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A molecular function of Zillion Different Screens protein explained

May 4, 2011 By

In a recent paper in Journal of Cell Biology entitled “Spatial regulation of Cdc55-PP2A by Zds1/Zds2 controls mitotic entry and mitotic exit in budding yeast“, Brandeis postdoctoral fellow Valentina Rossio and Assistant Professor of Biology Satoshi Yoshida reveal a molecular function of a mysterious protein Zds1.

The Zds1 protein in yeast  was identified some years ago in “a zillion different screens” for cell cycle mutants, stress response mutants, RNA metabolism mutants, etc., but the molecular function of the protein remained a mystery for more than 15 years. Rossio revealed that Zds1’s key target is a protein phosphatase 2A (PP2A) complex. She showed that Zds1 controls nucleocytoplasmic distribution of PP2A complex, and that this regulation is critical for cells to know when to enter and to exit from mitosis (picture below; cells lacking Zds proteins adopt an abnormal shape because of problems in mitosis). Rossio thinks all the other complicated phenotypes associated with ZDS1 can also be explained by PP2A regulation and is currently studying mechanistic details about the Zds1-PP2A interaction.

See also the accompanying commentary “Proteins keep Cdc55 in its place“

Filed Under: Biology, labs Tagged With: , , , , , , ,

Yeast genetics and familial ALS

April 27, 2011 By

In a recent paper in PLoS Biology, “A Yeast Model of FUS/TLS-Dependent Cytotoxicity“, Brandeis postdoc Shulin Ju and coworkers applied yeast genetics to examine the function of the human protein FUS/TLS. The gene for FUS/TLS is mutated in 5-10$ of cases of Familial ALS. The yeast model expressing the mutant protein recapitulates many important features of the pathology.

A particular feature of interest is that  FUS/TLS form cytoplasmic inclusions of this protein which is normally localized to the nucleus. Over-expression of a number of yeast proteins rescues the cells from the toxic effect without removing the inclusions. The results are suggested to implicate RNA processing or RNA quality control in the mechanism of toxicity, which I find really interesting in light of the talk Susan Lindquist (an author on this paper) gave at Brandeis about yeast prions and regulatory proteins earlier this month.

Other authors on the paper include Brandeis professors Dagmar Ringe and Gregory Petsko, and Brandeis alumni Dan Tardiff (PhD, Mol. Cell. Biol.,  ’07), currently a postdoc in the Lindquist lab at the Whitehead Institute,  and Daryl Bosco (PhD, Bioorganic Chem, ’03), currently on the faculty at U. Mass. Medical School.

For more information, please see the paper itself or the longer article about the research on Brandeis NOW.

Filed Under: Biochemistry, chemistry, labs, postdocs Tagged With: , , , , , , , , ,

Detecting Mutations the Easy Way

March 30, 2011 By

Recent Brandeis Ph.D graduate, Tracey Seier (Molecular and Cell Biology Program), Professor Sue Lovett, Research Assistant Vincent Sutera, together with former Brandeis undergraduates Noor Toha, Dana Padgett and Gal Zilberberg have developed a set of bacterial strains that can be used as “mutational reporters”.  Students in the Fall 2009 BIOL155a, Project Laboratory in Genetics and Genomics, course also assisted in the development of this resource. This work has recently been published in the journal Genetics.

These Escherichia coli strains carry mutations in the lacZ (β-galactosidase) gene that regain the ability to metabolize lactose by one, and only one, specific type of mutation. This set allows environmental compounds to be screened for effects on a broad set of potential mutations, establishing mutagen status and the mutational specificity in one easy step.

This strain set is improved over previous ones in the inclusion of reporters that are specific for certain types of mutations associated with mutational hotspots in gene. Mutations at these sites occur much more frequently than average and involve DNA strand misalignments at repeated DNA sequences rather than DNA polymerase errors. Such mutations are associated with human diseases, including cancer progression, and have been under-investigated because of the lack of specific assays. Using this strain set, Seier et al. also identified a mutagen, hydroxyurea, used in the treatment of leukemia and sickle cell disease, which affects only the “hotspot” class of mutations. This strain set, which will be deposited in the E. coli Genetic Stock Center,  will facilitate the screening of potential mutagens, environmental conditions or genetic loci for effects on a wide spectrum of mutational events.

 

 

Left: E. coli colonies showing lacZ mutant revertants (blue pimples) arising on a white colony on growth medium containing the beta-galactosidase indicator dye,  X-gal

 

Filed Under: Biology, grad students, labs, Undergrads Tagged With: , , , , , ,

Inaugural Neuro + MCB Graduate Student Social a Success

January 19, 2011 By

On Friday January 14th the first of an anticipated quarterly series of social events for Biology graduate students took place.  The concept for this entirely student-funded gathering was developed by myself (Scott Neal, MCB) and co-organizer Sean O’Toole (Neuro) with two goals in mind.  First, it would represent an opportunity to introduce first year students to their more senior classmates, many of whom they have not yet had occasion to interact with.  Additionally, it would generate a greater sense of community amongst all students in the Neuroscience and MCB graduate programs.  We strongly believe that social interaction is an integral part of graduate student life.  Too often students become isolated within their own labs and we wished to provide a means to change this.  By encouraging our colleagues to engage each other outside of the academic forum their graduate student experiences, and by extension their scientific productivity, might be improved.  This interaction may also foster inter-lab collaborations and promote mentorship opportunities.

Nearly half of all enrolled graduate students in the MCB and Neuroscience programs were welcomed to this event where they enjoyed snacks, beverages and conversation.  It provided an opportunity for graduate students to breach the normal social barriers (e.g. working in different buildings) and to learn about the interests of and approaches taken by our classmates as they develop their young careers. One attendee commented “We really need to do this more often; this was a great idea!”  Based on the success of this event we hope to expand future gatherings to include post-doctoral fellows and other life science graduate students.  These inclusions might create additional mentorship opportunities and will broaden the perspectives of all participants.

We all stand to benefit from camaraderie within the Brandeis Life Sciences community, whether it be from the ease at which we can walk down the hall to borrow a reagent or by the simple pleasure of recognizing each other and exchanging a brief “hello” as we rush to our next experiment.  Thank you to all of the students who participated and otherwise contributed to the success of this inaugural event.

Filed Under: events, grad students Tagged With: , ,

Phosphatases and DNA double strand break repair

December 8, 2010 By

When cells suffer DNA damage – as little as a single break in one chromosome – they respond by activating the DNA damage checkpoint, which prevents cells from entering mitosis until there is enough time to to repair the damage.  The principal biochemical events in the checkpoint pathway are the phosphorylations of protein kinases by other protein kinases and eventually the phosphorylation of other proteins that regulate mitosis.    When repair is complete, the checkpoint must be turned off.  Not surprisingly, the enzymes that turn off the checkpoint are phosphatases that can remove the phosphates added by the protein kinases.

The Haber lab has previously shown that, in budding yeast, a pair of PP2C phosphatases known as Ptc2 and Ptc3 were important in turning off a key protein kinase, Rad53.  A member of another phosphatase subgroup, the PP4 phosphatase Pph3, dephosphorylates a target of the checkpoint kinases, histone protein H2A.  There is one aspect that they didn’t understand at all: It seems that the intensity of the checkpoint signals must grow the longer it takes to repair DNA damage, because deletions of ptc2 and ptc3 or a deletion of pph3 prevented cells from turning off the damage signal when it took a long time – 6 hours – to repair the damage, but they had much less effect on different repair events that could complete in 3-4 hours or in less than 2 hours.  So they decided to see what would happen if they created a yeast strain lacking all three phosphatases (ptc2 ptc3 pph3), leading to a paper appearing this month in the journal Molecular and Cell Biology.

To their surprise, these cells had a new defect: they couldn’t complete the repair event itself, rather than simply being defective in resuming mitosis after repair was completed.  The mutants could not properly initiate the small amounts of DNA copying that are required for repair.  Again, the severity of the defect depends on the length of the delay it takes to initiate the repair event itself.  The figure (right) shows that the triple mutant is also much more sensitive to DNA damaging agents such as the anti-cancer drug camptothecin (CPT) and to methylmethansulfonate (MMS). These data show a complex connection between DNA damage signaling and the repair process itself, and reveal new roles for the phosphatases in DNA repair.  The work was carried out primarily by graduate student Jung-Ae Kim, now a postdoc at Rockefeller University, with help by another grad student, Wade Hicks, and by an undergraduate Sue Yen Tay, and postdoc Jin Li. The work was supported by a research and a graduate student training grant from the NIH.

Filed Under: Biology, grad students, labs Tagged With: , , , , , , , ,

BOLLI Bioethics & Law Course

November 30, 2010 By

In a country where baby boomers comprise 26.1% of the population, a commitment to lifelong learning has never been more important – both for the education of a large constituency of voters, and for the health of our nation. Adult learning has been shown to offer protective features against many diseases of aging and has recently become a priority for progressive academic institutions, such as Brandeis University.

At BOLLI (Brandeis Osher Lifelong Learning Initiative), adult learning is therefore a high priority. During interactive and informative classes, both historical and current issues are studied and debated. The program began in 2000, created to meet the “still unfulfilled demand for educational and intellectual stimulation for adults who are beyond the traditional university years.” In 2004, this Brandeis Adult Learning Institute (BALI) developed into the BOLLI program, “one of 122 Osher Lifelong Learning Institutes throughout the nation, offers a broad range of noncredit educational activities for retired, semi-retired and other adult participants. The program emphasizes peer leadership, individual and group participation and research, and an atmosphere of sociability and mutual encouragement.” [2]

This fall, a Bioethics & Law course is being co-taught by Charles Baron, Professor Emeritus of Boston College Law School, and by Milton Heifetz, a retired world-renowned neurosurgeon. Two Brandeis graduate students: Marilana Rufo, a Masters of Philosophy candidate, and Danna Zeiger, a Molecular and Cell Biology PhD Candidate, have enjoyed the opportunity to participate as BOLLI scholars in this Bioethics & Law course. The students of the class range from established lawyers to retired teachers and through a wide variety of ages and experiences. Each class elicits constant fervor over heated debates of scientific topics such as the bioethics of organ transplantation, human experimentation, and genetics and the law. In the genetics and law class, led by Danna Zeiger, the discussion was focused specifically on embryonic stem cell and embryo selection. Both of these controversial issues have been recently relevant in legal contexts, such as in the court-mandated freeze on stem cell research. Interesting legal issues, such as the restrictions of defects in embryos selected for preimplantation genetic diagnosis (PGD), the range of genetic defects known, and defects which are culturally controversial, such as deafness, were discussed and such legal cases were studied and debated. These issues are often hard for lay-voters to decipher and the BOLLI program affords the opportunity for adults from the community to learn about and discuss these often-jargon-filled but interesting controversies. To learn more or to become involved in the BOLLI program, see http://www.brandeis.edu/bolli/.

Filed Under: Biology, grad students, teaching Tagged With: , , ,

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