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  • 1
    Online Resource
    Online Resource
    Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 35 ( 2013-08-27), p. 14492-14497
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 35 ( 2013-08-27), p. 14492-14497
    Abstract: The growing world population and shrinkage of arable land demand yield improvement of rice, one of the most important staple crops. To elucidate the genetic basis of yield and uncover its associated loci in rice, we resequenced the core recombinant inbred lines of Liang–You–Pei–Jiu , the widely cultivated super hybrid rice, and constructed a high-resolution linkage map. We detected 43 yield-associated quantitative trait loci, of which 20 are unique. Based on the high-density physical map, the genome sequences of paternal variety 93–11 and maternal cultivar PA64s of Liang–You–Pei–Jiu were significantly improved. The large recombinant inbred line population combined with plentiful high-quality single nucleotide polymorphisms and insertions/deletions between parental genomes allowed us to fine-map two quantitative trait loci, qSN8 and qSPB1 , and to identify days to heading8 and lax panicle1 as candidate genes, respectively. The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yield-associated loci in rice.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1306579110
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing
    Oxford University Press (OUP) ; 2018
    In:  Molecular Biology and Evolution Vol. 35, No. 1 ( 2018-01-01), p. 149-158
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 35, No. 1 ( 2018-01-01), p. 149-158
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msx276
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 2024221-9
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation
    Springer Science and Business Media LLC ; 2023
    In:  BMC Biology Vol. 21, No. 1 ( 2023-04-18)
    Details
    In: BMC Biology, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2023-04-18)
    Abstract: Among six extant tiger subspecies, the South China tiger ( Panthera tigris amoyensis ) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers. Results In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher F ROH values for longer runs of homozygosity (ROH 〉 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records. Conclusions The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.
    Type of Medium: Online Resource
    ISSN: 1741-7007
    URL: Article
    DOI: 10.1186/s12915-023-01552-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2133020-7
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Nakamurella flava sp. nov., a novel endophytic actinobacterium isolated from Mentha haplocalyx Briq.
    Microbiology Society ; 2020
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 70, No. 2 ( 2020-02-01), p. 835-840
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 70, No. 2 ( 2020-02-01), p. 835-840
    Abstract: A Gram-stain-positive, aerobic, coccus-shaped, non-spore-forming actinobacterium, designated strain N5BH11 T , was isolated from a surface-sterilized sample of Mentha haplocalyx Briq. collected from Guizhou, PR China and tested by a polyphasic approach to determine its taxonomic position. Strain N5BH11 T grew optimally at 30 °C, pH 6.0–7.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain N5BH11 T belonged to the genus Nakamurella and had the highest 16S rRNA gene sequence similarity to Nakamurella flavida DS-52 T (98.1 %). The DNA G + C content of strain N5BH11 T was 71.6 mol%. The average nucleotide identity values between strain N5BH11 T and the type strains of Nakamurella panacisegetis , Nakamurella multipartita and Nakamurella lactea were 74.0, 76.5 and 73.6 %, respectively. The estimated DDH values between strain N5BH11 T and the type strains of N. panacisegetis , N. multipartita and N. lactea were 20.3%, 21.4 and 20.2 %, respectively. The cell-wall peptidoglycan contained meso -diaminopimelic acid, and MK-8(H 4 ) was the predominant menaquinone. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and unidentified phospholipids. The major fatty acids were iso-C 15 : 0 , anteiso-C 15 : 0 , C 16 : 0 and C 16 : 1 ω7 c . On the basis of the results of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain N5BH11 T represents a novel species of the genus Nakamurella , for which the name Nakamurella flava sp. nov. is proposed. The type strain is N5BH11 T (=KCTC 49196 T =CGMCC 4.7524 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.003831
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2020
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Description and genomic characterization of Jiella flava sp. nov., isolated from Acrostichum aureum
    Microbiology Society ; 2022
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 72, No. 10 ( 2022-10-03)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 72, No. 10 ( 2022-10-03)
    Abstract: Two endophytic bacteria, designated strains CQZ9-1 T and MQZ9-1, were isolated from semi-mangrove plant Acrostichum aureum collected from Maowei Sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, PR China. The two strains possessed almost identical 16S rRNA gene sequences (99.7 %). The average nucleotide identity (ANI), average amino acid identity (AAI) and the digital DNA-DNA hybridization (dDDH) values between the two strains were 100 %, indicating that they represented the same species. The 16S rRNA gene sequence similarities between strains CQZ9-1 T , MQZ9-1 and the most closely related type strains, Jiella mangrovi KSK16Y-1 T , Jiella sonneratiae MQZ13P-4 T and Jiella endophytica CBS 5Q-3 T were 98.0–98.1, 97.3–97.4 and 97.3–97.4 %, respectively. The results of phylogenetic analyses based on 16S rRNA gene sequences and genome sequences indicated that CQZ9-1 T and MQZ9-1 formed a distinct lineage with J. endophytica CBS5Q-3 T , Jiella pacifica 40Bstr34 T , J. mangrovi KSK16Y-1 T , J. sonneratiae MQZ13P-4 T , Jiella aquimaris JCM 30119 T and J. aquimaris 22II-16-19i. The draft genomes of strains CQZ9-1 T and MQZ9-1 were 4  162  933 bp and 4  164  266 bp in size, respectively, and their DNA G+C contents were both 63.8 %. Comparative genome analysis of the two strains and the type strains of related species revealed ANI, AAI and dDDH values below the cut-off levels of 95-96, 95.5 and 70 %, respectively. The ubiquinone detected in CQZ9-1 T was Q-10. The major cellular fatty acid of strains CQZ9-1 T and MQZ9-1 was found to be C 18:1 ω7 c . Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that CQZ9-1 T and MQZ9-1 represent a novel species of the genus Jiella , for which the name Jiella flava sp. nov. is proposed. The type strain is CQZ9-1 T (= CGMCC 1.18725 T = JCM 34331 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005514
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2022
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Cholesterol 25-hydroxylase acts as a host restriction factor on pseudorabies virus replication
    Microbiology Society ; 2017
    In:  Journal of General Virology Vol. 98, No. 6 ( 2017-06-01), p. 1467-1476
    Details
    In: Journal of General Virology, Microbiology Society, Vol. 98, No. 6 ( 2017-06-01), p. 1467-1476
    Type of Medium: Online Resource
    ISSN: 0022-1317 , 1465-2099
    URL: Article
    DOI: 10.1099/jgv.0.000797
    RVK:
    XA 53770
    RVK:
    WA 15000
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2017
    detail.hit.zdb_id: 2007065-2
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Positive Inotropic and Positive Lusitropic Effects of Dofetilide on Isolated Rat Ventricular Cells by Enhancing Na + /Ca 2+ Exchange
    Wiley ; 2006
    In:  The FASEB Journal Vol. 20, No. 5 ( 2006-03)
    Details
    In: The FASEB Journal, Wiley, Vol. 20, No. 5 ( 2006-03)
    Type of Medium: Online Resource
    ISSN: 0892-6638 , 1530-6860
    URL: Issue
    URL: Article
    DOI: 10.1096/fsb2.v20.5
    DOI: 10.1096/fasebj.20.5.A1200
    Language: English
    Publisher: Wiley
    Publication Date: 2006
    detail.hit.zdb_id: 1468876-1
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Characterization of Synonymous Codon Usage Bias in the Duck Plague Virus UL35 Gene
    S. Karger AG ; 2009
    In:  Intervirology Vol. 52, No. 5 ( 2009), p. 266-278
    Details
    In: Intervirology, S. Karger AG, Vol. 52, No. 5 ( 2009), p. 266-278
    Abstract: 〈 i 〉 Objective: 〈 /i 〉 The aim was to identify the codon usage bias between the newly identified duck plague virus (DPV) UL35 gene (GenBank accession No. EF643558) and the UL35-like genes of 27 other reference herpesviruses. 〈 i 〉 Methods: 〈 /i 〉 A comparative analysis of the codon usage bias of the 28 herpesviruses was performed by using the CodonW 1.4 program and CUSP (create a codon usage table) program of EMBOSS (The European Molecular Biology Open Software Suite). 〈 i 〉 Results: 〈 /i 〉 The results showed obvious differences of the synonymous codon usage bias in the 28 herpesviruses indicated by the Codon Adaptation Index, effective number of codons (ENc), and the value of G + C content at the 3rd codon position. The codon usage pattern of the DPV UL35 gene was phylogenetically conserved and similar to that of the UL35-like genes of the avian α-herpesvirus, with a strong bias towards the codons with A and T at the 3rd codon position. A cluster analysis of codon usage pattern of the DPV UL35 gene with other reference herpesviruses demonstrated that the codon usage bias of the UL35 genes of the 28 herpesviruses had a very close relation with their gene function. The ENc-plot revealed that the genetic heterogeneity in the DPV UL35 gene and the 27 reference herpesviruses were constrained by G + C content, while gene length exerted relatively weaker influences. In addition, comparisons of the codon preferences in the UL35 gene of DPV with those of 〈 i 〉 Escherichia coli 〈 /i 〉 , yeast and humans revealed that there were 33 codons showing distinct usage differences between the DPV and yeast, and 38 between the DPV and humans, but only 31 between the DPV and 〈 i 〉 E. coli 〈 /i 〉 . Therefore, the 〈 i 〉 E. coli 〈 /i 〉 system may be more suitable for the expression of the DPV UL35 gene. 〈 i 〉 Conclusion: 〈 /i 〉 Together, these results may improve our understanding of the evolution, pathogenesis and functional studies of DPV, as well as contribute significantly to the area of herpesvirus research and possibly studies with other viruses.
    Type of Medium: Online Resource
    ISSN: 0300-5526 , 1423-0100
    URL: Article
    DOI: 10.1159/000231992
    RVK:
    XA 10000
    Language: English
    Publisher: S. Karger AG
    Publication Date: 2009
    detail.hit.zdb_id: 1482863-7
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    His6-Tagged UL35 Protein of Duck Plague Virus: Expression, Purification, and Production of Polyclonal Antibody
    S. Karger AG ; 2009
    In:  Intervirology Vol. 52, No. 3 ( 2009), p. 141-151
    Details
    In: Intervirology, S. Karger AG, Vol. 52, No. 3 ( 2009), p. 141-151
    Abstract: 〈 i 〉 Objective: 〈 /i 〉 Duck plague virus (DPV), the causative agent of duck plague (DP), is an alphaherpesvirus that causes an acute, febrile, contagious, and septic disease of waterfowl. UL35 protein (VP26) is a major capsid protein encoded by the UL35 gene, which is located in the unique long (UL) region of the DPV genome. To investigate the specific roles of VP26, the UL35 gene was amplified from the DPV DNA by polymerase chain reaction (PCR) and subcloned into pET-32a(+). 〈 i 〉 Methods: 〈 /i 〉 The resultant prokaryotic expression vector, pET-32a(+)/UL35, includes an amino-terminal His6 as a fusion partner. 〈 i 〉 Escherichia coli 〈 /i 〉 BL21 (DE3) competent cells were transformed with the construct and protein expression was subsequently induced by the addition of isopropyl-β- 〈 i 〉 D 〈 /i 〉 -thiogalactopyranoside to the culture medium. Protein lysates were submitted to SDS-PAGE to evaluate recombinant protein expression. 〈 i 〉 Results: 〈 /i 〉 The band that corresponded to the predicted protein size (33 kDa) was observed on the SDS-PAGE gel. The recombinant His6-tagged VP26 fusion protein was expressed at a high level in an insoluble form (inclusion bodies) and constituted about 24% of the total cellular protein. Then, the fusion protein was purified to near homogeneity using single-step immobilized metal affinity chromatography on a nickel-nitrilotriacetic acid affinity resin, yielding about 620 mg per liter culture. After purification, New Zealand white rabbits were immunized with purified His6-tagged VP26 in order to raise polyclonal antibody against this recombinant protein. Using the resultant sera, Western blot analysis showed that the recombinant protein was recognized by the polyclonal antibody. 〈 i 〉 Conclusion: 〈 /i 〉 Thus, the polyclonal antibody prepared here may serve as a valuable tool to study the functional involvement of VP26 in the DPV life cycle.
    Type of Medium: Online Resource
    ISSN: 0300-5526 , 1423-0100
    URL: Article
    DOI: 10.1159/000221833
    RVK:
    XA 10000
    Language: English
    Publisher: S. Karger AG
    Publication Date: 2009
    detail.hit.zdb_id: 1482863-7
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Porcine IFITM1 is a host restriction factor that inhibits pseudorabies virus infection
    Elsevier BV ; 2020
    In:  International Journal of Biological Macromolecules Vol. 151 ( 2020-05), p. 1181-1193
    Details
    In: International Journal of Biological Macromolecules, Elsevier BV, Vol. 151 ( 2020-05), p. 1181-1193
    Type of Medium: Online Resource
    ISSN: 0141-8130
    URL: Article
    DOI: 10.1016/j.ijbiomac.2019.10.162
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
    detail.hit.zdb_id: 1483284-7
    SSG: 12
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