Kenneth H. Wolfe

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Ken Wolfe

FRS MRIA
Kenneth Wolfe Royal Society.jpg
Ken Wolfe at the Royal Society admissions day in London, July 2017
Born
Kenneth Henry Wolfe
Alma mater Trinity College Dublin (BA, PhD)
Awards EMBO Member (2010) [1]
Scientific career
Fields Comparative genomics
Yeast genetics
Bioinformatics [2]
Institutions University College Dublin
Trinity College Dublin
Indiana University Bloomington [3]
Thesis Rates of nucleotide substitution in higher plants and mammals  (1990)
Doctoral advisor Paul M. Sharp [4] [5] [6]
Other academic advisors Jeffrey D. Palmer [7]
Doctoral students
Website wolfe.ucd.ie

Kenneth Henry Wolfe FRS MRIA [11] [12] is an Irish geneticist and professor of genomic evolution at University College Dublin (UCD), Ireland. [13] [11] [14]

Contents

Education

Wolfe was educated at Trinity College Dublin, where he was awarded Bachelor of Arts degree in genetics in 1986 [3] followed by a PhD in 1990 [6] for research investigating synonymous substitution in vascular plants and mammals supervised by Paul M. Sharp. [4] [5] [6] [15]

Research and career

Wolfe's research focuses on comparative genomics, yeast genetics and bioinformatics. [2] [16] [17] Work in his laboratory investigates the evolution of eukaryotic genomes and chromosome organisation. [12] He is best known for his discovery that the genome of the yeast Saccharomyces cerevisiae underwent complete genome duplication about 100 million years ago, [18] an event that is now known to be the result of hybridization between two divergent species. [12] This finding reshaped our understanding both of yeast biology, and of mechanisms of genome evolution in eukaryotes. [12] His subsequent discoveries of similar ancient genome duplications (paleopolyploidy) [19] during human evolution, and in almost all families of flowering plants, led to the realisation that whole-genome duplication is widespread. [12] His group also studies the origin and evolution of mating systems in yeasts, and the process of mating-type switching in which one cell type can change into another by moving or replacing a section of chromosome. [12]

Wolfe was a postdoctoral researcher with Jeffrey D. Palmer [7] at Indiana University Bloomington before returning to Ireland in 1992 to establish his research group in the genetics department of Trinity College Dublin, [20] [3] where he remained for over 20 years. In 2013, he moved to University College Dublin's UCD School of Medicine and Conway Institute. [21] As of 2017 his most highly cited peer reviewed papers [2] [14] [16] have been published in leading scientific journals including Nature , [18] [22] PNAS , [23] The Plant Cell , [19] [24] Genome Research [25] and Nature Reviews Genetics . [7]

Former doctoral students from the Wolfe lab include Mario A. Fares, [4] Aoife McLysaght, [4] [8] [9] Estelle Proux-Wéra [4] and Cathal Seoighe. [5] [10]

Awards and honours

Wolfe was elected a Fellow of the Royal Society (FRS) in 2017, [12] a member of the Royal Irish Academy (MRIA) in 2000 [11] and a member of the European Molecular Biology Organization (EMBO) in 2010. [1] In 2011 he served as president of the Society for Molecular Biology and Evolution (smbe.org). [26]

Related Research Articles

Heterochromatin is a tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a role in the expression of genes. Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed; however, according to Volpe et al. (2002), and many other papers since, much of this DNA is in fact transcribed, but it is continuously turned over via RNA-induced transcriptional silencing (RITS). Recent studies with electron microscopy and OsO4 staining reveal that the dense packing is not due to the chromatin.

<span class="mw-page-title-main">Polyploidy</span> Condition where cells of an organism have more than two paired sets of chromosomes

Polyploidy is a condition in which the cells of an organism have more than one pair of (homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two complete sets of chromosomes, one from each of two parents; each set contains the same number of chromosomes, and the chromosomes are joined in pairs of homologous chromosomes. However, some organisms are polyploid. Polyploidy is especially common in plants. Most eukaryotes have diploid somatic cells, but produce haploid gametes by meiosis. A monoploid has only one set of chromosomes, and the term is usually only applied to cells or organisms that are normally diploid. Males of bees and other Hymenoptera, for example, are monoploid. Unlike animals, plants and multicellular algae have life cycles with two alternating multicellular generations. The gametophyte generation is haploid, and produces gametes by mitosis; the sporophyte generation is diploid and produces spores by meiosis.

<i>Saccharomyces cerevisiae</i> Species of yeast

Saccharomyces cerevisiae is a species of yeast. The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been originally isolated from the skin of grapes. It is one of the most intensively studied eukaryotic model organisms in molecular and cell biology, much like Escherichia coli as the model bacterium. It is the microorganism behind the most common type of fermentation. S. cerevisiae cells are round to ovoid, 5–10 μm in diameter. It reproduces by budding.

<i>Schizosaccharomyces pombe</i> Species of yeast

Schizosaccharomyces pombe, also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length. Its genome, which is approximately 14.1 million base pairs, is estimated to contain 4,970 protein-coding genes and at least 450 non-coding RNAs.

Gene duplication is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.

<span class="mw-page-title-main">Paleopolyploidy</span> State of having undergone whole genome duplication in deep evolutionary time

Paleopolyploidy is the result of genome duplications which occurred at least several million years ago (MYA). Such an event could either double the genome of a single species (autopolyploidy) or combine those of two species (allopolyploidy). Because of functional redundancy, genes are rapidly silenced or lost from the duplicated genomes. Most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are currently considered diploids, e.g., baker's yeast, Arabidopsis thaliana, and perhaps humans.

petite (ρ–) is a mutant first discovered in the yeast Saccharomyces cerevisiae. Due to the defect in the respiratory chain, 'petite' yeast are unable to grow on media containing only non-fermentable carbon sources and form small colonies when grown in the presence of fermentable carbon sources. The petite phenotype can be caused by the absence of, or mutations in, mitochondrial DNA, or by mutations in nuclear-encoded genes involved in oxidative phosphorylation. A neutral petite produces all wild type progeny when crossed with wild type.

<i>Hortaea werneckii</i> Species of fungus

Hortaea werneckii is a species of yeast in the family Teratosphaeriaceae. It is a black yeast that is investigated for its remarkable halotolerance. While the addition of salt to the medium is not required for its cultivation, H. werneckii can grow in close to saturated NaCl solutions. To emphasize this unusually wide adaptability, and to distinguish H. werneckii from other halotolerant fungi, which have lower maximum salinity limits, some authors describe H. werneckii as "extremely halotolerant".

Saccharomyces paradoxus is a wild yeast and the closest known species to the baker's yeast Saccharomyces cerevisiae. It is used in population genomics and phylogenetic studies to compare its wild characteristics to laboratory yeasts.

<span class="mw-page-title-main">Genome evolution</span> Process by which a genome changes in structure or size over time

Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics. Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes, both prokaryotic and eukaryotic, available to the scientific community and the public at large.

<span class="mw-page-title-main">Laurence Hurst</span>

Laurence Daniel Hurst is a Professor of Evolutionary Genetics in the Department of Biology and Biochemistry at the University of Bath and the director of the Milner Centre for Evolution.

Saccharomyces eubayanus, a cryotolerant type of yeast, is most likely the parent of the lager brewing yeast, Saccharomyces pastorianus.

Saccharomyces kudriavzevii, is a species of yeast in the Saccharomyces sensu stricto complex. Its type strain is NCYC 2889T. It is used in production of alcoholic beverages, including pinot noir wine, and hybrids of it are used in beer brewing. It is isolated widely from the bark of oak trees.

Aerobic fermentation or aerobic glycolysis is a metabolic process by which cells metabolize sugars via fermentation in the presence of oxygen and occurs through the repression of normal respiratory metabolism. Preference of aerobic fermentation over aerobic respiration is referred to as the Crabtree effect in yeast, and is part of the Warburg effect in tumor cells. While aerobic fermentation does not produce adenosine triphosphate (ATP) in high yield, it allows proliferating cells to convert nutrients such as glucose and glutamine more efficiently into biomass by avoiding unnecessary catabolic oxidation of such nutrients into carbon dioxide, preserving carbon-carbon bonds and promoting anabolism.

Paul Martin Sharp is Professor of Genetics at the University of Edinburgh, where he holds the Alan Robertson chair of genetics in the Institute of Evolutionary Biology.

Duncan Odom is a research group leader at the German Cancer Research Center (DKFZ) in Heidelberg, and the Cancer Research UK Cambridge Institute at the University of Cambridge. Previously he was as an associate faculty member at the Wellcome Trust Sanger Institute from 2011 to 2018.

<span class="mw-page-title-main">Aoife McLysaght</span> Irish geneticist and professor

Aoife McLysaght is an Irish geneticist and a professor in the Molecular Evolution Laboratory of the Smurfit Institute of Genetics, Trinity College Dublin in Ireland.

<span class="mw-page-title-main">Joseph Heitman</span>

Joseph Heitman is an American physician-scientist focused on research in genetics, microbiology, and infectious diseases. He is the James B. Duke Professor and Chair of the Department of Molecular Genetics and Microbiology at Duke University School of Medicine.

<span class="mw-page-title-main">Bernard Dujon</span> French geneticist

Bernard Dujon is a French geneticist, born on August 8, 1947, in Meudon (Hauts-de-Seine). He is Professor Emeritus at Sorbonne University and the Institut Pasteur since 2015. He is a member of the French Academy of sciences.

References

  1. 1 2 Anon (2010). "EMBO member: Kenneth H. Wolfe". people.embo.org. Heidelberg: European Molecular Biology Organization. Archived from the original on 31 January 2017.
  2. 1 2 3 Kenneth H. Wolfe publications indexed by Google Scholar OOjs UI icon edit-ltr-progressive.svg
  3. 1 2 3 Ken Wolfe's ORCID   0000-0003-4992-4979
  4. 1 2 3 4 5 6 7 8 Anon (2017). "Kenneth H. Wolfe academic genealogy". academictree.org. Archived from the original on 11 July 2017.
  5. 1 2 3 4 Kenneth H. Wolfe at the Mathematics Genealogy Project
  6. 1 2 3 Wolfe, Kenneth H. (1990). Rates of nucleotide substitution in higher plants and mammals (PhD thesis). Trinity College Dublin. OCLC   842511087. Copac   11666046.
  7. 1 2 3 Wolfe, Kenneth H. (2001). "Yesterday's polyploids and the mystery of diploidization". Nature Reviews Genetics. 2 (5): 333–341. doi:10.1038/35072009. ISSN   1471-0056. PMID   11331899. S2CID   20796914.(subscription required)
  8. 1 2 McLysaght, Aoife (2002). Evolution of vertebrate genome organisation (PDF) (PhD thesis). Trinity College Dublin. OCLC   842498402. Copac   11660313. Archived from the original (PDF) on 6 November 2017.
  9. 1 2 Wolfe, Ken (2017). "Wolfe lab alumni". wolfe.ucd.ie. Archived from the original on 11 July 2017.
  10. 1 2 Seoighe, Cathal (2000). Gene order evolution and genomic analysis of the model eukaryote, Saccharomyces cerevisiae, and other yeast species (PhD thesis). Trinity College Dublin. OCLC   842501444. Copac   11661350 ProQuest   301607379.
  11. 1 2 3 Anon (2000). "Kenneth H. Wolfe FTCD". ria.ie. Dublin: Royal Irish Academy. Archived from the original on 11 December 2017. Retrieved 14 July 2017.
  12. 1 2 3 4 5 6 7 Anon (2017). "Professor Kenneth Wolfe FRS". royalsociety.org. London: Royal Society. Archived from the original on 5 May 2017. One or more of the preceding sentences incorporates text from the royalsociety.org website where:
    "All text published under the heading 'Biography' on Fellow profile pages is available under Creative Commons Attribution 4.0 International License." -- "Royal Society Terms, conditions and policies". Archived from the original on 11 November 2016. Retrieved 9 March 2016.{{cite web}}: CS1 maint: bot: original URL status unknown (link)
  13. ↑ UCD Professor Kenneth Wolfe elected Fellow of the Royal Society on YouTube, University College Dublin
  14. 1 2 Kenneth H. Wolfe publications from Europe PubMed Central
  15. ↑ Sharp, Paul M.; Cowe, Elizabeth; Higgins, Desmond G.; Shields, Denis C.; Wolfe, Kenneth H.; Wright, Frank (1988). "Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity". Nucleic Acids Research . 16 (17): 8207–8211. doi:10.1093/nar/16.17.8207. ISSN   0305-1048. PMC   338553 . PMID   3138659.
  16. 1 2 Kenneth H. Wolfe publications indexed by the Scopus bibliographic database. (subscription required)
  17. ↑ Sherlock, Gavin; Schröder, Markus S.; Martinez de San Vicente, Kontxi; Prandini, Tâmara H. R.; Hammel, Stephen; Higgins, Desmond G.; Bagagli, Eduardo; Wolfe, Kenneth H.; Butler, Geraldine (2016). "Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species". PLOS Genetics . 12 (11): e1006404. doi: 10.1371/journal.pgen.1006404 . ISSN   1553-7404. PMC   5091853 . PMID   27806045. Open Access logo PLoS transparent.svg
  18. 1 2 Wolfe, Kenneth H.; Shields, Denis C. (1997). "Molecular evidence for an ancient duplication of the entire yeast genome". Nature. 387 (6634): 708–713. Bibcode:1997Natur.387..708W. doi: 10.1038/42711 . ISSN   0028-0836. PMID   9192896. S2CID   4307263.(subscription required)
  19. 1 2 Blanc, Guillaume; Wolfe, Kenneth H. (2004). "Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes". The Plant Cell. 16 (7): 1667–1678. doi:10.1105/tpc.021345. ISSN   1040-4651. PMC   514152 . PMID   15208399.
  20. ↑ "Trinity College Dublin Genetics Department". www.tcd.ie.
  21. ↑ "Ken Wolfe Profile". people.ucd.ie.
  22. ↑ Lander, E. S.; Linton, M.; Birren, B.; Nusbaum, C.; Zody, C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; Fitzhugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; Levine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J. P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A.; et al. (2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi: 10.1038/35057062 . hdl:2027.42/62798. ISSN   0028-0836. PMID   11237011.
  23. ↑ Wolfe, K. H.; Li, W. H.; Sharp, P. M. (1987). "Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs". Proceedings of the National Academy of Sciences . 84 (24): 9054–9058. Bibcode:1987PNAS...84.9054W. doi: 10.1073/pnas.84.24.9054 . ISSN   0027-8424. PMC   299690 . PMID   3480529.
  24. ↑ Blanc, Guillaume; Wolfe, Kenneth H. (2004). "Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution". The Plant Cell. 16 (7): 1679–1691. doi:10.1105/tpc.021410. ISSN   1040-4651. PMC   514153 . PMID   15208398.
  25. ↑ Blanc, G.; Hokamp, Karsten; Wolfe, Kenneth H. (2003). "A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome". Genome Research. 13 (2): 137–144. doi:10.1101/gr.751803. ISSN   1088-9051. PMC   420368 . PMID   12566392.
  26. ↑ Anon (2017). "SMBE Council members". smbe.org. Archived from the original on 10 October 2017. Retrieved 22 September 2017.
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