Stephen (Fringy) Richards will be giving a talk at UC Davis on June 4
“Genomic Innovation within the Phylum Arthropoda” June 4th at 4:00 PM in GBSF 4202 (see attached flyer).
Fringy is currently an Associate Professor at the Baylor College of Medicine, Human Genome Sequencing Center.
MIC 291: Selected Topics in Microbiology
Dr. Seemay Chou
(UCSF School of Medicine, Biochemistry & Biophysics)
“From bacteria to ticks: lessons in antimicrobial defense"
Wednesday, May 30, 2018
1022 Life Sciences
This week’s Ecology and Evolution Seminar series will be given by Rahel Sollmann, from the WFCB department here at UC Davis. For more about Rahel’s research, click here.
Her talk, titled: "Spatial capture-recapture: a flexible framework to study wildlife populations" will be tomorrow, Thursday, May 31 at 4:10 pm in Everson Hall.
Lecturer Positions in General Biology – BIO 1B
Department of Integrative Biology
University of California, Berkeley
The Department of Integrative Biology at UC Berkeley is generating an applicant pool of qualified temporary full or part-time lecturers to teach the General Biology laboratory class, BIO 1B (http://ib.berkeley.edu/courses/bio1b/), should the need arise. The pool will remain in place for one calendar year; those interested in remaining in the pool after the year must reapply. Appointments may be renewable based on need, funding, and performance. Positions range from 50% – 100%, depending on the number of sections taught. Vacancies may arise during Fall, Spring, or Summer.
The laboratory class currently covers three major sections: Evolution, Ecology, and Organismal Diversity. Exercises include investigations into population genetics, phylogenetic relationships, macroevolution, predator/prey interactions, competition, bioindicators, and structure and function of organisms. BIO 1B is a gateway course to the major field of Integrative Biology that consists of three one-hour lectures and one four-hour combined discussion and lab each week. The class has 48 sections with a maximum of 18 students in each section. Lecturers will be required to lead one discussion and lab per week, create quizzes, grade assignments, attend a Friday instructional meeting, be familiar with lecture, proctor exams, hold office hours and complete other instructional duties as assigned. Senior lecturers mentor new hires and Graduate Student Instructors (GSIs).
Minimum Basic Qualifications (by time of application): The completion of all Ph.D. degree requirements except the dissertation is required at the time of application.
Additional Qualifications (by start date): A Ph.D. or equivalent degree in biology or a closely related discipline is required by the time of appointment. Experience teaching a college-level course (previously employed as a graduate student instructor, teaching assistant, lecturer, etc.) of the biological sciences is also required.
Preferred Qualifications: Experience working with computer-based phylogenetic programs and familiarity with online course and grading systems is preferred. Preference will be given to those with experience teaching a class similar to UC Berkeley’s Bio 1B lab courses.
Minimum full-time annual salary is $53,402. Salary is commensurate with experience and education.
Appointments for fall semesters are usually reviewed in May and finalists are selected once funding is confirmed for the next academic year. Spring semester appointments are reviewed in September. Reviews for Summer are in January.
Application requirements to apply: Cover letter, curriculum vitae, statement of teaching philosophy, student evaluations of teaching, and names and email addresses of three references. One miscellaneous teaching document is optional. Please include career highlights in the cover letter that specifically address the subject matter of our course. The CV should include teaching experience with a listing of dates, courses, units, and title (Lecturer, Graduate Student Instructor/Teaching Assistant, Guest Lecturer, etc.). Statement of Teaching Philosophy should be no more than three pages. Student evaluations of teaching should include all respondents (quantitative and qualitative). For those with considerable teaching experience, complete student evaluations of teaching from the last three courses taught will suffice. The cover letter, CV, and complete student teaching evaluations are very important. To receive full consideration, please ensure your application is complete by the time of review. To apply:
Letters of recommendation may be requested of finalists. If reference letters are later solicited by the Department, they will be treated as confidential per University of California policy and California state law. Please refer potential referees, including when letters are provided via a third party (i.e., dossier service or career center), to the UC Berkeley statement of confidentiality
(http://apo.berkeley.edu/evalltr.html) prior to submitting their letters.
The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see:
http://policy.ucop.edu/doc/4000376/NondiscrimAffirmAct. The department is interested in candidates who will contribute to diversity and equal opportunity in higher education through their teaching.
New paper out from the lab. This is from a collaboration with Stan Marks in the Vet School at UC Davis. The work was led by Katti Horng with assistance from Holly Ganz.
Citation: 2018) Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ 6:e4827https://doi.org/10.7717/peerj.4827(
Abstract: Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.
Postdoc position to work on soil metagenomics https://www.isme-microbes.org/jobs/postdoctoral-position-soil-metagenomics
week’s Ecology and Evolution Seminarwill be given by Raquel Peixoto on May 17th at 4:10pm in 176 Everson Hall. Come hear the exciting work she’s been doing manipulating microbiomes to increase coral health! Her talk is titled “MARINE PROBIOTICS: INCREASING CORAL RESILIENCE TO BLEACHING THROUGH MICROBIOME MANIPULATION”
Raquel is an Associate Professor in Molecular Microbial Ecology at the Federal University of Rio de Janeiro and has spent most of the last year on sabbatical at UC Davis working with Jonathan Eisen
Of possible interest:
DEB/ECH 294 SEMINAR
Large scale analysis of food ingredient metatranscriptomes reveals insights about hazards and food quality
Kristen Beck, Ph.D.
Research Staff Member, Industrial and Applied Genomics
IBM Almaden Research Center, San Jose
Friday, May 18, 2018
11:00am * 1022 Life Sciences
Abstract: As the challenges of protecting global food supply chains become more complex, the technical approaches being used to understand and guard against threats are becoming more sophisticated. Food safety testing is beginning to adopt new technologies such as next generation sequencing of DNA or RNA in their monitoring procedures and the cost of next generation sequencing is only decreasing with time. Together, this makes providing food safety solutions a very data-intensive problem. By surveilling the microbiome of food ingredients, we can develop methods and best practices that can be used to improve food testing standards and security of the food supply chain. As part of the Consortium for Sequencing the Food Supply Chain, we’ve utilized hundreds of terabytes of raw sequencing and derivative data to show that microbes will respond to perturbations in their environment and can be useful as an indicator of food safety hazards. By monitoring food microbiomes, we can better understand food safety hazards and quality issues that may arise in the supply chain.
Bio: Dr. Beck is a research staff member in the Industrial and Applied Genomics group in the Accelerated Discovery Lab of IBM Research. She has been involved in food-related research for over a decade. She has published contributions in mechanistic studies of omega-3 fatty acids in tumorigenesis as well as composition of primate breast milks among other topics. Since joining IBM Research in 2015, she has been an essential member of the Consortium for Sequencing the Food Supply Chain and now serves as the IBM Technical Lead. Her current research focuses on analyzing next generation sequencing data to gain insights about microbial ecology in food ingredients as well as confidently determining of the presence of various hazards such as pathogenic organisms, antimicrobial resistance genes, and food fraud. She received a Ph.D. in Biochemistry, Molecular, Cellular, and Developmental Biology with a Designated Emphasis in Biotechnology from the University of California, Davis and is a proud almuna and trainee of the Biotechnology Program.