Mei Zeng Receives Genome Customization Award

Mei Zeng, a postdoc in Nelson Lau’s lab (Biology) has been selected to receive a postdoctoral fellowship award – the Genome Customization Award (TGCA) from Cellectis Bioresearch. The TGCA award was established by Cellectis Bioresearch in 2010 with the goal of spreading the use of meganucleases for genome customization throughout the life sciences

Meganucleases are endodeoxyribonucleases characterized by a large recognition site (12 to 40 base pairs) — so large that it  generally only occurs once in any given genome. The Lau group will apply the custom meganucleases to improve transgenesis of Xenopus tropicalis for RNA interference methodologies. The most widely used transgenesis method utilizes the yeast meganucleases I-SceI which cuts both the transgene vector and an unknown site in the genome into which the transgene gets integrated. This method has several limitations: it requires a large number of embryos for injection and screening,  the integration sites cut by I-Sce-I are unknown and likely stochastic, and it ultimately produces only 5-10% of germline transmission. The custom meganucleases engineered by Cellectis Bioresearch target a known single site (24bp) within the genome, allowing for increased specificity and efficiency of transgene intergration. Mei and colleagues hope to use the rational design to enforce the systemic constitutive expression of a short hairpin RNA cassette in a vertebrate model.

Marc Le Bozec, CEO of Cellectis Bioresearch, presented the award to Drs. Nelson Lau and Mei Zeng on March 16, 2011 at the grand opening of Cellectis Bioresearch Inc facilities in Cambridge, Massachusetts.

NEUCS-2011

Brandeis is one of the co-organizers of the third annual New England Undergraduate Computing Symposium which will be held on Saturday April 9th at Tufts University. This symposium is designed to build community among undergraduate Computer Science majors in New England and also to increase the diversity of our undergraduate majors by actively reaching out to under-represented groups and encouraging them to participate. Students register online at https://sites.google.com/site/neucs11/ by completing a simple form describing the project they plan to demo or present as a poster. We expect to have 60-80 students projects and around 150 students and faculty attending the symposium. If you are an undergrad that has written an interesting mobile app, or completed a creative project in one of your classes, or are working in a research lab on an exciting problem involving computation, please visit the site and register to present your project and/or demo your code.

NEUCS2010

(EL)2 2011

(EL)2 2011. the Experiential Learning, Engaged Learners Symposium held each Spring at Brandeis, will take place on the afternoon of Thursday, March 24th, in the Levin Ballroom and International Lounge. Brandeis President Frederick M. Lawrence will be the keynote speaker. Student presenters include undergraduates from Biology, Chemistry, Mathematics, Neuroscience, Physics, Psychology, as well as a wide range of other disciplines across the university, will present results from research, internships, and other learning experiences.

For more information, see the symposium website or download the symposium program (PDF).

yet more papers in the wild

More papers appearing recently:

Current Brandeis authors noted in boldface, past Brandeis trainees shown in italics

Older Adults are Better at Spotting Fake Smiles

Studies of aging and the ability to recognize others’ emotional states tend to show that older adults are worse than younger adults at recognizing facial expressions of emotion, a pattern that parallels findings on non-social types of perception. Most of the previous research focused on the recognition of negative emotions such as anger and fear. In a study “Recognition of Posed and Spontaneous Dynamic Smiles in Young and Older Adults” recently published in Psychology and Aging, Derek Isaacowitz’s Emotion Laboratory set out to investigate possible aging effects in recognizing positive emotions; specifically, the ability to discriminate between posed or “fake” smiles and genuine smiles. They video-recorded different types of smiles (posed and genuine) from younger adults (mean age = 22) and older adults (mean age = 70). Then we showed those smiles to participants who judged whether the smiles were posed or genuine.

Across two studies, older adults were actually better at discriminating between posed and genuine smiles compared to younger adults. This is one of the only findings in the social perception literature suggesting an age difference favoring older individuals. One plausible reason why older adults may be better at distinguishing posed and spontaneous smiles is due to their greater experience in making these nuanced social judgments across the life span; this may then be a case where life experience can offset the effects of negative age-related change in cognition and perception.

This was the first known study to present younger and older adult videotaped smiles to both younger and older adult participants; using dynamic stimuli provides a more ecologically valid method of assessing social perception than using static pictures of faces. The findings are exciting because they suggest that while older adults may lose some ability to recognize the negative emotions of others, their ability to discriminate posed and genuine positive emotions may remain intact, or even improve.

The Emotion Laboratory is located in the Volen Center at Brandeis. First author Dr. Nora Murphy (now Assistant Professor of Psychology at Loyola Marymount University) conducted the research as a postdoctoral research fellow, under the supervision of Dr. Isaacowitz, and second author Jonathan Lehrfeld (Brandeis class of 2008) completed his Psychology senior honors thesis as part of the project. The research was funded by the National Institute of Aging.

Claude Desplan to speak in Bauer Distinguished Lecturer Series

Claude Desplan, Silver Professor and Professor of Biology at NYU, will visit Brandeis the week of March 21-25 as part of the M.R.Bauer Foundation Distinguished Lecturer Series. Desplan’s work focuses on developmental biology in insects, and is particularly concerned with pattern formation. A recent topic of interest is the development of the neural network that supports color vision in the optic lobe of the fruit fly.

Desplan will speak on Monday, March 21 at 4:00 pm in Gerstenzang 121. The title of his talk will be “Processing of Color Information in Drosophilia”. Desplan will speak again at Neurobiology Journal Club on March 22 at 12:05 pm in Gerstenzang 121.

According to a post at ratemyprofessors.com:

Desplan is the funniest, nicest guy ever. At first you may not be able to understand him too too easily due to his french accent but after a few days that’s not a problem. Desplan went pretty slow and went over concepts that people didn’t seem to understand. Even then he held very helpful review sessions. Great professor.

 

Fostering leaders into a new scientific generation

Brandeis SACNAS Chapter Symposium
Saturday, March 26, 2011
10:00 am-3:00 pm
Shapiro Science Campus lobby

On March 26th the Brandeis SACNAS chapter will be holding their 2nd Brandeis SACNAS Chapter Symposium 2011: Fostering leaders into a new scientific generation. This year, we hope to expand our circle of influence even farther as we look forward to hosting students and mentors from Brandeis and other institutions in the greater Boston Region. We want to create a forum for students to network and learn about the different pathways that the sciences have to offer.

This year we will have Dr. Daniel Colon-Ramos, Assistant Professor of Cell Biology at Yale University, talk about his journey from early undergraduate to PhD. Dr. Jim Morris from Brandeis will discuss his track towards earning his MD/PhD at Harvard Medical School. Lastly, we will also hear from our own chapter President Kerwin Vega, fourth year undergraduate, as he speaks of his first steps towards pursuing a career in science and his networking experiences thus far. We will also host a Career Development Panel where professionals from various scientific backgrounds will briefly speak of their personal professional anecdotes as well as answer any questions. There will also be a poster session for students to present their work.

See story in The Jusiice

Molecular mechanisms of noisy transcription

In a recently published paper “Effect of promoter architecture on the cell-to-cell variability in gene expression” in PLoS Computational Biology, Alvaro Sanchez and co-workers investigated how the architecture of a model promoter region (characterized by number of transcription factor binding sites, the binding affinity and spacing on the DNA) affects the way in which individual cells respond to environmental stimuli. In particular, they examine, using stochastic chemical kinetics, how the intrinsic randomness in the binding and unbinding of transcription factors to their binding sites generates cell-to-cell differences in transcript and protein levels within a population. The analysis uses a combination of computational modeling and analytical mathematical methods. Sanchez, a recent Ph.D. graduate in Biophysics and Structural Biology performed this work with Jané Kondev (Physics), and in collaboration with Rob Phillips, Hernan Garcia and Daniel Jones (Caltech).

While previous population-average models explained well how promoter architecture affects the average response of a population of cells to changes in the concentration of transcription factors, the question of how the response of individual cells is determined by promoter region sequence remains generally unsolved and limited to simplified coarse-grain models. By way of an example, the authors of this study investigated the effect of cooperative binding between transcription factors in the level of variability in the transcriptional response to increasing concentrations of those factors. It is well known that cooperativity in gene regulation increases the sensitivity of the response of the promoter to changes in the intracellular concentration of transcription factors, leading to a switch-like response. By examining this architecture, Sanchez and co-workers found that cooperativity is also a source of large intrinsic cell-to-cell variability in gene expression: larger sensitivity comes accompanied with larger variability (even if all cells contain the exact same amount of repressor).

This investigation continues a collaboration between theorists at Brandeis and experimentalists at Caltech, which aims to connect the biochemical, molecular understanding of transcriptional regulation coming from in vitro biochemical experiments (which are also being done in the Gelles lab at Brandeis) with the phenotypic behavior of individual cells as determined by gene expression measurements in single live cells. Many of the predictions of this computational study are currently being tested in Rob Phillips’ lab.

 

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