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  1. Book ; Online ; E-Book: Bioinformatics and the cell

    Xia, Xuhua

    modern computational approaches in genomics, proteomics and transcriptomics

    2018  

    Author's details Xuhua Xia
    Keywords Life sciences ; Proteomics ; Bioinformatics ; Cell biology ; Evolutionary biology
    Subject code 570.285
    Language English
    Size 1 Online-Ressource (xiii, 489 Seiten), Illustrationen
    Edition Second edition
    Publisher Springer
    Publishing place Cham
    Publishing country Switzerland
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT019774576
    ISBN 978-3-319-90684-3 ; 9783319906829 ; 3-319-90684-4 ; 3319906828
    DOI 10.1007/978-3-319-90684-3
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article: Horizontal Gene Transfer and Drug Resistance Involving

    Xia, Xuhua

    Antibiotics (Basel, Switzerland)

    2023  Volume 12, Issue 9

    Abstract: Mycobacterium ... ...

    Abstract Mycobacterium tuberculosis
    Language English
    Publishing date 2023-08-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics12091367
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Selected Works in Bioinformatics

    Xia, Xuhua

    2011  

    Keywords Medical ethics & professional conduct ; Medical bioinformatics
    Size 1 electronic resource (192 pages)
    Publisher IntechOpen
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021044853
    ISBN 9789535155485 ; 9535155482
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  4. Article: Identification of host receptors for viral entry and beyond: a perspective from the spike of SARS-CoV-2.

    Xia, Xuhua

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1188249

    Abstract: Identification of the interaction between the host membrane receptor and viral receptor-binding domain (RBD) represents a crucial step for understanding viral pathophysiology and for developing drugs against pathogenic viruses. While all membrane ... ...

    Abstract Identification of the interaction between the host membrane receptor and viral receptor-binding domain (RBD) represents a crucial step for understanding viral pathophysiology and for developing drugs against pathogenic viruses. While all membrane receptors and carbohydrate chains could potentially be used as receptors for viruses, prioritized searches focus typically on membrane receptors that are known to have been used by the relatives of the pathogenic virus, e.g., ACE2 used as a receptor for SARS-CoV is a prioritized candidate receptor for SARS-CoV-2. An ideal receptor protein from a viral perspective is one that is highly expressed in epithelial cell surface of mammalian respiratory or digestive tracts, strongly conserved in evolution so many mammalian species can serve as potential hosts, and functionally important so that its expression cannot be readily downregulated by the host in response to the infection. Experimental confirmation of host receptors includes (1) infection studies with cell cultures/tissues/organs with or without candidate receptor expression, (2) experimental determination of protein structure of the complex between the putative viral RDB and the candidate host receptor, and (3) experiments with mutant candidate receptor or homologues of the candidate receptor in other species. Successful identification of the host receptor opens the door for mechanism-based development of candidate drugs and vaccines and facilitates the inference of what other animal species are vulnerable to the viral pathogen. I illustrate these approaches with research on identification of the receptor and co-factors for SARS-CoV-2.
    Language English
    Publishing date 2023-07-25
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1188249
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time.

    Xia, Xuhua

    Viruses

    2023  Volume 15, Issue 3

    Abstract: Almost all published rooting and dating studies on SARS-CoV-2 assumed that (1) evolutionary rate does not change over time although different lineages can have different evolutionary rates (uncorrelated relaxed clock), and (2) a zoonotic transmission ... ...

    Abstract Almost all published rooting and dating studies on SARS-CoV-2 assumed that (1) evolutionary rate does not change over time although different lineages can have different evolutionary rates (uncorrelated relaxed clock), and (2) a zoonotic transmission occurred in Wuhan and the culprit was immediately captured, so that only the SARS-CoV-2 genomes obtained in 2019 and the first few months of 2020 (resulting from the first wave of the global expansion from Wuhan) are sufficient for dating the common ancestor. Empirical data contradict the first assumption. The second assumption is not warranted because mounting evidence suggests the presence of early SARS-CoV-2 lineages cocirculating with the Wuhan strains. Large trees with SARS-CoV-2 genomes beyond the first few months are needed to increase the likelihood of finding SARS-CoV-2 lineages that might have originated at the same time as (or even before) those early Wuhan strains. I extended a previously published rapid rooting method to model evolutionary rate as a linear function instead of a constant. This substantially improves the dating of the common ancestor of sampled SARS-CoV-2 genomes. Based on two large trees with 83,688 and 970,777 high-quality and full-length SARS-CoV-2 genomes that contain complete sample collection dates, the common ancestor was dated to 12 June 2019 and 7 July 2019 with the two trees, respectively. The two data sets would give dramatically different or even absurd estimates if the rate was treated as a constant. The large trees were also crucial for overcoming the high rate-heterogeneity among different viral lineages. The improved method was implemented in the software TRAD.
    MeSH term(s) SARS-CoV-2/genetics ; Trees ; COVID-19 ; Phylogeny ; Evolution, Molecular
    Language English
    Publishing date 2023-03-05
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15030684
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Phylogeographic Reconstruction to Trace the Source Population of Asian Giant Hornet Caught in Nanaimo in Canada and Blaine in the USA.

    Freeman, Alexa / Xia, Xuhua

    Life (Basel, Switzerland)

    2024  Volume 14, Issue 3

    Abstract: The Asian giant hornet, ...

    Abstract The Asian giant hornet,
    Language English
    Publishing date 2024-02-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life14030283
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Multiple regulatory mechanisms for pH homeostasis in the gastric pathogen, Helicobacter pylori.

    Xia, Xuhua

    Advances in genetics

    2022  Volume 109, Page(s) 39–69

    Abstract: Acid-resistance in gastric pathogen Helicobacter pylori requires the coordination of four essential processes to regulate urease activity. Firstly, urease expression above a base level needs to be finely tuned at different ambient pH. Secondly, as nickel ...

    Abstract Acid-resistance in gastric pathogen Helicobacter pylori requires the coordination of four essential processes to regulate urease activity. Firstly, urease expression above a base level needs to be finely tuned at different ambient pH. Secondly, as nickel is needed to activate urease, nickel homeostasis needs to be maintained by proteins that import and export nickel ions, and sequester, store and release nickel when needed. Thirdly, urease accessary proteins that activate urease activity by nickel insertion need to be expressed. Finally, a reliable source of urea needs to be maintained by both intrinsic and extrinsic sources of urea. Two-component systems (arsRS and flgRS), as well as a nickel response regulator (NikR), sense the change in pH and act on a variety of genes to accomplish the function of acid resistance without causing cellular overalkalization and nickel toxicity. Nickel storage proteins also feature built-in switches to store nickel at neutral pH and release nickel at low pH. This review summarizes the current status of H. pylori research and highlights a number of hypotheses that need to be tested.
    MeSH term(s) Helicobacter pylori/genetics ; Helicobacter pylori/metabolism ; Urease/genetics ; Urease/metabolism ; Gene Expression Regulation, Bacterial ; Nickel/metabolism ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Hydrogen-Ion Concentration ; Urea/metabolism ; Homeostasis
    Chemical Substances Urease (EC 3.5.1.5) ; Nickel (7OV03QG267) ; Repressor Proteins ; Bacterial Proteins ; Urea (8W8T17847W)
    Language English
    Publishing date 2022-08-18
    Publishing country United States
    Document type Review ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 148-x
    ISSN 0065-2660
    ISSN 0065-2660
    DOI 10.1016/bs.adgen.2022.07.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  8. Article ; Online: Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria.

    Kruglikov, Alibek / Xia, Xuhua

    International journal of molecular sciences

    2024  Volume 25, Issue 4

    Abstract: The dynamic structures and varying functions of intrinsically disordered proteins (IDPs) have made them fascinating subjects in molecular biology. Investigating IDP abundance in different bacterial species is crucial for understanding adaptive strategies ...

    Abstract The dynamic structures and varying functions of intrinsically disordered proteins (IDPs) have made them fascinating subjects in molecular biology. Investigating IDP abundance in different bacterial species is crucial for understanding adaptive strategies in diverse environments. Notably, thermophilic bacteria have lower IDP abundance than mesophiles, and a negative correlation with optimal growth temperature (OGT) has been observed. However, the factors driving these trends are yet to be fully understood. We examined the types of IDPs present in both mesophiles and thermophiles alongside those unique to just mesophiles. The shared group of IDPs exhibits similar disorder levels in the two groups of species, suggesting that certain IDPs unique to mesophiles may contribute to the observed decrease in IDP abundance as OGT increases. Subsequently, we used quasi-independent contrasts to explore the relationship between OGT and IDP abundance evolution. Interestingly, we found no significant relationship between OGT and IDP abundance contrasts, suggesting that the evolution of lower IDP abundance in thermophiles may not be solely linked to OGT. This study provides a foundation for future research into the intricate relationship between IDP evolution and environmental adaptation. Our findings support further research on the adaptive significance of intrinsic disorder in bacterial species.
    MeSH term(s) Humans ; Intrinsically Disordered Proteins/chemistry ; Temperature ; Bacteria/genetics ; Bacteria/metabolism ; Protein Conformation
    Chemical Substances Intrinsically Disordered Proteins
    Language English
    Publishing date 2024-02-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25042000
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines

    Xuhua Xia

    Vaccines, Vol 9, Iss 734, p

    2021  Volume 734

    Abstract: The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components ...

    Abstract The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components of the vaccine need to have a 5′-UTR to load ribosomes efficiently onto the mRNA for translation initiation, optimized codon usage for efficient translation elongation, and optimal stop codon for efficient translation termination. Both 5′-UTR and the downstream 3′-UTR should be optimized for mRNA stability. The replacement of uridine by N1-methylpseudourinine ( <math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi mathvariant="sans-serif">Ψ</mi></semantics></math> ) complicates some of these optimization processes because <math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi mathvariant="sans-serif">Ψ</mi></semantics></math> is more versatile in wobbling than U. Different optimizations can conflict with each other, and compromises would need to be made. I highlight the similarities and differences between Pfizer/BioNTech and Moderna mRNA vaccines and discuss the advantage and disadvantage of each to facilitate future vaccine improvement. In particular, I point out a few optimizations in the design of the two mRNA vaccines that have not been performed properly.
    Keywords SARS-CoV-2 ; mRNA vaccine ; translation initiation ; codon optimization ; translation termination ; RNA secondary structure ; Medicine ; R
    Subject code 511
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines.

    Xia, Xuhua

    Vaccines

    2021  Volume 9, Issue 7

    Abstract: The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components ...

    Abstract The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components of the vaccine need to have a 5'-UTR to load ribosomes efficiently onto the mRNA for translation initiation, optimized codon usage for efficient translation elongation, and optimal stop codon for efficient translation termination. Both 5'-UTR and the downstream 3'-UTR should be optimized for mRNA stability. The replacement of uridine by N1-methylpseudourinine (Ψ) complicates some of these optimization processes because Ψ is more versatile in wobbling than U. Different optimizations can conflict with each other, and compromises would need to be made. I highlight the similarities and differences between Pfizer/BioNTech and Moderna mRNA vaccines and discuss the advantage and disadvantage of each to facilitate future vaccine improvement. In particular, I point out a few optimizations in the design of the two mRNA vaccines that have not been performed properly.
    Language English
    Publishing date 2021-07-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines9070734
    Database MEDical Literature Analysis and Retrieval System OnLINE

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