Archive for April, 2012

57 year experiment, Drosophila kept in dark for 1400 generations, many evolutionary changes (record longest postdoc!)

April 30, 2012 2 comments

Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment

Minako Izutsu1,2#, Jun Zhou3, Yuzo Sugiyama1, Osamu Nishimura1, Tomoyuki Aizu4, Atsushi Toyoda4, Asao Fujiyama4, Kiyokazu Agata1,2, Naoyuki Fuse1#*

1 Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan, 2 Laboratory for Molecular Developmental Biology, Graduate School of Science, Kyoto University, Kyoto, Japan, 3 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America, 4 Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan

Link to original paper in PLoS

Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.

Amazing experiment by Izutsu et al. where they kept flies in the dark for 57 years and then sequenced them. Goes a long way in explaining evolution of traits under certain conditions: think cave dwelling animals. Score one for evolution.

Sensory Volunteer Opportunity: Sensory Trial on Red Wine!

April 30, 2012 Leave a comment



My name is Aaron Whitlatch and I am a graduate student in Professor Mark Matthews’ Laboratory of the Viticulture and Enology Department.  I am looking for panelists who are willing to participate in a sensory study on red wine.  I currently have 12 people but still need at least 8 more.


The study will last only five weeks with one-hour commitments three days per week, so essentially the month of May.  It will include six training sessions over the first two weeks where you will smell and taste the wines with other panelists, generate descriptive terms and gain practice consistently using these terms.  Once the training is completed, nine tasting sessions in individual tasting booths will take place over the following three weeks.  These sessions don’t take as long as the training session and should be pretty easy.  It looks like Monday, Wednesday, Friday will be the days that work the best for most people.  


In order to take part in this study you have to (i) be over 21 years old, (ii) expectorate all the wines you are tasting, (iii) be willing to taste and smell, and (iv) be able to participate in all six training sessions.


After successful completion of the study you will receive a $50 gift card.  


If you are interested, please email me back at

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Harvard Library Urges University to Take A Stand Against Big Publishers

April 24, 2012 Leave a comment

Excerpt from “Harvard University says it can’t afford journal publishers’ prices” by Ian Sample

Exasperated by rising subscription costs charged by academic publishers, Harvard University has encouraged its faculty members to make their research freely available through open access journals and to resign from publications that keep articles behind paywalls.

A memo from Harvard Library to the university’s 2,100 teaching and research staff called for action after warning it could no longer afford the price hikes imposed by many large journal publishers, which bill the library around $3.5m a year.


The memo from Harvard’s faculty advisory council said major publishers had created an “untenable situation” at the university by making scholarly interaction “fiscally unsustainable” and “academically restrictive”, while drawing profits of 35% or more. Prices for online access to articles from two major publishers have increased 145% over the past six years, with some journals costing as much as $40,000, the memo said.

More than 10,000 academics have already joined a boycott of Elsevier, the huge Dutch publisher, in protest at its journal pricing and access policies. Many university libraries pay more than half of their journal budgets to the publishers Elsevier, Springer and Wiley.

As one of America’s premier institutions, it could potentially have long ranging consequences for the publishing business if Harvard decides to take a stand against absurd subscription prices. If Harvard and some other top tier institutions make a stand, it is likely that the University of California system will follow suit. Not sure when and how this will happen, but the current model for publishing is not sustainable with shrinking academic budgets.

Edit: commentary by Michael Eisen, co-founder of the PLoS journals and Open Access advocate.

Categories: Recent News

Bradford-Rominger award ceremony: A Bottoms-up Approach to Sustainability

April 24, 2012 Leave a comment

Mentor Seminar Spring 2012

April 24, 2012 Leave a comment

Greetings BMCDB!

Learn how to be a better mentor, teacher, and student!  Next week will be the first Entering Mentoring seminar for the Spring quarter.  This seminar is open to graduate students, postdocs, and even professors that want to enhance their abilities as a mentor.  This Spring we will hold 6 weekly 1-hour seminars covering topics common to all mentoring relationships.
Here are just a few benefits of participating in the Mentoring Seminar:

  1. Enhance your mentoring abilities through awareness and learn tools for effective mentoring
  2. Gain perspective on all mentoring relationships, including your own student/PI relationship
  3. Put on your CV that you took a HHMI Entering Mentoring Seminar
  4. Free coffee and bagels on Tuesday mornings!

Time:  Tuesday mornings from 9:00am to 10:00am
Dates: Tuesday May 1st through Tuesday June 5th (6 weeks long)
Place:  148 Briggs Hall
Our tentative weekly schedule will focus on the following topics:

  1. Establishing a good mentoring relationship, and elements of a good research project
  2. Learning to communicate effectively and adaptively
  3. Setting goals and expectations, and developing trust
  4. Identifying and resolving challenges in mentoring
  5. Evaluating your progress as a mentor
  6. Developing a mentoring philosophy and drawing parallels in mentoring

To sign up, subscribe to the EnteringMentoring listserve at: or email Brandon Zipp ( or Kristi Bezold ( for more information.
Feel free to email with any questions that you might have.  We look forward to seeing you next week!
Brandon and Kristi

BMCDB Exit Seminar Crystal Berger: “p53, a Target of Estrogen Receptor (ER) Alpha, Modulates DNA Damage-induced Growth Suppression in ER-positive Breast Cancer Cells”

April 24, 2012 Leave a comment

Crystal Berger (BMCDB) from Xinbin Chen’s lab will be giving her exit seminar this Thursday, April 26th from 2:30-3:30 in LSA 1022. 

 “p53, a Target of Estrogen Receptor (ER) Alpha, Modulates DNA Damage-induced Growth Suppression in ER-positive Breast Cancer Cells” 




Categories: Uncategorized

Announcement of new police chief and department reporting relationship

April 19, 2012 Leave a comment

Yesterday, we brought you the news that UCDPD chief Spicuzza would step down today. A new UCDPD chief has been announced: Matthew Carmichael (link to UCDPD site). He was the interim police chief, once Spicuzza was put on paid administrative leave, pending the investigation.

To the UC Davis Community:

Throughout the past several months, I have said many times that as chancellor of UC Davis I take full responsibility and am accountable for implementing whatever reforms are necessary following the period of self-examination and outside review of the events on our campus last November

In keeping with that commitment, I am pleased to announce today the appointment of Matthew Carmichael as our new chief of police. As many of you know, Matt has served admirably as our acting chief since last November 21. He will replace Annette Spicuzza, who announced her resignation as chief yesterday.

Matt will be introduced to the campus community this afternoon at the ARC Ballroom A. His appointment will take effect immediately for a term of one year. Toward the end of that period, we will undertake an open national recruitment for the position. Matt fully supports this approach and I am hopeful he will apply for the permanent position. Matt’s service as acting chief during the past five months has been extraordinary, during some very demanding circumstances.

With tremendous energy and enthusiasm, he has reached out to students, faculty and staff and has built many strong, positive relationships. He is highly respected as a leader, adviser and innovator not only within our department and across our campus, but also throughout the law enforcement community. In his short time as acting chief, Matt has taken many steps to bring positive change and a sense of openness to the department and its operations. In the coming months, I am fully confident that he will help us make great strides toward implementing the needed departmental reforms that the Reynoso task force recommended in its April 11 report.

Matt has a distinguished record of nearly three decades in law enforcement, the last 10 with the UC Davis Police Department. Before being named acting chief last November, Matt was a patrol lieutenant responsible for the Davis campus, where he also handled public information officer responsibilities. He began his professional law enforcement career in June 1985 as a reserve officer for the Pinole Police Department. He joined our campus’s Police Department in 2002. He has an associate’s degree in Administration of Justice from Napa Valley College.

As we move forward with the top-to-bottom review of our Police Department that I announced last week, I will reassign – effective May 1, 2012, on an interim basis – oversight of the department from our Office of Administrative and Resource Management to the Office of the Provost and Executive Vice Chancellor. The provost is our campus’s chief academic and operating officer, and this transfer will ensure that, going forward, the department will be closely aligned with our core academic mission and values.

As a first step toward a thorough review of our Police Department, we have called on the state Commission on Peace Officer Standards and Training (POST) to conduct a comprehensive audit of all Police Department operations. The results of this independent audit will help ensure that our department is meeting and performing its basic responsibilities and will also guide future efforts to improve the department.

At the same time, we are also launching a holistic review of our administrative policies and structures regarding decision-making within the university’s senior administration, as I had previously announced. We will have more to announce about this review in the days ahead.

As a campus, we have much work to do in the weeks and months ahead. I am confident that these actions announced today will help position our campus and our Police Department for success in the future.


Linda P.B. Katehi


Categories: UC Davis