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I'm Xiaolin Liu.

I will work on bacteria to study behavior if only I know how to tame them. --Max Delbruck

xiaolin

Email /  ResearchGate /  ORCiD

Experience

  • 2022.01-present, University of California, Santa Cruz, Postdoc.

  • 2019.10-2021.12, University of California, Santa Cruz, Visiting Ph. D.

  • 2015.09-2021.12, University of Chinese Academy of Sciences/ Yantai Institute of Coastal Zone Research, CAS, Ph. D.

  • 2011.09-2015.06, Shandong Normal University, B.S.

    • Presentation

  • 2024.01, Poster Presentation: Single amino acid change of PilO alters its repression on Helicobacter pylori motility. @Signal Transduction in Microorganism, Gordon Research Conference (GRC), 2024, Ventura, CA, US.

  • 2023.07, Oral Presentation: Analysis of the response of Helicobacter pylori to semi-solid agar uncovers new proteins that connect chemotaxis signaling and biofilm formation. @Receptorfest 2023, 2023, Pullman, WA, US.

  • 2022.11, Poster Presentation: Chemotaxis system regulated flagellar rotation, but not chemotaxis, contributes to the biofilm formation of Helicobacter pylori. @ASM Biofilm 2022, 2022, Charlotte, NC, US.

  • 2022.09, Poster Presentation: FliL has a conserved function in diverse microbes to negatively modulate motor output via its N-terminal region. @Signal Transduction in Microorganism, Gordon Research Conference (GRC), 2022, Ventura, CA, US.

  • 2022.05, Poster Presentation: Methylation-independent chemotaxis systems are the norm for gastric-colonizing bacteria. @UC Santa Cruz ANNUAL POSTDOC SYMPOSIUM 2022, Santa Cruz, CA, US.

  • 2021.01, Oral Presentation: Chemotaxis plays positive and negative roles on biofilm formation in Helicobacter pylori. @Bacterial Locomotion and Signal Transduction (BLAST), 2021, Virtual, US.

  • 2020.01, Poster Presentation: Boost or Inhibit: Oxalic acid from Sesbania rostrata seed exudates mediates the chemotactic response of Azorhizobium caulinodans ORS571 using multiple strategies. @Signal Transduction in Microorganism, Gordon Research Conference (GRC), 2020, Ventura, CA, US.

    • Awards

  • 2020, UCAS-BHBP Scholarship

  • 2019, National Scholarship for Graduate Students

  • 2019-2021, Scholarship from China Scholarship Council

  • 2019, Di-Ao Scholarship

  • 2018, Liu Ruiyu Marine Science Scholarship

  • 2017,2018, Level A Academic Scholarship for Graduate Students

    • Research

    I am very interested in two aspects of microbiology: first, the complex mechanisms of bacterial motility and chemotaxis; second, how bacterial cells in biofilms develop and organize intricate structures. Exploring both these realms not only expands our knowledge of microbial life but also holds promising implications for various fields, from healthcare to environmental science.

    Helicobacter pylori chemotaxis and biofilm formation

    1. Counterclockwise rotation of the flagellum promotes biofilm initiation in Helicobacter pylori
      Xiaolin Liu, Paphavee Lertsethtakarn, Vanessa T. Mariscal, Fitnat Yildiz, Karen M. Ottemann
      mBio 2024 | paper

    2. Bacterial flagella hijack type IV pili proteins to control motility
      Xiaolin Liu, Shoichi Tachiyama(co-first author), Xiaotian Zhou, Rommel A. Mathias, Sharmin Q. Bonny, Mohammad F. Khan, Yue Xin, Anna Roujeinikova, Jun Liu, Karen M. Ottemann
      Proceedings of the National Academy of Sciences of the United States of America 2024 | paper | News

    3. FliL functions in diverse microbes to negatively modulate motor output via its N-terminal region
      Xiaolin Liu, Anna Roujeinikova, Karen M. Ottemann
      mBio 2023 | paper
      BioRxiv 2022 | paper

    4. Methylation-independent chemotaxis systems are the norm for gastric-colonizing Helicobacter species
      Xiaolin Liu, Karen M. Ottemann
      Journal of Bacteriology 2022 (Editor's Pick)| paper

    5. The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation
      Shoichi Tachiyamaa, Kar L. Chan(co-first author), Xiaolin Liu, Skander Hathroubi, Briana Peterson, Mohammad F. Khan, Karen M. Ottemann, Jun Liu, Anna Roujeinikova
      Proceedings of the National Academy of Sciences of the United States of America 2022 | paper

    Azorhizobium caulinodans chemotaxis and host colonization

    1. The volatile organic compound acetoin enhances the colonization of Azorhizobium caulinodans ORS571 on Sesbania rostrata
      Li Sun, Dandan Wang(co-first author), Xiaolin Liu, Yanan Zhou, Weiwei Huang, Xin Guan, Xuexian Zhang, Zhihong Xie
      Science of the Total Environment 2023 | paper

    2. Systematic Analysis of Lysine Acetylation Reveals Diverse Functions in Azorhizobium caulinodans Strain ORS571
      Yanan Liu, Xiaolin Liu, Xiaoyan Dong, Zhiqiu Yin, Zhihong Xie, Yongming Luo
      Microbiology Spectrum 2022 | paper

    3. The effect of Azorhizobium caulinodans ORS571 and γ-aminobutyric acid on salt tolerance of Sesbania rostrata
      Yanan Liu, Xiaolin Liu, Xiaoyan Dong, Jiaming Yan, Zhihong Xie, Yongming Luo
      Frontiers in Microbiology 2022 | paper

    4. Azorhizobium caulinodans chemotaxis is controlled by an unusual phosphorelay network
      Emily N. Kennedy, Sarah A. Barr, Xiaolin Liu, Luke R. Vass, Yanan Liu, Zhihong Xie, Robert B. Bourret
      Journal of Bacteriology 2022 | paper

    5. The hypoxia-associated localization of chemotaxis protein CheZ in Azorhizorbium caulinodans
      Xiaolin Liu, Yanan Liu, Yixuan Wang, Dandan Wang, Kevin Scot Johnson, Zhihong Xie
      Frontiers in Microbiology 2021 | paper

    6. Eco-environment and sustainable management in the coastal zone (chapter 21)
      Zhihong Xie, Xiaolin Liu, Yanxia Wang
      China Science Publishing & Media with editors Yongming Luo, et al. 2021 | book

    7. Protein residues and a novel motif involved in the cellular localization of CheZ in Azorhizobium caulinodans ORS571
      Xiaolin Liu, Yanan Liu, Kevin Scot Johnson, Xiaoyan Dong, Zhihong Xie
      Frontiers in Microbiology 2020 | paper

    8. Effects of calcium and signal sensing systems on Azorhizobium caulinodans biofilm formation and host colonization
      Xiaolin Liu, Kaiye Zhang(co-first author), Yanan Liu, Desheng Zou, Dandan Wang, Zhihong Xie
      Frontiers in Microbiology 2020 | paper

    9. Azorhizobium caulinodans c-di-GMP phosphodiesterase Chp1 involved in motility, EPS production, and nodulation of the host plant
      Yu Sun, Yanan Liu (co-first author), Xiaolin Liu, Xiaoxiao Dang, Xiaoyan Dong, Zhihong Xie
      Applied Microbiology and Biotechnology 2020 | paper

    10. Oxalic acid from Sesbania rostrata seed exudates mediates the chemotactic response of Azorhizobium caulinodans ORS571 using multiple strategies
      Xiaolin Liu, Kaiye Zhang, Yanan Liu, Zhihong Xie
      Frontiers in Microbiology 2019 | paper

    11. A dual role of amino acids from Sesbania rostrata seed exudates in chemotaxis of Azorhizobium caulinodans ORS571
      Xiaolin Liu, Zhihong Xie, Yixuan Wang, Yu Sun, Xiaoxiao Dang, Haishuan Sun
      Molecular Plant-Microbe Interaction 2019 | paper

    12. Inactivation of the phosphatase CheZ alters cell-surface properties of Azorhizobium caulinodans ORS571 and symbiotic association with Sesbania rostrata
      Xiaolin Liu, Zhihong Xie
      Molecular Plant-Microbe Interaction 2019 | paper

    13. The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations
      Xiaoxiao Dang, Zhihong Xie, Wei Liu, Yu Sun, Xiaolin Liu, Yongqiang Zhu, Christian Staehelin
      BMC Genomics 2019 | paper

    14. A cheZ-like gene in Azorhizobium caulinodans is a key gene in the control of chemotaxis and colonization of the host plant
      Xiaolin Liu, Wei Liu, Yu Sun, Chunlei Xia, Claudine Elmerich, Zhihong Xie
      Applied and Environmental Microbiology 2018 | paper

    15. A Chemotaxis-Like Pathway of Azorhizobium caulinodans controls flagella-driven motility, which regulates biofilm formation, exopolysaccharide biosynthesis, and competitive nodulation
      Wei Liu, Yu Sun, Rimin Shen, Xiaoxiao Dang, Xiaolin Liu, Fu Sui, Yan Li, Zhenpeng Zhang, Gladys Alexandre, Claudine Elmerich, Zhihong Xie
      Molecular Plant-Microbe Interaction 2018 | paper

    16. Plant growth promotion properties of bacterial strains isolated from the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.) adapted to saline–alkaline soils and their effect on wheat growth
      Xiaolin Liu, Xiangyue Li (co-first author), Yan Li, Runzhi Li, and Zhihong Xie
      Canadian Journal of Microbiology 2017 | paper

    17. Azorhizobium caulinodans transmembrane chemoreceptor TlpA1 involved in host colonization and nodulation on roots and stems
      Wei Liu, Jinbao Yang, Yu Sun, Xiaolin Liu, Yan Li, Zhenpeng Zhang, Zhihong Xie
      Frontiers in Microbiology 2017 | paper

    18. Advances in phosphatase CheZ of bacterial chemotaxis signaling pathway
      Xiaolin Liu, Wei Liu, Zhihong Xie
      Acta Microbiologica Sinica 2016 | paper

    Service to the profession

  • 2023-current, Review editor, Frontiers in Cellular and Infection Microbiology

  • 2023, Guest editor, Journal of Visualized Experiments

    • Tools

    Bioinformatics Portals

    1. NCBI

    2. EBI

    3. Pasteur-tools

    4. abc

    5. IBIVU

    6. MPI-toolkit

    7. Online-tools

    8. National Microbiology Data Center

    Microbial genomic resources

    1. Microbesonline

    2. GTDB

    3. Mistdb

    4. UCSC microbial Genomie browser

    Protein

    1. Uniprot, a comprehensive resource for protein sequence and annotation data

    2. DeepTMHHM, Transmembrane prediction

    3. CDD, Conserved domain database

    4. Interpro, Database of protein families instead of old Pfam database

    5. SMART, a simple modular architecture research tool

    6. Annotree, a web tool to facilitate visualization of genome annotations across large phylogenetic trees

    7. TREND, Tree-based Exploration of Neighborhoods and Domains

    8. HMMER, fast and sensitive homology searches

    9. Phyre2, Protein Homology/analogY Recognition Engine V 2.0

    10. CD-vist, a sequence-based protein domain search tool

    11. SWISS-model, a fully automated protein structure homology-modelling server

    12. Predict Protein, prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions

    13. Jpred, Protein Secondary Structure Prediction server

    14. String, Database of protein association networks

    15. Aquerium, a domain-based protein family querier

    16. H. pylori protein interaction, published data

    Comparative and evolutionary genomics

    1. COG, Clusters of Orthologous Genes

    2. BioCyc, a database collection and website with extensive search and analysis tools

    3. Evolview, a webserver for visualization, annotation, and management of phylogenetic trees

    4. BacDive, the worldwide largest database for standardized bacterial information

    5. plannotate, plasmid annotation (feature identification)

    6. BDGP, promotor prediction

    Bioinformatics study

    1. MPI lectures on bioinformatics

    2. Bioinformatic software update

    3. Peking University lectures on bioinformatics

    Molecular biology, Mathmatics, Methods, and Grant application

    1. PRINCIPLES OF STATISTICS

    2. ImageJ

    3. R Graph gallery

    4. NEB resources &tools

    5. PaperBlast

    6. Addgene blog

    7. PACE, allows authors to effortlessly deliver images to exact publisher specifications in minutes

    8. Grant database, A grant database for National Natural Science Foundation of China by Sciencenet

    9. Grant database, A grant database for National Natural Science Foundation of China by Letpub

    10. A genome Mapping and SNP Calling Tutorial for Geneious

    11. Brief Introduction to Critical Point Drying

    Conference & Community

    1. BLAST, 2023, the Bacterial Locomotion and Signal Transduction (BLAST) group was founded in 1990 by Phil Matsumura, Joe Falke, Mike Manson, and Sandy Parkinson

    2. Sensory Transduction in Microorganisms, Gordon Research Conference, 2024, meet in alternate years when the BLAST is not held

    3. SEQanswers, a next generation sequencing community

    4. National Science Library, Chinese Academy of Sciences, a knowledge service platform for CAS

    Contact

    Santa Cruz, California, US

    Email: xliu241@ucsc.edu

    Email: liuxiaolin215@mails.ucas.ac.cn