Archive for April, 2013

Dr Famous published sexy but wrong paper – blog about it? via @pknoepfler

April 30, 2013 Leave a comment

We have all seen cases where a sexy research paper gets attention from the mainstream media. Often this results in oversimplifications of the results and overdrawn conclusions, while not providing a direct link to the original paper.

Now imagine that you have actually read this sexy paper.

Now imagine that the research has some serious issues.

Now imagine that the last author is a famous professor.

Will you devote  a blog entry to this paper or not?

On Paul Knoepfler blog you can answer this precise question (here).

Categories: UC Davis

Transgenic E. coli made to produce hydrocarbon fuels

April 24, 2013 Leave a comment

Super cool work from researchers in the UK

Excerpt from “Bacteria churn out first ever petrol-like biofuel” by Rebecca Summers

To be used as a mainstream alternative to fossil fuels – desirable because biofuels are carbon-neutral over their lifetime – engines would have to be redesigned, or an extra processing step employed to convert the fuel into a more usable form.

To try to bypass that, John Love from the University of Exeter in the UK and colleagues took genes from the camphor tree, soil bacteria and blue-green algae and spliced them into DNA from Escherichia coli bacteria. When the modified E. coli were fed glucose, the enzymes they produced converted the sugar into fatty acids and then turned these into hydrocarbons that were chemically and structurally identical to those found in commercial fuel.

“We are biologically producing the fuel that the oil industry makes and sells,” says Love.

“Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli”

Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing and are not fully compatible with modern, mass-market internal combustion engines. Rather, the ideal biofuels are structurally and chemically identical to the fossil fuels they seek to replace (i.e., aliphatic n– and iso-alkanes and -alkenes of various chain lengths). Here we report on production of such petroleum-replica hydrocarbons in Escherichia coli. The activity of the fatty acid (FA) reductase complex from Photorhabdus luminescens was coupled with aldehyde decarbonylase from Nostoc punctiforme to use free FAs as substrates for alkane biosynthesis. This combination of genes enabled rational alterations to hydrocarbon chain length (Cn) and the production of branched alkanes through upstream genetic and exogenous manipulations of the FA pool. Genetic components for targeted manipulation of the FA pool included expression of a thioesterase from Cinnamomum camphora (camphor) to alter alkane Cn and expression of the branched-chain α-keto acid dehydrogenase complex and β-keto acyl-acyl carrier protein synthase III from Bacillus subtilis to synthesize branched (iso-) alkanes. Rather than simply reconstituting existing metabolic routes to alkane production found in nature, these results demonstrate the ability to design and implement artificial molecular pathways for the production of renewable, industrially relevant fuel molecules.



Blueberry Sensory Panel

April 17, 2013 Leave a comment

Do you like blueberries?

We are looking for sensory panelist who can participate in our blueberry flavor research.

Each participant is expected to attend all training session in order to participate in the taste sessions starting from end of April to June.

  • Training session – starting from late April for 2 weeks with 3 training sessions per week (30-60 min each).
  • Taste session – May-June, 7 sessions over a 7 weeks period (20-45 min each). The exact dates cannot be determined until the day before harvest. But once the harvest date is fixed, the tasting days will be set once per week on the same day each week. (no taste session on the weekends)

Treats will be served, and gift cards given for attending sessions.

If you have time and are interested in participating, please contact Nobuko Sugimoto (

Nobuko Sugimoto

Postdoctoral Researcher

Department of Plant Sciences

1106 Wickson Hall

Categories: UC Davis

Career Options Seminar

April 8, 2013 Leave a comment

Greetings students and faculty (and please forward to postdocs),
We welcome you to join us at the upcoming Career Options Seminar! (Breakfast/Brunch will be served)
The Career Options Seminar series offers insight into a variety of career options for advanced degree holders. This is a fantastic opportunity to learn how your advanced degree can be used in different industries, network with invited speakers and jump-start your future career plans.

Michael Weickert –  Entrepreneur (President and CEO of S.E.A Medical Systems)

TUESDAY, April 9th @ 11am Life Sciences 1022

Be sure to tell your fellow grad students, techs, postdocs, and PI…We look forward to seeing you at the seminars!

If you are interested in having lunch with the speaker or if you have any questions, please don’t hesitate to email us (
Kind regards,

Hanine Rafidi, Michelle Tu, & Daniël Melters
COS Committee

Categories: Seminar Announcements

Seminars Page

April 8, 2013 Leave a comment

The Seminars page has been updated so check out what talks are happening this week! If there are seminar schedules missing that you would like listed on the site please email! Thanks!

Categories: Seminar Announcements

Trajectory of the infant gut microbiome

April 5, 2013 Leave a comment

Thanks to the Night Lab at UCol. Boulder for putting this together.

“The assembly of an infant gut microbiome framed against healthy human adults ”

“Here we present how a new born human gut microbial community develops from resembling the delivery method (vaginal) to look like, after almost 3 years of life, the one of an adult. This trajectory is created from the data published by Koenig JE et al. 2011 framed around the data generated by the Human Microbiome Project (HMP).”

BMCDB Students Chris Fortenbach and Weston Powell present at PSTP Retreat 4/9/2013

April 4, 2013 Leave a comment

Come hear BMCDB students Christ Fortenbach and Weston Powell present at the annual PSTP/VSTP Retreat next Tuesday 4/9/2013!

2013 VSTP/PSTP Annual Retreat

When: April 9, 2013, 1:00 p.m. to 5:00 p.m.

Where: Activities & Recreation Center (ARC), SE Corner of LaRue & Orchard Roads, UC Davis Campus


1:15 P.M.        Introduction or Welcome

John Payne, Ph.D., Director, PSTP Program

1:20 P.M.        Kimberly A. Dodd, VSTP Student

Protection from RVFV neurologic disease is dependent on a functional CD4+ T cell response

1:55 P.M.        Weston Powell, PSTP Student

Long, non-coding RNAs at the heart of Prader-Willi syndrome and Angelman syndrome

2:30 P.M.        Break & Poster Session

3:30 P.M.        Nanelle Barash, VSTP Student

Increased spatiotemporal resolution of Giardia intestinalis colonization dynamics using bioluminescent in vivo imaging

4:05 P.M.        Chris Fortenbach, PSTP Student

The effect of RGS9 overexpression on flicker responses of mouse bipolar cells