Meeting Professor Benham

Last week I had a meeting with professor Craig Benham, who studies the relationship between structure and function in macromolecules such as DNA. He has joint appointments at the Departments of Mathematics, Bioengineering, and the Center for Bioinformatics. We discussed the importance of DNA topology (in gene regulation specifically) and I have learned more about the methods developed by his group. Altogether, our meeting was very valuable for my research.

University of California system

The University of California (UC) is a public university system in the state of California. It has about 235,000 students enrolled at the campuses Berkeley, San Fransisco, Los Angeles, Davis, Santa Barbara, Irvine, Riverside, San Diego and Merced. UC Davis has about 32, 000 students.
The University of California's campuses boast large numbers of distinguished faculty in almost every field and it is widely regarded as one of the top public university systems in the world. By the Academic Ranking of World Universities, one of its campuses, UC Berkeley, is ranked second worldwide among public and private universities, and three—Berkeley, Los Angeles, and San Diego—are ranked among the top 15.

Robert Mondavi Institute

The Robert Mondavi Institute for Wine and Food Science (RMI) within the College of Agricultural and Environmental Sciences of UC Davis was established with a personal gift of $25 million in 2001 from Robert Mondavi, renowned California wine producer. The RMI houses the departments of Viticulture and Enology, and Food Science and Technology, both recognized as the best in the world in their respective areas of scholarship.

Roland left Davis, Lex moved into the lab

Last thursday Roland left Davis and returned to the Netherlands where he will continue with the project. Since our office is kind of empty and isolated now, Lex moved to a desk in the actual wet-lab last week. Working in the lab itself is a good way to get some interactions and to learn what kind of activities are going on in there, since I am right in the center of all the action now. No wet lab activities for me though, I will stick to the bio-informatics.

QUIZ: Davis heat map

What does this heat map represent ?
No cheating, so no Googling !!!

BGI@UCDavis

We spoke with Bart Weimer, a professor in the Department of Population Health and Reproduction in the UC Davis School of Veterinary Medicine, who has been appointed co-director of BGI@UCDavis, a partnership between UC Davis and BGI (Beijing Genomics Institute), the world's largest genome sequencing organization. Weimer will be responsible for the day-to-day operations of the center, to be located on UC Davis' Sacramento campus. The center has started sequencing at a small scale but intends to expand significantly in the coming years. One of the ambitious efforts is the 100K Genome project aimed at sequencing the genomes of 100,000 infectious microorganisms to speed diagnosis of foodborne illnesses, which has been launched by UCDavis, Agilent Technologies and the U.S. Food and Drug Administration.

Roland's seminar

Roland gave a seminar on Wednesday Sept. 12 at the Robert Mondavi Institute entitled "Bioinformatics analysis of Lactic Acid Bacteria genomes", attended by about 30 senior scientists, postdocs and students.

UC Davis Genome Center

We visited the Genome Center which has Core Facilities for Bioinformatics, DNA technologies, Expression analysis, Metabolomics and Proteomics. In addition the Genome Center houses many genomics and bioinformatics research groups who use the core facilities. Ryan Kim showed us their DNA sequencing equipment, which includes Illumina HiSeq and MiSeq, and PacBio machines. We spoke with Jonathan Eisen, one of the leading bioinformaticians at UC Davis.

Our project and team

At UC Davis they have sequenced the genome of a food-related Enterococcus faecium strain. Lex and Roland are assisting with genome assembly, annotation and comparative genomics. We are working with postdoc Eun Bae Kim (bioinformatician) and MSc student Lauren Kopit (lab work).

 

Eun Bae at the left

Trip to the country

Saturday Lex and I drove west from Davis through the countryside, dirt roads, fields of tomatoes and almond orchards, doing all the navigating with our smartphones. Dry-dry-dry. California has over 80% of the world production of almonds.We passed through the cute town of Winters, then past Lake Berryessa and over winding roads through the hills into the Napa Valley which is renowned for its vineyards and wineries.We passed hundreds of small and large wineries, and went to the Stag's Leap Wine Cellars for tasting.

Then we rushed on to Fairfield to catch the last tour of the Budweisser brewery. Budweisser is part of Anheuser-Busch, which in 2008 became part of InBev, the largest beer brewing company in the world. Very impressive, they have 120 huge chilled tanks holding a total of 25 million liters of beer !

Our workplace

Lex and I have our own large office with airco and good internet connections. That's all bioinformaticians need.

Maria Marco group

We are working in the lab of Maria Marco at the Robert Mondavi Institute, dept of Food Science and Technology, UC Davis.Marco’s team is investigating the ecology and molecular genetics of beneficial bacteria associated with plant surfaces and mammalian digestive tracts. Organisms of particular interest are Lactic Acid Bacteria (LAB) found in plant and gut environments. LAB are important for the production of (fermented) food products and specific strains are currently being applied as probiotics to deliver health benefits in the human gut. This lab aims to understand the molecular adaptations and activities of LAB in the context of the indigenous plant and gut microbiota to improve food production and maintain human health.

Meeting Professor David Mills

Today we had discussions with Professor David Mills, who is in the Departments of Viticulture & Enology and Food Science & Technology at  UC Davis. He is an expert in the molecular biology of Gram-positive microorganisms, with an emphasis on the lactic acid bacteria (LAB) and bifidobacteria used in food fermentations or active as probiotics. An overall goal of Dr. Mills research is to link genomic content, ecological context and specific strain behavior to better understand LAB biology in their “working” environments. Dr. Mills is the founder of the LAB Genomics Consortium USA and is a founding member of the UC Davis Milk Bioactives and Functional Glycobiology Programs. In 2012 Dr. Mills became the Peter J. Shields Endowed Chair in Dairy Food Science at UC Davis. 

Help: no coffee ! !

What a SHOCK! They don't drink coffee in the lab here. How can a Dutchman work or even survive without coffee ? So we bought 2 thermos bottles and will fill them with coffee every day before we go to work.

Farmers Market

At the Farmers Market at Davis the locals sell their produce, and there is a lot of music, dancing and family picnicking. Its all very green and healthy. This town resembles Wageningen in size and type of people and activities. Where else would you find a scientist in the Market trying to find volunteers for his food studies ? I think I will volunteer for the milk shake study.

Davis

Davis is located in the California Central Valley, exactly between San Francisco and Sacramento, the state capital. It is a small university town of about 65,000 inhabitants with nearly 30,000 employed by the University of California, Davis campus (some must be from outside Davis!). Davis is known for its liberal politics, for having many bicycles and bike paths, and for the beautiful UC Davis campus. 

It belongs to "America's Best Biking Cities".

Davis has dry, hot summers and cool, rainy, winters like those of a Mediterranean climate. 

Arrived in Davis

Lex and I arrived in Davis this weekend, and are now trying to adjust to the time difference and high temperature (33-35 oC). Today is Labour Day, which means that all Americans do NOT work, so we have an extra day to recuperate.

NGI-NBIC Distinguished Visiting Scientist Award for Prof. Roland Siezen

NGI-NBIC Distinguished Visiting Scientist Award for Prof. Roland Siezen

A Distinguished Visiting Scientist stipend for the period 2010-2013 has been awarded by NGI-NBIC to Prof. Dr. Roland Siezen of the Bacterial Genomics group at the Center of Molecular and Biomolecular Informatics (CMBI), UMC St. Radboud Nijmegen. He will visit international host institutes to set up new collaborations in genomics and bioinformatics of food- and health/disease-related bacteria, in particular in relation to microbial diversity. This will also involve exchange and developments of bioinformatics tools and databases. These host institutes at universities in South Africa and USA are of high international reputation, with excellent scientific infrastructure and computational facilities.

Prof. Siezen’s goals are to increase the international visibility of the NGI, NBIC, the Kluyver Centre and TI Food and Nutrition programmes and science at the host institutes by giving guest lectures, and by discussing NBIC/Kluyver/TIFN research projects with local scientists and students. The collaborations should lead to joint international publications (1-2 per host institute) with these NGI institutes.

The first visit in March 2011 was to the Centre of Excellence in Biomedical Tuberculosis Research of Stellenbosch University in South Africa, and to the South African National Bioinformatics Institute (SANBI), University of the Western Cape in Capetown. He was accompanied by PhD student Anita Schürch of the Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), in Bilthoven, the Netherlands. 

The second visit in September 2012 will be to the Food Science and Technology Department, University of California, Davis, USA. Host scientist will be Dr. Maria Marco. Prof. Siezen will be accompanied by NBIC PhD student Lex Overmars of the CMBI, Nijmegen.