Tag Archives: coccidioides

Job: Environmental Microbiology – UC Riverside

UC Riverside faculty position in Environmental Microbiology part of Hiring Cluster BREATHE: Environ./Medical Microbiology, Environ./Medical History, Pulmonary Physiology, Pulmonary/Mucosal Immunol

Job #JPF00639 School of Medicine – Biomedical Sciences

Environmental Microbiology – experience working in natural systems, and in soil and/or air microbial ecology. A range of expertise between bacterial, archaeal, and fungal organisms, is preferred, including aeromicrobiology, and organisms with airborne spores (e.g., Coccidioides, Aspergilli, Pseudomonas, Clostridium, etc.). In addition, the environmental microbiologist should have experience working with plant-microbe interactions relevant to invasive plants.


Note the Deadline for application is being moved to January 15, 2017.


The University of California at Riverside (UCR) is implementing a major expansion of our faculty and investing in state-of-the-art research facilities to support their work. This expansion will build critical mass in 34 vital and emerging fields of scholarship, foster truly cross-disciplinary work, and further diversify the faculty at one of America’s most diverse research universities. We encourage applications from scholars committed to excellence and seeking to help define the research university for the next generation. For more information about our hiring initiative or to submit an application, please visit clusterhiring.ucr.edu or academicpersonnel.ucr.edu.

This announcement aims to fill up to five positions to help establish and build the BREATHE research group (Bridging Regional Ecology and Aerosolized Toxins to understand Health Effects) in interdisciplinary areas bringing together research in air quality, pulmonary biology and health, and public policy. Growth in research areas associated with this cluster will complement the impending move of the California Air Resources Board (CARB) to the UCR campus. The placement of each successful candidate may be in departments in the College of Natural and Agricultural Sciences (CNAS) such as Plant Pathology and Microbiology, Environmental Sciences, and Biology; the School of Medicine (SOM) including the Division of Biomedical Sciences and Division of Clinical Sciences; the Bourns College of Engineering (BCOE) such as Chemical and Environmental Engineering; the School of Public Policy; and the College of Humanities and Social Sciences (CHASS), such as History, depending on the preferences of the candidate and interested host departments. Candidates are expected to develop an internationally recognized and externally funded research program in one or more areas related to air quality, lung function and health, and policy, as well as demonstrate an interest in building and working with interdisciplinary research teams. All candidates must have a PhD, MD, or MD/PhD in a relevant field and be strongly committed to both undergraduate and graduate teaching. Preference will be given to applicants whose research interests complement those of existing faculty in the School of Medicine, College of Engineering Center for Environmental Research and Technology (CE-CERT), School of Public Policy, and the Center for Conservation Biology, and strengthen our initiative to develop an extramurally funded research center in air quality, health, and policy. Successful candidates must also have clear potential or demonstrated ability to work successfully with and benefit a diverse student body.

The next four positions to be filled in the BREATHE cluster will be in the areas of (1) Environmental Microbiology, (2) Environmental or Medical History, (3) Mammalian Pulmonary physiology, and (4) Pulmonary or mucosal immunology at the Assistant Professor level. The successful candidates will have the ability to teach coursework and have expertise in the relevant areas. In addition, they will play a central role in helping assemble the cohort of affiliated researchers across the campus. This announcement solicits applications for these positions; applicants must indicate which of the four positions they are applying to:

  1. Environmental Microbiology – experience working in natural systems, and in soil and/or air microbial ecology. A range of expertise between bacterial, archaeal, and fungal organisms, is preferred, including aeromicrobiology, and organisms with airborne spores (e.g., Coccidioides, Aspergilli, Pseudomonas, Clostridium, etc.). In addition, the environmental microbiologist should have experience working with plant-microbe interactions relevant to invasive plants.
  2. Environmental or Medical History – history of science, medicine, and/or the environment, with preference for individuals interested in the connections among environment and health, and public policy, employing a mix of disciplinary approaches from such fields as environmental history, history of medicine, history of science, medical geography or historical geography.
  3. Mammalian pulmonary physiology – research focus can be on, but is not limited to, lung physiology, including comparative, ecological or evolutionary approaches, exercise physiology, as well as clinical topics such as infectious lung diseases, lung microbiome, chronic lung disease, asthma, or related diseases.
  4. Pulmonary or mucosal immunology – pulmonary inflammation or immunity, lung microbiome, chronic lung disease, asthma, or related diseases, with priority on research that also assesses the impact of inhaled particulates and pollutants, as well as other environmental, cultural or related factors.

The University of California is an Equal Opportunity / Affirmative Action Employer with a strong institutional commitment to the achievement of excellence and diversity among its faculty and staff. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability, protected veteran status, or any other characteristic protected by law.

UCR is a world-class research university with an exceptionally diverse undergraduate student body. Its mission is explicitly linked to providing routes to educational success for underrepresented and first-generation college students. A commitment to this mission is a preferred qualification.

Advancement through the faculty ranks at the University of California is through a series of structured, merit-based evaluations, occurring every 2-3 years, each of which includes substantial peer input.

To apply: Please send a full curriculum vitae, indication of the specific position applied for, a description of proposed research, teaching philosophy and letters from three professional references. A statement addressing potential contribution to academic diversity must be included. Application materials for the Assistant Professor position should be submitted through http://aprecruit.ucr.edu/apply/JP00639. Applications will be reviewed beginning November 14, 2016. Positions will remain open until filled. Anticipated start date is July 1, 2017. Salary is commensurate with education and experience.

A cacophony of comparative genomics papers

A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation sequencing will enable and can start to imagine what happens when even cheaper 3rd generation sequencing technologies are applied. I’m behind in reviewing these papers for you, dear reader, but I hope you’ll click through and take a look at some of these papers if you are interested in the topics.

In the following set of papers we have some nice examples of comparative genomics of closely related species and among a clade of species. The papers mentioned below include our work on the human pathogens Coccidioides and Histoplasma (Sharpton et al) studied at several evolutionary distances, a study on Saccharomycetaceae (Souciet et al) clade of yeast species, and a comparison of two species of Candida (Jackson et al): the commensal and opportunistic fungal pathogen Candida albicans with a very closely related species Candida dubliensis.  There is also a nice comparison of strains of Saccharomyces cerevisiae looking at effects of domestication and examples of horizontal transfer.

There is also a report of de novo sequencing of a filamentous fungus using several approaches, traditional Sanger sequencing, 454, and Illumina/Solexa (DiGuistini et al).

Finally, a paper from a few months ago (Ma et al), gives a fantastic look at one of the early branches in the fungal tree – the Mucorales (formerly Zygomycota) – via the genome of Rhizopus oryzae.  This paper is a really excellent example of what we can learn about a group of species by contrasting genomic features in the early branches in the tree with the more well studied Ascomycete and Basidiomycete fungi.  More genome sequences will help us build on these findings and clarify if some of the observations are unique to the lineage or universal aspects of the earliest fungi.

I hope you enjoy!

Novo, M., Bigey, F., Beyne, E., Galeote, V., Gavory, F., Mallet, S., Cambon, B., Legras, J., Wincker, P., Casaregola, S., & Dequin, S. (2009). Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118 Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0904673106 (via J Heitman)

Jackson, A., Gamble, J., Yeomans, T., Moran, G., Saunders, D., Harris, D., Aslett, M., Barrell, J., Butler, G., Citiulo, F., Coleman, D., de Groot, P., Goodwin, T., Quail, M., McQuillan, J., Munro, C., Pain, A., Poulter, R., Rajandream, M., Renauld, H., Spiering, M., Tivey, A., Gow, N., Barrell, B., Sullivan, D., & Berriman, M. (2009). Comparative genomics of the fungal pathogens Candida dubliniensis and C. albicans Genome Research DOI: 10.1101/gr.097501.109

DiGuistini, S., Liao, N., Platt, D., Robertson, G., Seidel, M., Chan, S., Docking, T., Birol, I., Holt, R., Hirst, M., Mardis, E., Marra, M., Hamelin, R., Bohlmann, J., Breuil, C., & Jones, S. (2009). De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biology, 10 (9) DOI: 10.1186/gb-2009-10-9-r94 (open access)

Sharpton, T., Stajich, J., Rounsley, S., Gardner, M., Wortman, J., Jordar, V., Maiti, R., Kodira, C., Neafsey, D., Zeng, Q., Hung, C., McMahan, C., Muszewska, A., Grynberg, M., Mandel, M., Kellner, E., Barker, B., Galgiani, J., Orbach, M., Kirkland, T., Cole, G., Henn, M., Birren, B., & Taylor, J. (2009). Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives Genome Research DOI: 10.1101/gr.087551.108 (open access)

Souciet, J., Dujon, B., Gaillardin, C., Johnston, M., Baret, P., Cliften, P., Sherman, D., Weissenbach, J., Westhof, E., Wincker, P., Jubin, C., Poulain, J., Barbe, V., Segurens, B., Artiguenave, F., Anthouard, V., Vacherie, B., Val, M., Fulton, R., Minx, P., Wilson, R., Durrens, P., Jean, G., Marck, C., Martin, T., Nikolski, M., Rolland, T., Seret, M., Casaregola, S., Despons, L., Fairhead, C., Fischer, G., Lafontaine, I., Leh, V., Lemaire, M., de Montigny, J., Neuveglise, C., Thierry, A., Blanc-Lenfle, I., Bleykasten, C., Diffels, J., Fritsch, E., Frangeul, L., Goeffon, A., Jauniaux, N., Kachouri-Lafond, R., Payen, C., Potier, S., Pribylova, L., Ozanne, C., Richard, G., Sacerdot, C., Straub, M., & Talla, E. (2009). Comparative genomics of protoploid Saccharomycetaceae Genome Research DOI: 10.1101/gr.091546.109 (open access)

Ma, L., Ibrahim, A., Skory, C., Grabherr, M., Burger, G., Butler, M., Elias, M., Idnurm, A., Lang, B., Sone, T., Abe, A., Calvo, S., Corrochano, L., Engels, R., Fu, J., Hansberg, W., Kim, J., Kodira, C., Koehrsen, M., Liu, B., Miranda-Saavedra, D., O’Leary, S., Ortiz-Castellanos, L., Poulter, R., Rodriguez-Romero, J., Ruiz-Herrera, J., Shen, Y., Zeng, Q., Galagan, J., Birren, B., Cuomo, C., & Wickes, B. (2009). Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication PLoS Genetics, 5 (7) DOI: 10.1371/journal.pgen.1000549 (open access)

Dermatophyte genome sequences

The first of several dermatophyte fungal genomes, Microsporum gypseum, has been released at the Broad’s Dermatophyte site.  Two Tricophyton species and another Microsporum genome should follow soon. These dermatophyte fungi are Onygenales (Ascomycota) fungi (like Coccidioides and Histoplasma), although their placement in the phylogenies shown in the whitepaper and related review paper is a bit ambiguous. I’m sure that can be improved with a few more gene sequences gleaned from the genomes.

The 23 Mb M. gypseum genome is a bit smaller than the sizes of C. immitis (28 Mb), H. capsulatum (32 Mb), or Paracoccidioides brasiliensis (29 Mb).  While no annotation is currently available for the M. gypseum genome, this genome will help in establishing what genes were ancestral in the Onygenales and comparing patterns of gene family gains and losses in fungi that specialize on animal hosts.

Some more comparison across different kinds of dermatophyte fungi that are very distantly related like dandruff causing fungus Malasezzia globosa (Basidiomycota) will be really interesting as well.

Thanks Joe H and FGI folks for passing along announcement and to the Broad/FGI folks for the work to make this sequence available.

Coccidioides in the news

The NY Times has an article on the high rate of Coccidioides incidence at the state prison in Pleasant Valley, California. The infection rate has been documented by Pappagianis et al in an in-depth study of Coccidioidomycosis in the California state prisons. The disease has stalled some plans for constructing a new prison the edge of the San Joaquin Valley so the state is definitely taking note.

Cocci map
Also see Figure here with prettier links.

Thanks Liz!

More Cocci genomes

The Broad Institute has made available additional genomes of strains of Coccidioides immitis and C. posadasii. There are now genome sequences for 4 strains of C. immitis sequenced and 3 strains of C. posadasii including the C735 strain from the JCVI/TIGR. including the reference strain RS that is assembled into 7 supercontigs (there are probably 5 chromosomes) and annotated with ~10,000 genes. However we think at least ~1-2k of the annotated genes in strain RS are likely reptitive sequences and not real genes based on comparisons with the TIGR annotations of C. posadasii C735 strain and de novo repeat finding and analysis – John talked about this in his talk at Asilomar.

Thse available strain sequences are going to allow for some interesting analyses that have yet to be applied in fungi. This includes doing some whole genome scans for selection using more sensitive population genetic tests than the gross-level non-synonymous /synonymous ratio tests that we’ve been relegated to with the current comparisons and it is starting to feel a bit like when “all you have is a hammer…”. Now all we have to do is get the whole genome multi-strain alignment quirks worked out and probably have to do our own quick annotation since only the two reference strains are annotated.

Cocci arthrocondia