Archive for May, 2012

Mapping The Tomato Genome Promises A Tastier Future

May 30, 2012 Leave a comment

The EU Tomato Genome Sequencing Consortium has announced that they have completed sequencing the genome of “Heinz 1706” as well as it’s wild relative Solanum pimpinellifolium. The sequence will be published tomorrow (May 31st) in Nature. The hopes are that having access to the tomato genome will make breeding easier, and hopefully lead to tastier tomatoes. Currently tomato breeding is one of the most complex and interwoven processes that most Americans have no clue is even happening. As it stands most commercial tomatoes have to be completely rebred every couple of years just to be the same consistent tomato that we are familiar with. The publishing of the tomato genome will hopefully not only make the whole process easier, but also help producers to emphasize genes that enhance flavor and not just appearance, yield, and durability.

From “Tomato genome sequence bears fruit” By Rebecca Hill

According to the leaders of the UK arm of the Tomato Genome Consortium, Graham Seymour at the University of Nottingham and Gerard Bishop, formerly of Imperial College London, the sequence will make precision breeding possible not just in tomatoes, but also in other crop species from the Solanaceae family, such as aubergines (Solanum melongena) and peppers (Capsicum spp.).

They also hope it will help in the development of tomatoes that can survive pests, pathogens and even climate change, as well as high-yield crops that still have a good flavour. “It’s really all about making a better tomato,” says Allen Van Deynze, a molecular geneticist at the Seed Biotechnology Center at the University of California, Davis. “This work enables a lot of things we just couldn’t do before.”

Launched in 2003, the project has taken some time to get results, but it has produced an “amazingly complete” sequence, the leaders say. With more than 80% of the genome sequenced, and more than 90% of the genes within it identified, and refinements still taking place, the group hopes to make this a gold-standard reference sequence. “It’s one of the better genomes out there,” says Van Deynze.

From Nature Editorial “You Say Tomato

The scientists have analysed many more traits in these variants than just taste. They have built up a phenotypic resource that details all the desirable (and undesirable) properties you might want to see in a tomato — from pest-resistance to speed of ripening. The resource will be extremely valuable for those who want to exploit the tomato genome, the sequence of which we publish this week (seepage 635). The paper reports the sequences of both the inbred tomato strain Heinz 1706 — generated by the company whose founder Henry Heinz changed the world of tomato ketchup — and its wild ancestorSolanum pimpinellifolium. (Among the many aphorisms ascribed to Heinz is this fitting one: to improve the product in glass or can, you must improve it while it is still in the ground.)

Plant genomes are more challenging to sequence than those of animals because they tend to be larger and more complicated. But at around 900 megabases — just over one-quarter of the size of the human genome — the tomato genome proved manageable. Still, more than 300 scientists from 90 institutes across 14 countries have been slaving away at the task since 2003. It is a fabulous effort that has the potential to radically advance plant science. First, however, the biology behind the genome needs to be understood.

Understanding the basis of tomato genomics is important for three reasons. First, it will help scientists to unravel the extraordinary diversity of the tomato plant, and of the natural world in general. The tomato belongs to one of the planet’s most diverse plant genera — Solanum, which includes more than 1,000 species ranging from the potato (Solanum tuberosum) to woody nightshade (Solanum dulcamara). Comparing sequences may help researchers to understand evolutionary processes

From “Tomato Genome Sequenced” from Science Daily

Tomato is a member of the Solanaceae or nightshade family, and the new sequences are expected to provide reference points helpful for identifying important genes in tomato’s Solanaceae relatives. The group includes potato, pepper, eggplant and petunia and is among the world’s most important vegetable plant families in terms of both economic value and production volume.

Beyond improvement of the tomato, the genome sequence also provides a framework for studying closely related plants, such as potato, pepper, petunia and even coffee. These species all have very similar sets of genes, yet they look very different.

How can a similar set of “genetic blueprints” empower diverse plants with different adaptations, characteristics and economic products? This challenging question is being explored by comparing biodiversity and traits of tomato and its relatives.

The Tomato Genome Consortium started its work in 2003, when scientists analyzed the DNA sequence of tomato using the most modern equipment available at the time. Fortunately, with the recent introduction of so-called “next generation sequencing” technologies, the speed of data output increased 500-fold and enabled the project to move on efficiently to its conclusion.

“The tomato genome sequence provides insights into fleshy fruit evolution”  The Tomato Genome Consortium Sato et al.

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanumpimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

The genes shown represent a fruit ripening control network regulated by transcription factors (MADS-RINCNR) necessary for production of the ripening hormone ethylene, the production of which is regulated by ACC synthase (ACS). Ethylene interacts with ethylene receptors (ETRs) to drive expression changes in output genes, including phytoene synthase (PSY), the rate-limiting step in carotenoid biosynthesis. Light, acting through phytochromes, controls fruit pigmentation through an ethylene-independent pathway. Paralogous gene pairs with different physiological roles (MADS1/RINPHYB1/PHYB2ACS2/ACS6ETR3/ETR4PSY1/PSY2), were generated during the eudicot (γ, black circle) or the more recent Solanum (T, red circle) triplications. Complete dendrograms of the respective protein families are shown in Supplementary Figs 16 and 17.

Solving The Mystery of “Falling Bubbles” In Stouts

May 29, 2012 Leave a comment

Falling stout bubbles explained

By Jason Palmer

Science and technology reporter, BBC News

Irish mathematicians may have solved the mystery of why bubbles in stout beers such as Guinness sink: it may simply be down to the glass.

Simulations suggest an upward flow at the glass’s centre and a downward flow at its edges in which the liquid carried the bubbles down with it.

But the reasons behind this flow pattern remained a mystery.


“If you imagine your pint is full of bubbles, then the bubbles will start to rise,” Dr Lee said.

But the bubbles in a standard pint glass find themselves in a different environment as they rise straight up.

“Because of the sloping wall of the pint, the bubbles are moving away from the wall, which means you’re getting a much denser region next to the wall,” Dr Lee explained.

“That is going to sink under its own gravity, because it’s less buoyant, and that sinking fluid will pull the bubbles down.”

The bubbles, that is, are “trying” to rise, but the circulation that creates drives fluid down at the wall of the glass.

“You’ll see sinking bubbles not because the bubbles themselves are sinking, but because the fluid is and it’s pulling them down with it.”

The same flow pattern occurs with other beers such as lagers, but the larger bubbles of carbon dioxide are less subject to that drag.

Simulations of bubble circulation
Calculations show that a glass shaped “upside-down” would exhibit the opposite effect on bubbles

Why do bubbles in Guinness sink?

(Submitted on 23 May 2012)

Stout beers show the counter-intuitive phenomena of sinking bubbles while the beer is settling. Previous research suggests that this phenomena is due the small size of the bubbles in these beers and the presence of a circulatory current, directed downwards near the side of the wall and upwards in the interior of the glass. The mechanism by which such a circulation is established and the conditions under which it will occur has not been clarified. In this paper, we demonstrate using simulations and experiment that the flow in a glass of stout depends on the shape of the glass. If it narrows downwards (as the traditional stout glass, the pint, does), the flow is directed downwards near the wall and upwards in the interior and sinking bubbles will be observed. If the container widens downwards, the flow is opposite to that described above and only rising bubbles will be seen.

Reminder: BMCDB blog Photo Contest 2012

May 29, 2012 Leave a comment

The Annual Meeting & BBQ are fast approaching and so is the deadline for the BMCDB blog Photo Contest 2012!

Have you already submitted your science photo? If not, send it to with a short description.

Also, have you already voted on the current contestants?

And yes, you can win money, but only if you participate of course!

Categories: Photo Contest, UC Davis

Stem Cell Essay Contest: $50 prize & essay is published via @pknoepfler

May 29, 2012 Leave a comment

On the stem cell blog of the  Knoepfler lab, there is an exciting competition:

Want to win $50 and become a published author?

Enter the Knoepfler Lab Stem Cell Blog Essay Contest.

The challenge?

Write a no more than 500 word, convincing, non-fiction essay on stem cells thinking entirely outside the box.

Otherwise, the angle you take is totally up to you.

Surprise me.

Make me think.

There will be two winners.

Category 1 = age 18 or younger

Category 2 = age 19 or older


The winners will each get two prizes.

1) you will get a $50 iTunes gift card


2) you will have you essay published on this website for 1,000s of the top scientists, patient advocates, grant funders, politicians, and educators in the world interested in stem cells to read. Talk about potentially opening doors and a great thing to put on your resume/CV or college application too.

Rules (read carefully).

Essays over 500 words will not be considered.

References/citations of other papers (if you choose to have any, limit of 5) do not count toward the word limit.

Fictional essays will not be considered.

The sole judge will be me and all decisions final.

No plagiarism.  No personal attacks, no obscenities, and especially no boring essays.

In the event of a tie for any given age category, each of the tied winners for a given age group will get a $25 gift card and both will be published.

With your entry, tell me whether you are in category 1 or 2, otherwise your essay will not be considered. With your essay you must supply a statement indicating your name, your age, your mailing address for the prize, and your email address as well as a statement agreeing to have your essay published on this website. Essays lacking this info or statement will not be considered.

Deadline. June 30, 2012. No exceptions.

Entries must be emailed to me at:

Only one entry per person (those sending more will be disqualified).

No members of the Knoepfler Lab are eligible of course.

If you want to stay up to date with the work of the Knoepfler lab, you can follow dr. Paul Knoepfler on twitter too.

Categories: Lab Profiles, UC Davis

Nominations Solicited for Acting Vice Chancellor – Student Affairs

May 26, 2012 Leave a comment

Dear UC Davis Community, I am seeking nominations and letters of interest for an experienced academic leader from within UC Davis to serve as Interim Vice Chancellor – Student Affairs. As you may know, Vice Chancellor Fred Wood, who has admirably served UC Davis for more than a quarter century, has accepted the Chancellor’s position at the University of Minnesota – Crookston, effective July 2, 2012. We must move swiftly to ensure continuity of leadership in Student Affairs. Therefore, I ask that nominations be forwarded to me by June 4, 2012, so that I may submit an item to the Regents for approval of a one-year interim appointment while we conduct a national recruitment for a permanent replacement. This position reports directly to me and will serve as a member of the Council of Deans and Vice Chancellors during the interim appointment. I am seeking an individual who is a member of the campus’s Academic Senate with demonstrated accomplishment in academic leadership and management in student-related positions; excellent management, organizational, planning, supervisory and problem-solving skills; excellent oral and written communication skills; knowledge of budgeting, financial controls, and fiscal accountability; knowledge of student development theory and student concerns, challenges, interests and issues; ability to work collaboratively and inclusively with faculty, staff, students, the media, and the broader community; and the ability to relate effectively to a wide variety of people of diverse backgrounds, including an understanding and respect for cultural, ethnic, and individual differences. The position requires a minimum of five years of academic administrative experience. With the assistance of an advisory committee composed of student, faculty and administration representatives, we will review the nominations and letters of interest submitted. Our goal will be to fill the Interim Vice Chancellor – Student Affairs position by July 2, 2012. Nominations and letters of interest should be submitted to Linda Fairfield at Thank you for your assistance in recruiting this critical position.

Sincerely, Linda P.B. Katehi Chancellor

Categories: Recent News, UC Davis

Take A Moment To Remember This Memorial Day Weekend

May 25, 2012 Leave a comment

A note from V&E’s resident veteran, Luke Bohanan


Before we set off in our different directions to enjoy (or work through) this Memorial day weekend, I would like to take a moment of you time, to get on my soap box.
Yesterday I went with a few of my Student Veterans club members to the Memorial Union to lay flowers at the Aggie veterans memorial tucked away in the corner next to the fireplace in the Griffin lounge in the MU.  There, a stainless steel plaque lists the names of 134 UC Davis Graduates that were killed in combat from World War I through 2006, accompanied by a book encased in glass that talks about each service member.  I had never realized that the MU, the Memorial Union, was originally dedicated to these heroes, and I realized how easy it is to forget what memorial day is all about.  For me, the break is always bitter sweet.  Every year since 2003 I have lost at least one of the original 400 some odd soldiers that I crossed the boarder with in Iraq, many of whom I worked closely with, and all of whom I have called my brother.
So, if you have time this weekend, or later on, I invite you to go down to the MU Griffin lounge and take a moment to think about those who sacrificed so much to stand up when the call came out.  Also, if you are at a party, bbq, camping trip, or stuck behind your computer, take a moment, and take a moment and have a drink for all the great men and women who fought so hard and are no longer here to drink with us.
Here is a link to the article about the re-dedication of the wall, if you are interested.

Thank you, and have fun this weekend.

Special Seminar: RNA on Steroids 2 pm Friday, 5/25, LS1022.

May 24, 2012 Leave a comment

RNA on Steroids
2 pm Friday, 5/25, LS1022.
Dr Loren Williams, Director, NASA Center for Ribosomal Evolution and Adaptation, GA Tech, Atlanta

Dr Williams works on rewinding the “tape of life”: to shed light on the nature of protein synthesis prior to the last universal common ancestor of life. His center focuses on the characteristics of ancient macromolecules and their assemblies, specifically on aboriginal mechanisms of peptide synthesis by RNA – an attempt to uncover clues about key steps in the transition from the RNA world to the protein. In part, Dr Williams work carries the potential of discovering and characterizing the oldest traceable macromolecules and machines of life, and the earliest discernable connection between RNA and protein. The formation of the Peptidyl Transferase Center  marked the beginning of the translation machinery and the beginning of the end of the RNA world. Therefore, working on the resurrection and the structures of ancestral Peptidyl Transferase Centers allows Dr Williams to test ideas about primitive living systems, as well as the origin of protein.