1/25 at #UCDavis: Monica Borucki – Recovering Viral Population Diversity to Improve Biosurveillance and Predict Viral Emergence

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Dr. Monica Borucki


“Recovering Viral Population Diversity to Improve Biosurveillance and Predict Viral Emergence”

Wednesday, January 25, 2017

4:10 pm

1022 Life Sciences

Abstract: RNA viruses constantly evolve to optimize interactions with their hosts and potentially expand host range. Understanding the role of quasispecies in viral evolution is a necessary step toward optimizing detection of emergent viruses, developing effective countermeasures, and ultimately predicting the potential impact of emerging or novel viruses. Deep Illumina sequencing and computational analysis of viral quasispecies was used to define the role intra-host viral diversity plays in the adaptation of viruses to new host environments, with a focus on viral families of medical significance that exhibit the propensity for cross species transmission. Analysis of samples from a naturally occurring rabies host jump, and from in vitro and in vivo passage of a coronavirus and a paramyxovirus indicate that viral diversity plays a pivotal role in viral adaptation. In each case the genetic changes that characterized the emergent genotype were present as rare variants in the virus population prior to selection. These results suggest that recovering the full genetic diversity could improve biosurveillance by building a knowledge base of mutations that may play a role in viral emergence. Similarly, the presence of ancestral genotypes as rare members of the population may provide insights useful for forensic studies and outbreak investigation.

Dr. Borucki is a Biomedical Scientist in the Biosciences and Biotechnology Division of LLNL. Her research focuses on the mechanisms of viral evolution and emergence, biosurveillance, and viral forensics. Before coming to LLNL, she served as a Research Geneticist at USDA-ARS and adjunct faculty at Washington State University where she investigated the epidemiology and virulence of food pathogen, Listeria monocytogenes.

Borucki 1-25-17.doc

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Job Opening – Research Faculty Position, FSU Coastal & Marine laboratory

The Florida State University
Coastal and Marine Laboratory
Research Faculty Position Open: Marine Community Ecologist

The Florida State University Coastal and Marine Laboratory (FSUCML) (http:///www.marinelab.fsu.edu) invites applications for a Marine Community Ecologist research faculty position (12 month renewable appointment). We seek a highly motivated coastal ecologist with notable research achievements. The successful applicant will be expected to make a commitment to excellence in scholarship, student mentoring and outreach and have the ability to develop a well-funded, independent research program. Salary will be provided at 100% for the first two years and 75% from the 3rd year forward, with the expectation that the remaining 25% of salary will be met through external funding. A competitive start-up package will be offered. Applicants must have a Ph. D. degree with significant postdoctoral experience.

The Coastal and Marine Laboratory is committed to research focused on coastal and marine issues of ecological importance that provides the scientific basis for policy decisions. The primary area of interest is in experimental community ecology with a focus on local habitats. The FSUCML is embedded in an area of rich terrestrial and marine biodiversity with an abundance of complex and interconnected estuarine and marine habitats including tidal salt marshes and flats, seagrass meadows, oyster reefs, and hard-bottom reefs dominated by soft coral and sponge communities. It is expected that successful candidates would focus on ecological processes related to these local habitats and environments.

Applicants are asked to provide a single document in PDF format containing a letter of application, a curriculum vita, a two-page narrative describing their research interests and plans, and a brief graduate student mentoring statement. Applicants are encouraged to present their research in a way that is complementary to, and can form a basis for integrative collaboration with faculty at the FSUCML and on the FSU main campus.

Applications must be sent electronically to lhedwards. Applicants should also have three letters of recommendation sent tolhedwards. The closing date for applications is 15 February 2017 .

Florida State University is committed to the diversity of its faculty, staff, and students, and to sustaining a work and learning environment that is inclusive. Women, minorities, and people with disabilities are encouraged to apply. FSU is an Equal Opportunity/Access/Affirmative Action Employer.

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At #UCDavis tomorrow: Kyria Boundy-Mills “Discovery and Innovation at the Phaff Yeast Culture Collection”

Kyria Boundy-Mills, Ph.D.
Curator, Phaff Yeast Culture Collection

January 18, 2017
Time: 4:10-5PM
Location: Room 1022 LSA
Title: “Discovery and Innovation at the Phaff Yeast Culture Collection”

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Job Opening at Smithsonian Environmental Research Center – Marine Disease/Parasite Ecologist


The Smithsonian Environmental Research Center (SERC) is seeking a scholar with expertise in marine diseases (pathogens) and/or marine parasites to develop a new research program in marine disease ecology. The candidate will leverage the capabilities of existing SERC labs and bridge interests at SERC and throughout the Smithsonian Institution to better understand human drivers of coastal disease processes.

Deadline: January 31, 2017

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Ken Cadwell – “Transkingdom interactions in the gut” at #UCDavis 1/26

Friday, January 26th
Noon in GBSF 1005

“Transkingdom interactions in the gut”

Dr. Ken Cadwell from NYU.

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At #UCDavis today: Li Zhao – Evolution of de novo genes in Drosophila

CPB Seminar ReminderTuesday, January 17, 2017
1022 Life Sciences

Speaker: Li Zhao
Postdoctoral Scholar, Begun Lab, UC Davis
Title: Evolution of de novo genes in Drosophila
Host: David Begun

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1/23 Talk by Alberto Pepe (Authorea), Shields Library, 12-1:30

One week from today for

Alberto Pepe

Data-driven, Interactive Scientific Articles in a Collaborative Environment with Authorea

Monday, January 23rd, 12-1:30pm

Shields Library’s Data Science Initiative space on the 3rd floor

Most tools that scientists use for the preparation of scholarly manuscripts, such as Overleaf and ShareLaTex, function offline and do not account for the born-digital nature of research objects. Authorea allows scientists to collaboratively write rich data-driven manuscripts on the web that offers readers a dynamic, interactive experience with an article’s full text, images, interactive figures, data, and code. In this talk, I will show you how Authorea differs from Overleaf and ShareLatex and how we are bringing scientific writing into the 21st century. For a quick overview, here’s how we are different. Please bring your laptop as attendees will be included in the demo (not mandatory but suggested).

Alberto Pepe is the co-founder of Authorea. He recently finished a Postdoctorate in Astrophysics at Harvard University. During his postdoctorate, Alberto was also a fellow of the Berkman Center for Internet and Society and the Institute for Quantitative Social Science. Alberto is the author of 30 publications in the fields of Information Science, Data Science, Computational Social Science, and Astrophysics. He obtained his Ph.D. in Information Science from the University of California, Los Angeles with a dissertation on scientific collaboration networks which was awarded with the Best Dissertation Award by the American Society for Information Science and Technology (ASIS&T). Prior to starting his Ph.D., Alberto worked in the Information Technology Department of CERN, in Geneva, Switzerland, where he worked on data repository software and also promoted Open Access among particle physicists. Alberto holds a M.Sc. in Computer Science and a B.Sc. in Astrophysics, both from University College London, U.K. Alberto was born and raised in the wine-making town of Manduria, in Puglia.

Sponsored by Innovating Communication in Scholarship

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At #ucdavis 1/12: Judie Bronstein “Mutualism: What Do We Know, and Where Do We Go From Here?”

Tomorrow’s Ecology and Evolution speaker will

be Judie Bronstein from University of Arizona.

Title: Mutualism: What Do We Know, and Where Do We Go From Here?
Room: 100 Hunt Hall
Date and Time: 4:10pm on Thursday January 12th

According to her webpage
"We study all things mutualistic. Projects in the lab focus on
ecological, evolutionary, and behavioral questions about mutualism.
We’re particularly interested in coevolutionary dynamics, community
organization, context dependency, climate change effects, and the
continuum from cooperation to conflict. We are linked more by a common
conceptual context rather than any single type of interaction or group
of organisms."

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UC Conservation Genomics: CALeDNA Program

Of possible interest:

Dear UC Conservation Genomics Consortium investigators, members, and friends,

We are excited to share the news that our citizen science program, CALeDNA, has officially launched! Now, we need your help to make it visible.

I am attaching a press release statement. But here is the short version for you.

We have made a website that educates the public about the value of biodiversity monitoring and the technique we are using, non-invasive environmental DNA sequencing. It trains them on how to collect samples for us. A volunteer does the training on the website and downloads our app. We send them a kit and a map of places to go based on their interests of places to hike to when they register with us. We need 1000 volunteer citizen scientists to collect 18,000 samples across the state during 2017. We have several bioblitz events planned, some with iNaturalist, and some across the 39 UC natural reserves, national and state parks, and private preserves. By the end of the year we will have sampled across much of the state during both the dry and the rainy season. We will sequence and analyze the samples, producing publications and policy recommendations, engaging stakeholders of various kinds and promoting the technology and optimized analysis approach.

Any undergraduate course, nature club, or friends who like to get outdoors can participate. In some cases, we can even help pay for the gas to drive to a reserve. We need your help to recruit citizen scientists and engage them in our program. We have a bioblitz at Pillar Point the weekend of Feb 9-11 that we need volunteers to join for. Then throughout April and May we need people to visit the fascinating UC Reserves. We’ll handle the paperwork to register with them.

If you are teaching courses this quarter and would be willing to share a promotional slide at the start of your class, or willing to incorporate fieldwork with us as part of your class, let me know and I’m more than happy to work with you. We would also appreciate recommendations on places to advertise the CALeDNA program. Finally, please share this with your colleagues and labs–perhaps they will want to participate too!

Thank you for being part of this Consortium and for learning about our new CALeDNA launch. Wishing you a great New Year!

With warm regards,



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Job: Senior Research Associate in metagenomics and next-gen sequencing

Posting this for colleagues at Phylagen.

For full disclosure – I am a consultant for Phylagen.


Senior Research Associate
Phylagen, Inc. http://phylagen.com
San Francisco, CA
Position Description
Phylagen is an early stage biotech company developing microbiome analytics and data generation approaches with applications to a diverse set of industries and brands.
We are bringing on an innovative lab scientist – ideally with a M.S or Ph.D. in biology, molecular biology, microbiology, biochemistry, or related field (translating to 4-5 years lab experience). We want someone deeply knowledgeable in microbiome sample handling, high-throughput sequencing library preparation,  and next-generation sequencing platforms.
The position will entail processing samples from different environments, developing and optimizing protocols for amplicon and shotgun metagenomic libraries, and translating processes to automated and high-throughput pipelines for the generation of high-quality sequence data. Expertise in sequencing platform tuning or laboratory automation is a bonus.
We are looking someone who is flexible – a fast learner with relevant experience that will allow them to contribute quickly. We offer a competitive salary, equity, and benefits package. You will be a key player in a cutting edge, rapidly growing venture-backed microbiome startup.
Apply on LinkedIn (https://goo.gl/DPNph1) or send CV to jobs@phylagen.com.
Company Description
Phylagen is an early stage biotech startup focused on building game-changing microbiome science and technology with applications across a diverse set of industries and brands. We are harnessing the unseen world of microbes to improve our daily lives by combining advanced DNA sequencing and big data analytics to analyze the microbiome in ways previously not possible. This enables us to solve diverse problems across health care, food processing, transportation, and other industries.
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