosaminidase,alkaline protease,chitinase,and catalase,causing reduced decomposition and nutrient release in cattle and pig *** findings advance our understanding of decomposition and nutrient recycling from manure-contaminated antibiotics,which will help facilitate sustainable agricultural production and soil carbon sequestration.

关键词： Residual antibiotics Livestock manure decomposition Microbial community Co-occurrence network Enzyme activities

Antioxidative capacity and enzyme activity in Haematococcus pluvialis cells exposed to superoxide free radicals

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Chinese Journal of Oceanology and Limnology 2010年第1期28卷 1-9页

作者：刘建国张晓丽孙延红林伟 Research and Development Center of Marine biotechnology Institute of OceanologyChinese Academy of Sciences graduate University of Chinese Academy of sciences

The antioxidative capacity of astaxanthin and enzyme activity of reactive oxygen eliminating enzymes such as superoxide dismutase (SOD),peroxidase (POD),catalase (CAT) and ascorbate peroxidase (APX) were studied in three cell types of Haematococcus pluvialis exposed to high concentrations of a superoxide anion radical (O2ˉ).The results show that defensive enzymes and astaxanthin-related mechanisms were both active in *** during exposure to reactive oxygen species (ROS) such as Oˉ*** reacted with ROS much faster than did the protective enzymes,and had the strongest antioxidative capacity to protect against lipid *** defensive mechanisms varied significantly between the three cell types and were related to the level of astaxanthin that had accumulated in those ***-enriched red cells had the strongest antioxidative capacity,followed by brown cells,and astaxanthin-deficient green *** there was no significant increase in expression of protective enzymes,the malondialdehyde (MDA) content in red cells was sustained at a low level because of the antioxidative effect of astaxanthin,which quenched Oˉ2 before the protective enzymes could *** green cells,astaxanthin is very low or absent;therefore,scavenging of ROS is inevitably reliant on antioxidative ***,in green cells,these enzymes play the leading role in scavenging ROS,and the expression of these enzymes is rapidly increased to reduce excessive ***,because ROS were constantly increased in this study,the enhance enzyme activity in the green cells was not able to repair the ROS damage,leading to elevated MDA *** the four defensive enzymes measured in astaxanthin-deficient green cells,SOD eliminates Oˉ2,POD eliminates H2O2,which is a by-product of SOD activity,and APX and CAT are then initiated to scavenge excessive ROS.

关键词： astaxanthin Haematococcus pluvialis lipid peroxidation reactive oxygen species (ROS)

Rapid progress of DNA replication studies in Archaea,the third domain of life

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Science China(Life sciences) 2012年第5期55卷 386-403页

作者： ISHINO Yoshizumi ISHINO Sonoko Department of Bioscience and biotechnology Graduate School of Bioresource and Bioenvironmental Sciences Kyushu University

Archaea,the third domain of life,are interesting organisms to study from the aspects of molecular and evolutionary *** cells have a unicellular ultrastructure without a nucleus,resembling bacterial cells,but the proteins involved in genetic information processing pathways,including DNA replication,transcription,and translation,share strong similarities with those of ***,archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic ***,the hyperthermophilic archaea provide very stable proteins,which are especially useful for the isolation of replisomal multicomplexes,to analyze their structures and *** review focuses on the history,current status,and future directions of archaeal DNA replication studies.

关键词： Archaea DNA replication DNA polymerase replication fork replisome hyperthermophile

genomic analysis of modern maize inbred lines reveals diversity and selective breeding effects

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Science China(Life sciences) 2025年第2期68卷 578-581页

作者： Lisen Li Deqian Fan Chenglong Zhu Zhuoya Liu Wenji Huang Peidong Xin Huishan Yue Mengying Li Yufei Wang Wenjie Xu Jiangmin Zheng Ye Li Ziwei Yu Jianzhong Ling Qiang Qiu Wen Wang Chenguang Feng Xiaojing Song Kun Wang Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection School of Ecology and EnvironmentNorthwestern Polytechnical UniversityXi’an 710072China Shanghai Fisheries Research Institute Shanghai Fisheries Technical Extension StationShanghai 200433China East China Sea Fisheries Research Institute Chinese Academy of Fishery SciencesShanghai 200090China Laboratory for Marine Biology and biotechnology Qingdao Marine Science and Technology CenterQingdao 266237China

Dear Editor,Maize(Zea mays L.)is one of the most widely cultivated crops worldwide(Ranum et al.,2014),accounting for about 37.2%of the global cereal crop *** production yield has increased over sevenfold since single-... 详细信息

关键词： breeding crops cultivated

Identification and Characterization of hmr19 Gene Encoding a Multidrug Resistance Efflux Protein from Streptomyces hygroscopicus *** Strain 10-22

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Acta Biochimica et Biophysica Sinica 2004年第8期36卷 519-528页

作者： Lei QIN , Heng-An WANG1 , Zhong-Qin WU, Xiao-Feng ZHANG, Mei-Lei JIN,Zi-Xin DENG2, and Guo-Ping ZHAOShanghaiResearch Center of biotechnology, Shanghai Institute for Biological sciences, Chinese Academy of sciences,graduate School of the Chinese Academy of sciences, Shanghai 200233, China 1School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 201101, China 2School of Life Science and biotechnology, Shanghai Jiaotong University, Shanghai 200030, China ShanghaiResearch Center of biotechnology Shanghai Institute for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences School of Agriculture and Biology Shanghai Jiaotong University

The hmr19 gene was cloned from Streptomyces hygroscopicus subsp. yingchengensis strain 10- 22, a bacterium strain producing agricultural antibiotics. Sequence similarity comparison indicates that hmr19 gene may encode a predicted protein with 14 putative transmembrane α-helical spanners, belonging to the drug:H+ antiporter-2 family of the major facilitator superfamily. The expression of hmr19 in the mycelium of strain 10-22 was detected by Western blotting analysis. Gene replacement technology was employed to construct an hmr19 disruption mutant. The growth inhibition test against different antibiotics indicated that the mutant strain was 5–20 fold more susceptible to tetracycline, vancomycin and mitomycin C than the parental wild type strain. The mutant took up tetracycline much faster and accumulated more antibiotics than the wild type strain 10-22. While with the addition of an energy uncoupler, carbonyl cyanide m- chlorophenylhydrazone, the characteristics of the accumulation of [3H]tetracycline in these two strains were almost the same. It was thus concluded that hmr19 encoded a multidrug resistance efflux protein.

关键词： multidrug resistance (MDR) gene replacement (knockout) Streptomyces Streptomyces hygroscopicus subsp. yingchengensis strain 10-22

Cloning of the cDNA encoding adenosine 5'-monophosphate deaminase 1 and its mRNA expression in Japanese flounder Paralichthys olivaceus

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Chinese Journal of Oceanology and Limnology 2013年第1期31卷 118-127页

作者：蒋克勇孙姝娟刘梅王宝杰孟晓林王雷 R&D Center of Marine biotechnology Institute of OceanologyChinese Academy of Sciences graduate University of Chinese Academy of sciences

AMP deaminase catalyzes the conversion of AMP into IMP and ammonia. In the present study, a full-length cDNA of AMPD1 from skeletal muscle of Japanese flounder Paralichthys olivaceus was cloned and characterized. The 2 526 bp cDNA contains a 5'-UTR of 78 bp, a 3'-UTR of 237 bp and an open reading frame (ORF) of 2 211 bp, which encodes a protein of 736 amino acids. The predicted protein contains a highly conserved AMP deaminase motif (SLSTDDP) and an ATP-binding site sequence (EPLMEEYAIAAQVFK). Phylogenetic analysis showed that the AMPD1 and AMPD3 genes originate from the same branch, but are evolutionarily distant from the AMPD2 gene. RT-PCR showed that the flounder AMPD1 gene was expressed only in skeletal muscle. QRT-PCR analysis revealed a statistically significant 2.54 fold higher level of AMPD1 mRNA in adult muscle (750±40 g) compared with juvenile muscle (7.5±2 g) (P<0.05). HPLC analysis showed that the IMP content in adult muscle (3.35±0.21 mg/g) was also statistically significantly higher than in juvenile muscle (1.08±0.04 mg/g) (P<0.05). There is a direct relationship between the AMPD1 gene expression level and IMP content in the skeletal muscle of juvenile and adult flounders. These results may provide useful information for quality improvement and molecular breeding of aquatic animals.

关键词： AMPD1 cDNA cloning mRNA expression IMP skeletal muscle Japanese flounder

Sequencing and expression analysis of CD3γ/δ and CD3ε chains in mandarin fish, Siniperca chuatsi

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Chinese Journal of Oceanology and Limnology 2013年第1期31卷 106-117页

作者：郭政聂品 State Key Laboratory of Freshwater Ecology and biotechnology Institute of HydrobiologyChinese Academy of Sciences graduate University of Chinese Academy of sciences

The genomic and cDNA sequences of the CD3γ/δ and CD3ε homologues in the mandarin fish, Siniperca chuatsi, were determined. As in other vertebrate CD3 molecules, the deduced amino acid sequences of mandarin fish CD3γ/δ and CD3ε contained conserved residues and motifs, such as cysteine residues and CXXC and immunoreceptor tyrosine-based activation motifs. However, mandarin fish CD3γ/δ and CD3ε showed some differences to their mammalian counterparts, specifically the absence of a negatively charged residue in the transmembrane region of CD3γ/δ. Additionally, while an N-glycosylation site was present in CD3c, the site was not observed in CD3γ/δ. The CD3γ/δ and CD3ε subunit sequences contain six and five exons, respectively, consistent with homologues from Atlantic salmon, Salmo salar. Phylogenetic analysis also revealed that CD3γ/δ and CD3ε in mandarin fish are closely related to their counterparts in Acanthopterygian fish. Real-time PCR showed CD3γ/δ and CD3ε were expressed mainly in the thymus and spleen in normal healthy fish and, to a lesser extent, in mucosal-associated lymphoid tissues, such as the intestine and gills. When lymphocytes isolated from head kidney were treated with the mitogens phytohemagglutinin, concanavalin, and polyriboinosinic polyribocytidylic acid, mRNA expression levels of CD3γ/δ and CD3ε were significantly elevated within 12 h of treatment. This indicated the presence of T lymphocytes in the head kidney of teleost fish, and also the recognition of mitogens by the lymphocytes. Mandarin fish infected with the bacterial pathogen Flavobacterium columnare also showed an increase in the expression of CD3γ/δ and CD3ε mR_NA, indicating that CD3γ/δ and CD3ε lymphocytes are involved in the immune response of this species.

关键词： CD3γ/δ CD3ε mandarin fish mitogen Flavobacterium columnare

Statistical optimization of medium composition and culture condition for the production of recombinant anti-lipopolysaccharide factor of Eriocheir sinensis in Escherichia coli

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Chinese Journal of Oceanology and Limnology 2011年第6期29卷 1249-1259页

作者：姜珊刘梅王宝杰蒋克勇王雷 R&D Center of Marine biotechnology Institute of Oceanology Chinese Academy of sciences graduate University of Chinese Academy of sciences

Anti-lipopolysaccharide factors （ALFs） are important antimicrobial peptides that are isolated from some aquatic species. In a previous study, we isolated ALF genes from Chinese mitten crab, Eriocheir sinensis. In this study, we optimized the production of a recombinant ALF by expressing E. sinensis ALF genes in Eseherichia coli maintained in shake-flasks. In particular, we focused on optimization of both the medium composition and the culture condition. Various medium components were analyzed by the Plackett-Burman design, and two significant screened factors, （NH4）2SO4 and KH2PO4, were further optimized via the central composite design （CCD）. Based on the CCD analysis, we investigated the induction start-up time, the isopropylthio-D-galactoside （IPTG） concentration, the post-induction time, and the temperature by response surface methodology. We found that the highest level of ALF fusion protein was achieved in the medium containing 1.89 g/L （NH4）2SO4 and 3.18 g/L KH2PO4, with a cell optical density of 0.8 at 600 nm before induction, an IPTG concentration of 0.5 mmol/L, a post-induction temperature of 32.7~C, and a post-induction time of 4 h. Applying the whole optimization strategy using all optimal factors improved the target protein content from 6.1% （without optimization） to 13.2%. We further applied the optimized medium and conditions in high cell density cultivation, and determined that the soluble target protein constituted 105% of the total protein. Our identification of the economic medium composition, optimal culture conditions, and details of the fermentation process should facilitate the potential application of ALF for further research.

关键词： anti-lipopolysaccharide factor optimization medium composition culture conditions statisticalmethodology

Construction of two selectable markers for integrative/conjugative plasmids in Flavobacterium columnare

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Chinese Journal of Oceanology and Limnology 2012年第2期30卷 269-278页

作者：张金邹红王良发黄贝李楠王桂堂聂品 State Key Laboratory of Freshwater Ecology and biotechnology Institute of HydrobiologyChinese Academy of Sciences graduate University of Chinese Academy of sciences

Flavobacterium columnare, the etiological agent of colunmaris disease, is one of the most important and widespread bacterial pathogens of freshwater fish. In this study, we constructed two artificial selectable markers （chloramphenicol and spectinomycin resistance） for gene transfer in F. columnare. These two new artificial selectable markers, which were created by placing the chloramphenicol or spectinomycin resistance gene under the control of the native acs regulatory region of F. columnare, were functional in both F. columnare and Escherichia coli. The integrative/conjugative plasmids constructed by using these markers were introduced into F. columnare G4 via electroporation or conjugation. The integrated plasmid DNA was confirmed by Southern blotting and PCR analysis. These two markers can be employed in future investigations into gene deletion and the pathogenicity of virulence factors in F. columnare.

关键词： Flavobacterium columnare selectable marker integrative/conjugative plasmid gene disruption