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)

At #UCDavis today: Rich Corsi Living in a Material World: Why the Surfaces that Surround You Affect What You Breathe

Living in a Material World:

Why the Surfaces that Surround You Affect What You Breathe

Richard L. Corsi, Ph.D., The University of Texas at Austin

Environmental & Water Resources Fall Seminar Series

Tuesday, October 3, 12:10 pm, 3102b Ghausi Hall

From infancy to twilight years, the air that we breathe and surfaces that we touch inside buildings have a substantial impact on our lifetime exposure to air pollution, including pollution of outdoor origin. As such, there is value in understanding the processes that affect the sources and fate of air pollutants indoors, with a goal of manipulating these processes to improve the air that we breathe.

An important feature of indoor atmospheres is the relatively large ratio of surface area to volume of air, particularly in comparison to the same ratio for the outdoor atmosphere. From building materials to architectural coatings, flooring to furniture, and HVAC system components to human occupants, indoor surfaces vary considerably from one another and within and between buildings. These surfaces are sources of air pollutants and reservoirs (sinks) onto and into which pollutants adsorb, absorb and persist. They contain reaction sites that permanently remove pollutants while forming others. They also allow for direct contaminant transfer following physical contact. Importantly, indoor materials and their surfaces are dynamic, with changes that occur over time scales of minutes to decades and that can dramatically influence surface interactions with pollutants in indoor air.

This presentation will begin with a discussion of the importance of indoor air quality, including the broader impacts associated with its improvement and the intellectual merit of its continued study. The importance of indoor materials and their impacts on indoor air quality will be explored using several examples from past and ongoing research that reflect different interfacial phenomena and influencing factors. The potential for smart use of materials for improvement of indoor air quality will also be discussed as a rich topic for future research.

There are materials around you that are affecting the amount and nature of pollutants that you are inhaling as you read this abstract. Get to know them.

Richard L. Corsi is a proud graduate of the Department of Civil and Environmental Engineering at UC Davis (MS 1985, PhD 1989). He is a Distinguished Engineering Alumni Medal recipient of the College of Engineering at UC Davis (2016) and was named a Distinguished Alumnus of Humboldt State University in 2006. Dr. Corsi is past Chair of the Department of Civil, Architectural and Environmental Engineering at the University of Texas at Austin and currently holds the Joe J. King Chair in Engineering. His research focuses on sources, fate, human exposure and innovative control strategies related to indoor air quality. In recent years his team has focused significantly on ozone-initiated chemistry and indoor air quality. He serves as Vice-President of the Academy of Fellows of the International Society of Indoor Air Quality and Climate. In 2015, Dr. Corsi was inducted into the University of Texas Academy of Distinguished Teachers (top 5%), and in 2016 he received a Regents Outstanding Teaching Award from the University of Texas System.

Richard Harris of NPR at #UCDavis 10/25 “Common Errors that Bedevil Biomedical Research and How to Fix Them,”

Got this and am following the instructions:


We are pleased to announce that Dr. Richard Harris, Distinguished Science Writer- NPR Correspondent on Science, Medicine, and the Environment, will be presenting the Storer Lectureship in Life Sciences Series, “Common Errors that Bedevil Biomedical Research and How to Fix Them,” at 4:10 p.m. on Wednesday, October 25, 2017 in the Student Community Center, Multipurpose Room. Please see the attached flyer for additional information. Richard will be signing his book, “Rigor Mortis- How Sloppy Science creates Worthless Cures, Crushes Hope and Wastes Billions, ” immediately after the lecture.

Richard Harris_flyer fnl.pdf

Call for applications: UC President’s Postdoctoral Fellowship Program

Attached is the 2018-19 Call for Applications for the UC President’s Postdoctoral Fellowship Program awards.

Please feel free to forward the attached call for applications to your professional networks that include:

Graduate students;

PhD candidates;

Postdoctoral appointees;

Department/Division chairs; and

Campus Diversity Officers.

The application deadline is November 1, 2017.

University of California



THE PROGRAM. The University of California President’s Postdoctoral Fellowship Program was established in 1984 to encourage outstanding women and minority Ph.D. recipients to pursue academic careers at the University of California. The current 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. The contributions to diversity may include public service towards increasing equitable access in fields where women and minorities are underrepresented. In some fields, the contributions may include 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 and research 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 in the United States.

AWARDS AND APPOINTMENTS. Fellowships are awarded for research conducted at any one of the University of California’s ten campuses.

The award includes a salary starting at approximately $48,200 depending on field and experience, benefits including health insurance and paid vacation/sick leave, and up to $5,000 for research‐related and program travel expenses. Each award is for a minimum of 12‐months and may be renewable for an additional term upon demonstration of academic/research productivity.

ELIGIBILITY. Applicants must receive a Ph.D. from an accredited university before the start of their fellowship. Successful applicants must present documents demonstrating that they are legally authorized to work in the United States. Individuals granted deferred action status under the Deferred Action for Childhood Arrivals program are encouraged to apply.

Apply online at: ppfp.ucop.edu

DEADLINE: November 1, 2017


Los Angeles
San Diego
San Francisco
Santa Barbara
Santa Cruz

More information:
President’s Postdoctoral Fellowship Program University of California visit online: ppfp.ucop.edu/info/
email: ppfpinfo

University Partnerships for Faculty Diversity

Partner Programs with University of Minnesota, Carnegie Mellon University, University of Colorado, Boulder, University of Maryland, University of Michigan, The California Alliance, UC Chancellor’s Postdoctoral Fellowship Programs, and the UC‐affiliated National Labs.
Please visit: http://ppfp.ucop.edu/info/about-ppfp/partnerships.html

2018-19 Call for Applications.pdf