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Research Funding For Undergrads: MRSEC Summer Materials Undergraduate Research Fellowships

January 30, 2017 By

The Division of Science wishes to announce that, in 2017, we will offer seven MRSEC Summer  Materials Undergraduate Research Fellowships (SMURF) for Brandeis students doing undergraduate research, sponsored by the Brandeis Materials Research Science and Engineering Center.

The fellowship winners will receive $5,000 stipends (housing support is not included) to engage in an intensive and rewarding research and development program that consists of full-time research in a MRSEC lab, weekly activities (~1-2 hours/week) organized by the MRSEC Director of Education, and participation in SciFest VII on Aug 3, 2017.

The due date for applications is February 27, 2017, at 6:00 PM EST.

To apply, the application form is online and part of the Unified Application: https://goo.gl/9LcSpG (Brandeis login required).


Eligibility
Students are eligible if they will be rising Brandeis sophomores, juniors, or seniors in Summer 2017 (classes of ’18, ’19, and ’20). No prior lab experience is required. A commitment from a Brandeis MRSEC member to serve as your mentor in Summer 2017 is required though. The MRSEC faculty list is: http://www.brandeis.edu/mrsec/people/index.html

Conflicting Commitments
SMURF recipients are expected to be available to do full time laboratory research between May 30 – August 4, 2017. During that period, SMURF students are not allowed to take summer courses, work another job or participate in extensive volunteer/shadowing experiences in which they commit to being out of the lab for a significant amount of time during the summer. Additionally, students should not be paid for doing lab research during this period from other funding sources.

Application Resources
Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQ may be addressed to Steven Karel <divsci at brandeis.edu>.

Filed Under: awards, Biochemistry, Biology, chemistry, labs, Physics, Undergrads Tagged With: , , , , , , , , , , , , , , , , , , ,

Mitosis: One Polo controls it all

November 17, 2014 By

On November 6, 2014, Cell Cycle published a paper from the Yoshida lab entitled “The budding yeast Polo-like kinase Cdc5 is released from the nucleus in anaphase for timely mitotic exit.” This study was authored by Vladimir V. Botchkarev Jr., Valentina Rossio, and Satoshi Yoshida.

The cell cycle is one of the most fundamental biological processes whose ultimate goal is cell division with equal content of DNA in both daughter cells. The process of cell division is regulated by many intracellular events which must occur in a sequential order. These events include mitotic entry, faithful chromosome segregation, mitotic exit, and cytokinesis. Over the past 25 years, the Polo-like kinase (Polo) has been established to play important regulatory roles in each of these processes. Although many mitotic substrates of Polo have been discovered, the mechanism by which Polo can coordinate all of these mitotic events has remained largely elusive.

To understand the mechanism by which Polo can target its many substrates in a sequential order during mitosis, we decided to study the budding yeast Polo kinase Cdc5, which has high conservation with the human Polo-like kinase 1.

We found that Cdc5-GFP dynamically changes its localization during the cell cycle: Cdc5 is found in the cytoplasm in S- through early G2-phase, it accumulates in the nucleus at metaphase, and is released again to the cytoplasm in anaphase. Blocking nuclear import of Cdc5 in metaphase leads to a prolonged metaphase duration, suggesting that nuclear Cdc5 is required for chromosome segregation. In contrast, blocking nuclear release of Cdc5 in anaphase results in a prolonged anaphase duration, a defect in activation of the cytoplasmic Mitotic Exit Network, and a defect in cytokinesis. This indicates that Cdc5 is released from the nucleus to the cytoplasm in anaphase for timely mitotic exit and cytokinesis. We further found that activation of the Cdc14 phosphatase, a known nuclear substrate of Cdc5, is required for Cdc5 nuclear release in anaphase.

Collectively, our work reveals that the budding yeast Polo-like kinase Cdc5 controls the timing of mitotic events by dynamically changing its sub-cellular localization. Furthermore, our data suggests the existence of a positive feedback look between Cdc5 and Cdc14 to regulate timely mitotic exit. Read more …

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

Chromosome Tethering in Yeast

August 26, 2014 By

On July 14, 2014, PLOS ONE  published a paper from the Haber and Kondev labs. The paper, Effect of chromosome tethering on nuclear organization in yeast, was authored by Baris Avsaroglu, Gabriel Bronk, Susannah Gordon-Messer, Jungoh Ham, Debra A. Bressan, James E. Haber, and Jane Kondev.

by Baris Avsaroglu

Chromosopone.0102474_350mes are folded into the cell nucleus in a non-random fashion. In yeast cells the Rabl model is used to describe the folded state of interphase chromosomes in terms of tethering interactions of the centromeres and the telomeres with the nuclear periphery. By combining theory and experiments, we assess the importance of chromosome tethering in determining the spatial location of genes within the interphase yeast nucleus. Using a well-established polymer model of yeast chromosomes to compute the spatial distributions of several genetic loci, we demonstrate that telomere tethering strongly affects the positioning of genes within the first 10 kb of the telomere. Further increasing the distance of the gene from the telomere reduces the effect of the attachment at the nuclear envelope exponentially fast with a characteristic distance of 20 kb. We test these predictions experimentally using fluorescently labeled genetic loci on chromosome III in wild type and in two mutant yeast strains with altered tethering interactions. For all the cases examined we find good agreement between theory and experiment. This study provides a quantitative test of the polymer model of yeast chromosomes, which can be used to predict long-ranged interactions between genetic loci relevant in transcription regulation and DNA recombination.

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

Patching Up Broken Chromosomes

August 12, 2014 By

Olga Tsaponina and James Haber’s recent paper “Frequent Interchromosomal Template Switches during Gene Conversion in S. cerevisiae” was published online by Molecular Cell on July 24, 2014.

by James Haber

“The process of copying DNA every time our cells divide is exceptionally accurate, but in copying 6,000,000,000 base pairs of the genome mistakes do occur, including both mutations and the formation of chromosome breaks. These breaks must be repaired to maintain the integrity of our chromosomes.  In our recent paper we have demonstrated that the mechanism of patching up a broken chromosome is associated with a surprisingly high level of alterations of the sequence.  Many of these changes result from “slippage” of the DNA polymerases copying the DNA during the repair process; for example in copying a sequence of 4 Gs, the polymerase occasionally jumps over one, to lose a base from the sequence (a frameshift mutation).

graphical_abstract_350In this paper we focused on more dramatic slippage events in which the copying machinery jumped from one chromosome to a related but divergent sequence on another chromosome and then jumped back, creating a chimeric sequence.  These interchromosomal template switches (ICTS) occur at a low rate when the distant sequence is only 71% identical, but if we make that segment 100% identical we could find such jumps 10,000 times more frequently, in about 1 in 300 events.  This result reveals how unstable the copying machinery in DNA repair is compared to normal DNA replication. This was very surprising and provides an explanation for many complex rearrangements associated with cancers.  In carrying out this work we identified the first protein that is needed to permit these frequent jumps: a chromatin remodeling enzyme known as Rdh54 that previously did not have a well-defined role in DNA repair in somatic cells.

Finally, we learned a new role for the proteins that survey the genome for mismatched bases that arise during replication and found that one of these proteins, Msh6, is required to specify which strand of DNA containing a mismatch is the “good one” that should be used as the template to correct the mismatch.

This work was supported by the National Institutes of Health General Medical Institute”.

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

Eapen wins HHMI International Student Research Fellowship

August 15, 2013 By

Vinay Eapen from the Haber Lab in Biology has been awarded an HHMI International Student Research Fellowship. These fellowships, highly sought-after, are among the few available to international students studying at major research universities in the US – there were only 42 recipients nationwide. Eapen is a graduate student entering his fourth year in the Molecular and Cell Biology PhD program at Brandeis, and already has 4 publications from Brandeis to his credit resulting from his studies of the DNA damage checkpoint and autophagy in yeast.

 

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

Rosenstiel Award 2012- Dr. Steven J. Elledge

March 13, 2013 By

The 2012 Rosenstiel award is being awarded to Dr. Steven J. Elledge of Harvard University and the Howard Hughes Medical Institute for his seminal contributions towards understanding the eukaryotic DNA damage response[1] [2] .
Cells are constantly challenged by damage to their DNA. It of no surprise therefore, that both prokaryotic and eukaryotic cells have evolved sophisticated and remarkably complex responses to deal with damaged DNA. It is for elucidating these mechanisms that Dr. Elledge is being honored with the Rosenstiel award this year.
Dr. Elledge’s interest with the DNA damage response began as a graduate student at MIT in the laboratory of Graham Walker, where he identified and cloned genes involved in DNA repair mechanism known as the SOS reponse in the bacterium E.coli[3, 4] . It was during this time that Dr. Elledge also invented an extremely useful molecular biology tool known as ‘phasmids’ which allowed for the ability to rapidly clone E.coli genes by packaging them in phages[5].
After MIT, Dr Elledge began his postdoctoral work at Stanford University where he discovered the Ribonucleotide reductase(RNR) genes in budding yeast[6, 7]. These genes are induced following DNA damage to promote the synthesis of deoxyribonucleotides which helps facilitate DNA repair. Dr. Elledge followed up on this work as a professor at Baylor University by a series of important papers that shed light on how cells arrest division after DNA damage. Most notably in 1994, his group identified the Rad53 checkpoint kinase that is activated after DNA damage and contributes to cell cycle arrest [8]. In 1998, his group also identified the mammalian homolog of Rad53 (Chk2) [9, 10].In 1999, the Elledge group reported that the DNA damage checkpoint in yeast occurs in two parallel pathways laying the foundation of our understanding of the DNA damage checkpoint[11]. More recently, work from the Elledge lab identified novel factors in the DNA damage response by performing a siRNA screen in mammalian cells[12].
Dr Steve Elledge has been an investigator of the Howard Hughes Medical Institute since 1993. In 2003 he moved to Harvard Medical School as Professor in the Departments of Genetics and as a Geneticist in the Department of Medicine, Brigham and Women’s Hospital. Dr. Elledge was elected in 2003 to both the U.S. National Academy of Sciences and the American Academy of Arts and Sciences. In addition to the Rosenstiel award, he has received the DAMD Breast Cancer Innovator Award (2003), the National Academy of Sciences Award in Molecular Biology (2002), the John B. Carter, Jr. Technology Innovation Award (2002), and the Paul Marks Prize for Cancer Research (2001[2]).

Editor’s Note: On Mar 20, 2013, Elledge was named to receive a 2013 Canada Gairdner International Award.

1. Brownlee, C., Biography of Stephen J. Elledge. Proc Natl Acad Sci U S A, 2004. 101(10): p. 3336-7.
2. Haber, J.E., The 2005 Genetics Society of America Medal. Steven J. Elledge. Genetics, 2005. 169(2): p. 506-7.
3. Elledge, S.J. and G.C. Walker, Proteins required for ultraviolet light and chemical mutagenesis. Identification of the products of the umuC locus of Escherichia coli. J Mol Biol, 1983. 164(2): p. 175-92.
4. Elledge, S.J. and G.C. Walker, The muc genes of pKM101 are induced by DNA damage. J Bacteriol, 1983. 155(3): p. 1306-15.
5. Elledge, S.J. and G.C. Walker, Phasmid vectors for identification of genes by complementation of Escherichia coli mutants. J Bacteriol, 1985. 162(2): p. 777-83.
6. Elledge, S.J. and R.W. Davis, Identification of the DNA damage-responsive element of RNR2 and evidence that four distinct cellular factors bind it. Mol Cell Biol, 1989. 9(12): p. 5373-86.
7. Elledge, S.J. and R.W. Davis, DNA damage induction of ribonucleotide reductase. Mol Cell Biol, 1989. 9(11): p. 4932-40.
8. Allen, J.B., et al., The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast. Genes Dev, 1994. 8(20): p. 2401-15.
9. Hirao, A., et al., DNA damage-induced activation of p53 by the checkpoint kinase Chk2. Science, 2000. 287(5459): p. 1824-7.
10. Matsuoka, S., M. Huang, and S.J. Elledge, Linkage of ATM to cell cycle regulation by the Chk2 protein kinase. Science, 1998. 282(5395): p. 1893-7.
11. Sanchez, Y., et al., Control of the DNA damage checkpoint by chk1 and rad53 protein kinases through distinct mechanisms. Science, 1999. 286(5442): p. 1166-71.
12. Adamson, B., et al., A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol, 2012. 14(3): p. 318-28.

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