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  1. Article: Understanding pre-mRNA splicing through crystallography

    Espinosa, Sara / Lingdi Zhang / Rui Zhao / Xueni Li

    Methods. 2017 Aug. 01, v. 125

    2017  

    Abstract: Crystallography is a powerful tool to determine the atomic structures of proteins and RNAs. X-ray crystallography has been used to determine the structure of many splicing related proteins and RNAs, making major contributions to our understanding of the ... ...

    Abstract Crystallography is a powerful tool to determine the atomic structures of proteins and RNAs. X-ray crystallography has been used to determine the structure of many splicing related proteins and RNAs, making major contributions to our understanding of the molecular mechanism and regulation of pre-mRNA splicing. Compared to other structural methods, crystallography has its own advantage in the high-resolution structural information it can provide and the unique biological questions it can answer. In addition, two new crystallographic methods – the serial femtosecond crystallography and 3D electron crystallography – were developed to overcome some of the limitations of traditional X-ray crystallography and broaden the range of biological problems that crystallography can solve. This review discusses the theoretical basis, instrument requirements, troubleshooting, and exciting potential of these crystallographic methods to further our understanding of pre-mRNA splicing, a critical event in gene expression of all eukaryotes.
    Keywords crystallography ; eukaryotic cells ; proteins ; RNA ; X-ray diffraction
    Language English
    Dates of publication 2017-0801
    Size p. 55-62.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2017.04.023
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

    Lingdi Zhang / Christian V. Forst / Aubree Gordon / Gabrielle Gussin / Adam B. Geber / Porfirio J. Fernandez / Tao Ding / Lauren Lashua / Minghui Wang / Angel Balmaseda / Richard Bonneau / Bin Zhang / Elodie Ghedin

    Microbiome, Vol 8, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: Abstract Background The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, the host, and resident ... ...

    Abstract Abstract Background The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, the host, and resident bacteria with pathogenic potential are known to complicate and worsen disease, resulting in coinfection and increased morbidity and mortality of infected individuals. When pathogenic bacteria acquire antibiotic resistance, they are more difficult to treat and of global health concern. Characterization of ARG expression in the upper respiratory tract could help better understand the role antibiotic resistance plays in the pathogenesis of influenza-associated bacterial secondary infection. Results Thirty-seven individuals participating in the Household Influenza Transmission Study (HITS) in Managua, Nicaragua, were selected for this study. We performed metatranscriptomics and 16S rRNA gene sequencing analyses on nasal and throat swab samples, and host transcriptome profiling on blood samples. Individuals clustered into two groups based on their microbial gene expression profiles, with several microbial pathways enriched with genes differentially expressed between groups. We also analyzed antibiotic resistance gene expression and determined that approximately 25% of the sequence reads that corresponded to antibiotic resistance genes mapped to Streptococcus pneumoniae and Staphylococcus aureus. Following construction of an integrated network of ARG expression with host gene co-expression, we identified several host key regulators involved in the host response to influenza virus and bacterial infections, and host gene pathways associated with specific antibiotic resistance genes. Conclusions This study indicates the host response to influenza infection could indirectly affect antibiotic resistance gene expression in the respiratory tract by impacting the microbial community structure and overall microbial gene expression. Interactions between the host systemic responses to influenza infection and antibiotic resistance gene expression highlight the importance of viral-bacterial co-infection in acute respiratory infections like influenza. Video abstract
    Keywords Antibiotic resistance ; Upper respiratory tract infection ; Microbiome ; Influenza infection ; Metatranscriptome ; Microbial ecology ; QR100-130
    Subject code 572
    Language English
    Publishing date 2020-03-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Improved thermostability of an acidic xylanase from Aspergillus sulphureus by combined disulphide bridge introduction and proline residue substitution

    Wenhan Yang / Yongzhi Yang / Lingdi Zhang / Hang Xu / Xiaojing Guo / Xu Yang / Bing Dong / Yunhe Cao

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Volume 9

    Abstract: Abstract As a feed additive, xylanase has been widely applied in the feed of monogastric animals, which contains multiple plant polysaccharides. However, during feed manufacture, the high pelleting temperatures challenge wild-type xylanases. The aim of ... ...

    Abstract Abstract As a feed additive, xylanase has been widely applied in the feed of monogastric animals, which contains multiple plant polysaccharides. However, during feed manufacture, the high pelleting temperatures challenge wild-type xylanases. The aim of this study was to improve the thermostability of Aspergillus sulphureus acidic xylanase. According to the predicted protein structure, a series of disulphide bridges and proline substitutions were created in the xylanase by PCR, and the mutants were expressed in Pichia pastoris. Enzyme properties were evaluated following chromatographic purification. All the recombinant enzymes showed optima at pH 3.0 and 50 °C or 55 °C and better resistance to some chemicals except for CuSO4. The specific activity of the xylanase was decreased by introduction of the mutations. Compared to the wild-type enzyme, a combined mutant, T53C-T142C/T46P, with a disulphide bond at 53–142 and a proline substitution at 46, showed a 22-fold increase of half-life at 60 °C. In a 10-L fermentor, the maximal xylanase activity of T53C-T142C/T46P reached 1,684 U/mL. It was suggested that the T53C-T142C/T46P mutant xylanase had excellent thermostability characteristics and could be a prospective additive in feed manufacture.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2017-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Author Correction

    Lingdi Zhang / Hengbo Zhou / Xueni Li / Rebecca L. Vartuli / Michael Rowse / Yongna Xing / Pratyaydipta Rudra / Debashis Ghosh / Rui Zhao / Heide L. Ford

    Nature Communications, Vol 9, Iss 1, Pp 1-

    Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression

    2018  Volume 1

    Abstract: In the original version of this Article, the title of the legend to Fig. 7 incorrectly read ‘Knockdown of B55α increases breast cancer metastasis’ instead of ‘Knockdown of B55α decreases breast cancer metastasis’. This has now been corrected in both the ... ...

    Abstract In the original version of this Article, the title of the legend to Fig. 7 incorrectly read ‘Knockdown of B55α increases breast cancer metastasis’ instead of ‘Knockdown of B55α decreases breast cancer metastasis’. This has now been corrected in both the PDF and HTML versions of the Article.
    Keywords Science ; Q
    Language English
    Publishing date 2018-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression

    Lingdi Zhang / Hengbo Zhou / Xueni Li / Rebecca L Vartuli / Michael Rowse / Yongna Xing / Pratyaydipta Rudra / Debashis Ghosh / Rui Zhao / Heide L Ford

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 14

    Abstract: Eya proteins are characterised by phosphatase activity associated with both the evolutionary conserved region and the less conserved N-terminal domain (NTD). Here the authors show that NTD mediates the interaction with PP2A and regulates c-Myc ... ...

    Abstract Eya proteins are characterised by phosphatase activity associated with both the evolutionary conserved region and the less conserved N-terminal domain (NTD). Here the authors show that NTD mediates the interaction with PP2A and regulates c-Myc phosphorylation and stability, potentially switching PP2A from a tumour suppressor to an oncogene.
    Keywords Science ; Q
    Language English
    Publishing date 2018-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Author Correction

    Xueni Li / Shiheng Liu / Jiansen Jiang / Lingdi Zhang / Sara Espinosa / Ryan C. Hill / Kirk C. Hansen / Z. Hong Zhou / Rui Zhao

    Nature Communications, Vol 9, Iss 1, Pp 1-

    CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing

    2018  Volume 1

    Abstract: The originally published version of this Article contained several errors in Figure 2, panel a: the basepair register in SL3-4 of yeast U1 snRNA was depicted incorrectly; the basepair for A287-U295 in yeast U1 snRNA was erroneously present; basepairs for ...

    Abstract The originally published version of this Article contained several errors in Figure 2, panel a: the basepair register in SL3-4 of yeast U1 snRNA was depicted incorrectly; the basepair for A287-U295 in yeast U1 snRNA was erroneously present; basepairs for U84-G119, G309-U532, A288-U295 and U289-A294 in yeast U1 snRNA were missing; the bulging nucleotide in SL3 of human U1 snRNA was depicted as G instead of C; and the dashed boxes defining the 5′ ss binding site and Sm site in both human and yeast snRNAs were not drawn accurately. These have now been corrected in both the PDF and HTML versions of the Article.
    Keywords Science ; Q
    Language English
    Publishing date 2018-04-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Author Correction

    Lingdi Zhang / Hengbo Zhou / Xueni Li / Rebecca L. Vartuli / Michael Rowse / Yongna Xing / Pratyaydipta Rudra / Debashis Ghosh / Rui Zhao / Heide L. Ford

    Nature Communications, Vol 9, Iss 1, Pp 1-

    Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression

    2018  Volume 1

    Abstract: In the original version of this Article, the title of the legend to Fig. 7 incorrectly read ‘Knockdown of B55α increases breast cancer metastasis’ instead of ‘Knockdown of B55α decreases breast cancer metastasis’. This has now been corrected in both the ... ...

    Abstract In the original version of this Article, the title of the legend to Fig. 7 incorrectly read ‘Knockdown of B55α increases breast cancer metastasis’ instead of ‘Knockdown of B55α decreases breast cancer metastasis’. This has now been corrected in both the PDF and HTML versions of the Article.
    Keywords Science ; Q
    Language English
    Publishing date 2018-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  8. Article ; Online: Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression

    Lingdi Zhang / Hengbo Zhou / Xueni Li / Rebecca L Vartuli / Michael Rowse / Yongna Xing / Pratyaydipta Rudra / Debashis Ghosh / Rui Zhao / Heide L Ford

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 14

    Abstract: Eya proteins are characterised by phosphatase activity associated with both the evolutionary conserved region and the less conserved N-terminal domain (NTD). Here the authors show that NTD mediates the interaction with PP2A and regulates c-Myc ... ...

    Abstract Eya proteins are characterised by phosphatase activity associated with both the evolutionary conserved region and the less conserved N-terminal domain (NTD). Here the authors show that NTD mediates the interaction with PP2A and regulates c-Myc phosphorylation and stability, potentially switching PP2A from a tumour suppressor to an oncogene.
    Keywords Science ; Q
    Language English
    Publishing date 2018-03-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  9. Article ; Online: Author Correction

    Xueni Li / Shiheng Liu / Jiansen Jiang / Lingdi Zhang / Sara Espinosa / Ryan C. Hill / Kirk C. Hansen / Z. Hong Zhou / Rui Zhao

    Nature Communications, Vol 9, Iss 1, Pp 1-

    CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing

    2018  Volume 1

    Abstract: The originally published version of this Article contained several errors in Figure 2, panel a: the basepair register in SL3-4 of yeast U1 snRNA was depicted incorrectly; the basepair for A287-U295 in yeast U1 snRNA was erroneously present; basepairs for ...

    Abstract The originally published version of this Article contained several errors in Figure 2, panel a: the basepair register in SL3-4 of yeast U1 snRNA was depicted incorrectly; the basepair for A287-U295 in yeast U1 snRNA was erroneously present; basepairs for U84-G119, G309-U532, A288-U295 and U289-A294 in yeast U1 snRNA were missing; the bulging nucleotide in SL3 of human U1 snRNA was depicted as G instead of C; and the dashed boxes defining the 5′ ss binding site and Sm site in both human and yeast snRNAs were not drawn accurately. These have now been corrected in both the PDF and HTML versions of the Article.
    Keywords Science ; Q
    Language English
    Publishing date 2018-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

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  10. Article ; Online: CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing

    Xueni Li / Shiheng Liu / Jiansen Jiang / Lingdi Zhang / Sara Espinosa / Ryan C. Hill / Kirk C. Hansen / Z. Hong Zhou / Rui Zhao

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 13

    Abstract: U1 snRNP is critical for 5′ splicing site recognition in pre-mRNA splicing. Here the authors describe the cryo-EM structure of the yeast U1 snRNP and suggest that PrpF39 is an alternative splicing factor essential for the successful recruitment of U1 ... ...

    Abstract U1 snRNP is critical for 5′ splicing site recognition in pre-mRNA splicing. Here the authors describe the cryo-EM structure of the yeast U1 snRNP and suggest that PrpF39 is an alternative splicing factor essential for the successful recruitment of U1 snRNP by other alternative splicing factors.
    Keywords Science ; Q
    Language English
    Publishing date 2017-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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