David S. Holmes, PhD.

Principal Investigator and Full Professor

Extremophile Genomics and Astrobiology Laboratory

PhD in Biochemistry, California Institute of Technology, USA.

dsholmes2000@yahoo.com

Líneas de Investigación

  • Extremophile genomics
  • Cell adaptations in extreme environments
  • Thermodynamic limits of life
  • Astrobiology

Bioinformatics and Genome Biology

We are studying the evolution of microorganisms (extremophiles) that live in extraordinary environments, such as high temperature, acid pH and high salt. Extremophiles exhibit many interesting characteristics that are not only of fundamental interest but also make them useful in many biotechnological applications. For example, understanding their ability to use hydrogen, iron, and sulfur as energy sources helps generate models of the emergence of life on earth and provides insight into the potential for life on exoplanets and moons (Astrobiology). Examination of their unusual physiological capacities is also advancing our understanding of how some extremophiles can operate as a consortium to liberate copper in industrial biomining (bioleaching) operations.

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Biography

David Holmes is Full Professor in the Centro de Genómica y Bioinformática, at the Universidad Mayor where he is director of the Laboratory of Extremophile Genomics and Astrobiology. He received a BA (Genetics, First Class Honors) from Trinity College Dublin, Ireland and a PhD in Biochemistry from the California Institute of Technology, USA. He did postdoctoral research in the Dept of Chemistry and Chemical Engineering at Caltech. He then held several academic positions from Assistant Professor to Full Professor in the USA and also worked for 6 years at the Research and Development Labs of General Electric. Dr. Holmes has over 180 publications. One of his papers became a Scientific Citation Classic. He has graduated 40 Masters and PhD students and has served on numerous editorial and scientific boards.

David’s current research focusses on the genomics of extremophiles including those that live in environments with ultra-low pH, high temperature, and high concentration of salt. Research questions include i) what are the thermodynamic limits of life? ii) how can an understanding of the extraordinary metabolisms of extremophiles suggest models for the emergence of life on Earth? and iii) how can extreme environments on Earth be used as surrogates to search for potential life-supporting habitats on exoplanets and moons?

David’s awards include a Helen G. and Arthur McCallum Fellowship; a Lucy Mason Clark Fellowship; a Damon Runyon Fellowship; Member of the Recombinant DNA Advisory Panel to the Governor of New York State; Scientific Advisory Board, International Museum of Life, Boston; NSF review panel; United Nations Visiting Scholar to India, Chile, and Russia; Kings Mille Jones prize in Natural Sciences; Life Time Achievement Award in Biotechnology (Indonesia); Life Time Achievement Award in Bioinformatics (Spain); He has been cited as one of the most influential scientists in the development of Bioinformatics in Latin American and was elected a Fellow of the American Academy of Microbiology in 2015.

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Selected publications

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus. Eva Vergara, Gonzalo Neira, Carolina González, Diego Cortez, Mark Dopson and David S. Holmes. Genes 2020, 11(4), 389; https://doi.org/10.3390/genes1...

Héctor Osorio, Erin Mettert, Patricia Kiley, Mark Dopson, Eugenia Jedlicki and David S. Holmes. Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front. Microbiol., 10 (2019): 1642.

Mario Esparza, Eugenia Jedlicki, Carolina González, Mark Dopson, and David S. Holmes. Uptake and Assimilation of Inorganic Carbon in Extremely Acidic Environments: Case of the Polyextremophile Acidithiobacillus ferrooxidans. Front. Microbiol., 04 April 2019 | https://doi.org/10.3389/fmicb.2019.00603.

Himel Nahreen Khaleque, Carolina González, Raihan Shafique, Anna Kaksonen, David S Holmes, Elizabeth Lindsay Watkin. Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus through Comparative Genome Analysis. Front. Microbiol., 2019 Feb 8;10:155. doi: 10.3389/fmicb.2019.00155. eCollection 2019.

Himel N. Khaleque, Carolina González, Anna H. Kaksonen, Naomi J. Boxall, David S. Holmes and Elizabeth L.J. Watkin. Genome-based classification and renaming of two extremely acidophilic, iron- and sulfur-oxidizing halophiles 'Acidihalobacter prosperus' strain V6 and 'Acidihalobacter ferrooxidans' strain V8 as two new species, Acidihalobacter aeoliana sp. nov., and Acidihalobacter vulcanensis sp. nov., respectively. Int J Syst Evol Microbiol. 2019 Mar 5. doi: 10.1099/ijsem.0.003313.

Jorquera R, González C, Clausen P, Petersen B, Holmes DS. Improved ontology for eukaryotic single-exon coding sequences in biological databases. Database (Oxford), 1; 2018:1-6.

Francisco Issotta, Paulo C. Covarrubias, Ana Moya-Beltrán, Sören Bellenberg, Christian Thyssen, Wolfgang Sand, Harold Nuñez, Cristóbal Mena, David S. Holmes, Raquel Quatrini and Mario Vera. 16S rRNA and Multilocus Phylogenetic Analysis of the Iron Oxidizing Acidophiles of the Acidiferrobacteraceae Family. Solid State Phenomena 262:339-343, (2017). ISSN 1662-9787. Trans Tech Publications, Switzerland.

Matias Castro, Ana Moya-Beltrán, Paulo C. Covarrubias, Mónica González, Francisco Issotta, Oscar A. Salgado, Lillian G. Acuña, Gonzalo Encina, David S Holmes, David Barrie Johnson, Raquel Quatrini. Draft genome sequence of Acidithiobacillus albertensis DSM14366 type strain. Standards in Genomic Sciences 12:77 (2017).

Raquel Quatrini; Lorena Escudero; Ana Moya-Beltrán; Pedro A. Galleguillos; Francisco Issotta; Mauricio Acosta; Juan Pablo Cárdenas; Harold Nuñez; David S. Holmes; Cecilia Demergasso. Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile. Standards in Genomic Sciences, 12:84 (2017).

Braulio Valdevenito-Maturana, Jose Antonio Reyes-Suarez, Jaime Henriquez, David S. Holmes, Raquel Quatrini, Ehmke Pohl, Mauricio Arenas-Salinas. MUTANTELEC: an In Silico Mutation Simulation Platform for Comparative Electrostatic Potential Profiling of Proteins. J. of Computational Chemistry 38, 467–474, (2017).

Mark Dopson, David S Holmes, Marcelo Lazcano, Timothy J McCredden, Kieran T Mulroney, Elizabeth LJ Watkin. Multiple osmotic stress responses in Acidihalobacter prosperous results in a greater tolerance to chloride ions than in Acidithiobacillus ferrooxidans. Front. Microbiol., 05 January, doi.org/10.3389/fmicb.2016.02132 (2017).

Sophie R. Ullrich, Anja Poehlein, Carolina González, Judith S. Tischler, Francisco Ossandon, Rolf Daniel, David S. Holmes, Michael Schlömann, Martin Mühling. Gene loss and horizontal gene transfer contributed to the genome evolution of the extreme acidophile “Ferrovum”. Front. Microbiol. 7:797. doi: 10.3389/fmicb.2016.00797 (2016).

J. P. Cárdenas, R. Quatrini and D. S. Holmes. Genomic and Metagenomic Challenges and Opportunities for Bioleaching: a mini-review. Res Microbiol. Sep;167(7):529-38 (2016).

Carolina González†, Marcelo Lazcano†, Jorge Valdés and David S. Holmes. Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use as Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation. Front. Microbiol. 7:2035. doi: 10.3389/fmicb.2016.02035 (2016).

Jorquera R., Ortiz R., Ossandon F., Cárdenas J.P., Sepúlveda R and Holmes D. S. SinEx DB: A Database for Single Exon Coding Sequences in Mammalian Genomes. DataBase, baw095 doi:10.1093/database/baw095 (2016).

Juan Pablo Cárdenas, Raquel Quatrini and David S. Holmes. Aerobic lineages of the oxidative stress response protein rubrerythrin emerged in an ancient microaerobic, (hyper)thermophilic environment. Front Microbiol. Nov 18; 7:1822 (2016).

Alberto J.M. Martin, Calixto Dominguez, J. Sebastian Contreras-Riquelme, David S. Holmes, Tomas Perez-Acle. A graphlet-based metric for the comparison of dynamic Gene Regulatory Networks. Plos One. Oct 3;11(10):e0163497 (2016).

Francisco Issotta, Pedro Galleguillos, Ana Moya-Beltrán, Carol S. Davis-Belmar, George Rautenbach, Paulo C. Covarrubias, Mauricio Acosta G., Francisco J. Ossandon, Yasna Contador, David S. Holmes, Sabrina Marín-Eliantonio, Raquel Quatrini, Cecilia Demergasso. Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile. Stand Genomic Sci. 2016 Feb 27;11:19. eCollection (2016).

Sophie R. Ullrich, Anja Poehlein, Carolina González, Judith S. Tischler, Francisco Ossandon, Rolf Daniel, David S. Holmes, Michael Schlömann, Martin Mühling. Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus “Ferrovum”. PLoS One. 2016 Jan 25;11(1): e0146832. doi: 10.1371

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