Tag Archives: Misc.

Community Ecologist faculty position at Sonoma State

Hat tip to Sharon Strauss for forwarding this:

Sonoma State University – Community Ecology
Review of Applications begins Dec 3 2017

The Department of Biology at Sonoma State University seeks to hire a highly motivated and productive scientist for a tenure-track Assistant Professor position in Community Ecology. The candidate must have a proven track record of publication in peer-reviewed journals and will be expected to develop and maintain an externally funded research program. We are interested in candidates that work in terrestrial (above ground and/or below ground) or marine systems. We are especially interested in candidates whose research program uses a range of techniques that include field approaches to examine community processes. We seek a dynamic teacher-scholar with a strong commitment to undergraduate and graduate education and the ability to attract and mentor students in our graduate program. Teaching responsibilities include introductory, upper-division, and graduate classes, and for this position may include ecology or marine ecology. The candidate will also have the opportunity to contribute to other courses, which could include an offering in their area of specialty. See full job announcement at our web site: http://web.sonoma.edu/aa/docs/poas/tt/poa_104478.pdf.

Sonoma State University is located in Sonoma County, which offers access to a wide range of environments for research, and is home to the Center for Environmental Inquiry, which manages Galbreath Wildlands Preserve (3,670 acres) and Fairfield Osborn Preserve (450 acres). In addition, the Department of Biology has greenhouse facilities that are used for both teaching and research.


ABGG Seminar: Rebecca Calisi Rodriguez, TODAY @ 12:10 in 1150 Hart Hall

This week’s Animal Behavior Graduate Group seminar:

Parental Care: From Genome to Phenome

…and then off to save the world!

Rebecca M. Calisi Rodríguez

Assistant Professor of Neurobiology, Physiology, and Behavior

University of California, Davis

Friday, November 3rd, 12:10 in 1150 Hart Hall
Coffee and cookies will be available

Important changes in behavior occur when we become parents. For animals that exhibit parental care, raising offspring successfully involves transitioning from aggressive and sexual behaviors to more caring and nurturing ones. But how do the brain and body pull off this great feat? In the first part of this seminar, Calisi will discuss her work in characterizing a neurohormone, gonadotropin inhibitory hormone (GnIH), over the course of parental care in both a bird and rodent model, demonstrating how results of these studies could change the way we study the neural control of parental care behavior. Then, she will touch upon how this work has inspired current investigations in her lab of how the genomic activity of tissues vital to reproduction – the hypothalamus in the brain, the pituitary, and the gonads – change over the parental care stage using the avian model of the common pigeon. In the second part of her talk, Calisi will shift gears to discuss another exciting area of research in her lab. This research focuses on using pigeons as biomonitors of dangerous, human-made contaminants, with the goal of identifying problem urban and rural areas and communities in need of resources and assistance.

10/27 – microBOOmes: UC Davis Genome Center Halloween Symposium on Microbiomes


Friday October 27, 2017

UC Davis Genome Center

Halloween Symposium on Microbiomes

GBSF 1005 and Lobby

Bring your pumpkins and costumes for prizes

Space will be provided for posters – please bring one and display

2017 GC Halloween Symposium-Flyer


8:30-8:55 Coffee and refreshments; Pumpkin and Poster set-up


8:55-9:00 Jonathan Eisen Opening Remarks


9:00-9:30 Dawn Sumner Ghostly landscapes where animals dare not tread: Phototrophic mats in ice-covered lakes, Antarctica
9:30-10:00 Christian Santos Medellin Tales from the underground: host-microbiome interactions across the soil-root continuum
10:00-10:30 Break


10:30-11:00 Angela Zivkovic Changes in Gut Microbiota Composition in Response to Eating a Mediterranean Diet vs. a Fast Food Diet


11:00-11:30 Philip Brooks Composition of gut microbiota affects C. jejuni-mediated inflammation and autoimmunity in murine models


11:30-1:00 Lunch and pumpkin voting & posters


1:00-2:00 Tanja Woyke – KEYNOTE TALK Targeting taxonomic ‘blind spots’ & functional traits via single-cell approaches


2:30-3:00 Ruihong Zhang Powerful Microbes and Biodigesters for Turning Waste into Energy


3:00-3:30 Eric Velazquez “Enterobacteriaceae underlie variation in susceptibility to infection.”


3:30-4:00 Matt Settles From amplicons to metagenomes, a Core facilities perspective of the biome


4:00-4:15 Closing remarks and announcements of winners



At U. Idaho: Assistant or Associate Professor of Arthropod Molecular Systematics

Assistant or Associate Professor of Arthropod Molecular Systematics

The Department of Entomology, Plant Pathology and Nematology at the University of Idaho, Moscow, Idaho is hiring a tenure‐track Assistant or Associate Professor of Arthropod Molecular Systematics. Rank is negotiable.

Position summary: Qualified candidates will use molecular systematics approaches to examine topics such as the impact of newly emerging arthropod pests within Idaho and the Pacific Northwest (PNW) and the effect of changing environments on species diversity. The work will further understanding of arthropods relevant to the population and economy of Idaho and the region. Responsibilities will include teaching undergraduate and graduate courses in the use of molecular techniques in systematics and taxonomy and supervision and development of the collections of the W. F. Barr Entomology Museum as a regional resource for education and research. The incumbent will also work with stakeholders across the state and the PNW.

Responsibilities: Develop an innovative, externally funded, internationally recognized program in molecular systematics. Potential research focus areas could include use of molecular phylogenetic techniques to study life history, evolution, biodiversity, invasion biology, or evolutionary relationships among arthropod groups. Familiarity with high‐ throughput sequencing, quantitative analysis of molecular data or other research methodologies relevant to the position is expected. Research may be directed at any group of arthropods important to the population and the economy of Idaho and

the PNW. Teaching duties would include undergraduate and graduate courses in Entomology that are appropriate to the expertise and interests of the new faculty member and that meet the needs of the department. Mentoring of undergraduate and graduate students and post‐doctoral scholars is expected. The new faculty member would also be expected to interact with stakeholder groups interested in arthropod systematics and biology. The incumbent will lead the W. F. Barr Entomology Museum to develop the collection as a resource for both educational and research needs. He/she would be expected to participate in Departmental, College and University governance and to be an active participant in professional scientific societies.

Minimum qualifications: A Ph.D. in Entomology or related discipline with emphasis on arthropod molecular systematics is required. Qualified candidates will have a strong record of scholarly achievement that includes high‐impact publications. Demonstrated excellence in written and oral communication skills and experience with entomological collections are expected. Desired qualifications include the ability to secure extramural funding, teaching experience at the undergraduate and/or graduate level,

demonstrated ability to mentor students and trainees and the ability to work cooperatively and effectively in a team environment with colleagues and stakeholders.

Closing date: 12/14/2017

Instructions to applicants: Along with your on‐line application, write a letter of application addressing your qualifications (for both the minimum and desired qualifications listed) and interests, including a clear description of your research and teaching philosophies. In addition, your application materials must include a CV and the names and contact information for at least three (3) professional references.

For information contact Dr. Ed Lewis, Chair Department of Entomology, Plant Pathology and Nematology (eelewis) or Dr. Nilsa A. Bosque‐Pérez, Chair Search Committee (nbosque)

SystematicsPosition Announcement.pdf

4th Annual #UCDavis Human Genomics Symposium


Office of Continuing Medical Education

4th Annual UC Davis
Human Genomics Symposium

Complimentary – Deadline, Friday, November 10
Link to Registration

November 17, 2017
Friday, 9:00am-4:00pm
Education Building, Lecture Hall 1222
4610 X Street, Sacramento, CA

Conference Flyer

Conference Webpage
Genomic Medicine Webpage
UC Davis Education Building Map


Mildred Cho, PhD Carrie Northover, PhD
Metaphors Matter
Mildred Cho, PhD

Associate Director
Center for Biomedical Ethics
Stanford University
Participant-powered Research
Carrie Northover, PhD
Director, Research Services

Katherine A. Rauen, MD, PhD

Chief, Genomic Medicine
UC Davis MIND Institute

John McPherson, PhD
Associate Director for Basic Sciences
UC Davis Comprehensive Cancer Center

University of California, Davis, Health is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.

University of California, Davis, Health designates this live activity for a maximum of 5 AMA PRA Category 1 Credits™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.

UC Davis Health, Office of Continuing Medical Education
4610 X Street #2301, Sacramento, CA 95817

#UCDavis Chancellor’s Postdoctoral Fellowship Program (CPFP)

The UC Davis Chancellor’s Postdoctoral Fellowship Program offers postdoctoral research fellowships and faculty mentoring to outstanding scholars in all fields whose research, teaching, and service will contribute to the diversity and equal opportunity at the University of California. These contributions may include public service addressing the needs of our increasingly diverse society, efforts to advance equitable access to higher education, or research focusing on underserved populations or understanding inequalities related to race, gender, disability or LGBT. The program is seeking applicants with the potential to bring to their academic careers the critical perspective that comes from their non-traditional educational background or understanding of the experiences of members of groups historically underrepresented in higher education.

The UC Davis Chancellor’s Postdoctoral Fellowship Program partners with sister programs sponsored by the UC Office of the President, the University of Michigan, and other UC campuses.

Visualize metagenomic data

Uzon picture

We are reaching out to hear from others what tools they are using to assign and visualize gene functions in environmental samples of microbial communities.


Our dataset is simple. We did a metagenomic analysis of two pools (samples/sites). First, we co-assembled the whole metagenome for each pool. Then, we used anvi’o to bin individual bacterial and archaeal genomes within the pools. These genomes (bins) were then fed into RAST. This online software gives you a table of known genes for each bin. At the moment we have an array of tables with known microbial genes for each pool that we would like to visualize/summarize in an aesthetically pleasing way. We tried to use summary statistics in MG-RAST, but the upload failed eight times in a row (including several attempts of uploading individual bins as fasta files, co-assembled metagenomes as fasta files, and sequence reads before assembly as fastq files). The upload failures were identified as cashing problems or internal errors.


We went back to using anvi’o using NCBI COG assignments, following their infant gut pangenome tutorial (http://merenlab.org/tutorials/infant-gut/) which in the end gives you a similar output to RAST in tabular format.


What software are people using out there to compare, assign and visualize gene functions across samples and across bins? Can these tabular outputs be used as inputs for any software producing visually pleasing figures?


(The foto is taken from http://www.airpano.com/360Degree-VirtualTour.php?3D=kamchatka-uzon)