Odor Recognition & Brute-Force Conversions

Frontiers in Computational Neuroscience will be publishing an interesting paper written by Honi Sanders and John Lisman (with co-authors Brian E. Kolterman, Roman Shusterman, Dmitry Rinberg, Alexei Koulakov) titled, “A network that performs brute-force conversion of a temporal sequence to a spatial pattern: relevance to odor recognition“. Honi Sanders has written a preview of this paper.

by Honi Sanders

Lisman_ProvisionalPDF_BLThere are many occasions in which the brain needs to process information that is provided in a sequence. These sequences may be externally generated or internally generated. For example, in the case of understanding speech, where words that come later may affect the meaning of words that come earlier, the brain must somehow store the sentence it is receiving long enough to process the sentence as a whole. On the other hand, sequences of information also are passed from one brain area to another.  In these cases too the brain must store the sequence it is receiving long enough to process the message as a whole.

One such sequence is generated by the olfactory bulb, which is the second stage of processing of the sense of smell.  While individual cells in the olfactory bulb will fire bursts in response to many odors, the order in which they fire is specific to an individual odor. How such a sequence can be recognized as a specific odor remains unclear.  In Sanders et al, we present experimental evidence that the sequence is discrete and therefore contains a relatively small number of sequential elements; each element is represented in a given cycle of the gamma frequency oscillations that occur during a sniff. This raises the possibility of a “brute force” solution for converting the sequence into a spatial pattern of the sort that could be recognized by standard “attractor” neural networks.  We present computer simulations of model networks that have modules; each model can produce a persistent snapshot of what occurs during a given gamma cycle. In this way, the unique properties of the sequence can be determined at the end of sniff by the spatial pattern of cell firing in all modules.

The authors thank Brandeis University High Performance Computing Cluster for cluster time. This work was supported by the NSF Collaborative Research in Computational Neuroscience, NSF IGERT, and the Howard Hughes Medical Institute.

Genetics Training Grant Retreat to be held Friday, 9/26/14

The annual Genetics Training Grant seminar is being held on Friday, September 26th at the Shapiro Campus Center Auditorium at Brandeis University. Four cutting-edge synthetic biologists: Timothy Lu, Ron Weiss, William Shih and Ahmad Khalil will share their research for the Synthetic Biology: Insights and Applications” symposium.
Brandeis graduate students and post-docs will have the opportunity to meet the speakers and present their work in a poster session after the talks. We encourage researchers from all departments to contribute. If you are currently, or previously were on the Genetics Training Grant, presentation of a poster is expected. 

Schedule for GTG Retreat

9:30-10:30 Ron Weiss (MIT, Dept. of Biological Engineering)
“Synthetic biology: from parts to modules to therapeutic systems.”
10:30-11:00 Coffee Break
11:00-12:00 Timothy Lu (MIT, Dept. of Biology Engineering)
“Synthetic biology for human health applications.”
12:00-1:30 Break/Lunch
1:30-2:30 William Shih (Wyss Institute)
“DNA nanostructures as building blocks for molecular biophysics and future therapeutics.”
2:30-3:30 Ahmad Khalil (Boston University, Biomedical Engineering)
“Building molecular assemblies to control the flow of biological information.”
3:30-5:00 Poster session
Shapiro Science Center 2nd floor.
All life sciences students are invited to present.

John Wardle Named Division of Science Head

John Wardle, Division of ScienceSusan Birren, Dean of Arts and Sciences, has announced that John Wardle, Professor of Physics, will be the new Head of the Division of Science.

The following is Susan’s email:

“I am pleased to announce that John Wardle will be the new Head of the Division of Science.  John is an astrophysicist and Professor of Physics and is a former chair of the Physics department.  In his new role he will oversee science-wide programs and initiatives, including the summer undergraduate research program and will work with Division of Science faculty and staff to identify new directions for the division.  I am delighted that he has agreed to take on this role and I hope that you will join with me in welcoming him.

We all owe a debt of gratitude to Eve Marder who, as the first Head of the Division, created and steered many of the priorities of the Division.  During her time as Head, Eve ably represented the Sciences at Brandeis and beyond, worked to make the Summer Undergraduate Science Program a flourishing success, changed the way we trained students and postdocs in the ethical conduct of research, and worked tirelessly to secure funding and recognition for the Sciences.  Thank you Eve!”

Gina Turrigiano Named One of the “30 Most Influential Neuroscientists Alive Today”

Gina Tturrigiano405urrigiano has been named one of the “30 Most Influential Neuroscientists Alive Today” by the Online Psychology Degree Guide.

The guidelines for selecting the neuroscientists include: leadership, applicability (neuroscientists that have created technologies that have improved people’s lives); awards & recognition by the international science community and other notable accomplishments such as personal or educational achievements.

Gina Turrigiano is the author of numerous papers, has been awarded a MacArthur Foundation fellowship and the HFSP Nakasone Award, and in 2013 was elected to the National Academy of Sciences.

Men, Women and Emotional Stress Responses

Psychoneuroendocrinology (November 2014) is publishing a fascinating paper authored by Sarah Lupis, Michelle Lerman and Jutta Wolf titled Anger responses to psychosocial stress predict heart rate and cortisol stress responses in men but not women.

473People can experience a wide range of emotions when under stress, including feelings of anger and fear. In recent years researchers have sought to understand how these emotion stress responses are linked to biological stress responses. In particular, some evidence suggests that anger and fear may be linked to cardiovascular changes in differential ways. It is less clear, however, how emotions during stress may predict increases in levels of the stress hormone cortisol. These deficits in our understanding are partly due to the methodological difficulties in measuring emotion in the context of stress. Much prior research has relied solely on retrospective self-report (after the stress has passed, a questionnaire asks a study participant to reflect on how he felt in the moment of stress). By this time, the participant may have forgotten how he felt, or may already be utilizing coping strategies to process those emotions. In addition, he may not feel comfortable reporting how the stressor made him feel, leading to less-than-honest responses. Unsurprisingly, prior research has not shown consistent links between these self-report measures and biological stress responses. In the current study, we therefore added facial coding of emotion expression to assess emotions occurring during stress. Our aim was to determine how expressions of anger and fear were linked to heart rate and cortisol stress responses.

We recruited 32 healthy Brandeis students and exposed them to a brief psychosocial stressor. A certified coder assessed facial expressions shown during the stressful situation. Heart rate and cortisol levels were measured throughout. After the stressor, the participants also self-reported how they felt during the stressor. A first notable finding showed that what participants self-reported feeling and the expressions they actually showed did not correlate. With regards to self-report, men who reported feeling fear showed blunted cortisol stress responses. Consistent with prior research, self-report was otherwise not associated with heart rate or cortisol stress responses. When looking at facial expressions, a consistent pattern appeared: men who showed more anger during the stressful situation also showed exaggerated heart rate and cortisol stress responses. For women, neither anger nor fear were linked to biological stress responses (see Figure).

Our findings first emphasize the importance of assessing emotion using multiple means. In this case, facial expressions revealed an emotion-stress link for males that would not be apparent using self-report alone. Facial coding may thus be a useful addition to current stress paradigms. Further, if men who react with anger in stressful situations do respond with exaggerated stress responses, it could have important down-stream health effects. Exaggerated, prolonged, or dysfunctional stress responses could, over time, lead to changes in basal stress systems. This kind of ‘allostatic load’ is associated with negative health outcomes including diabetes and cardiovascular disease. Anger and fear do not seem to drive these responses in females, and further study is needed to determine if similar relationships exist for a different set of emotions, perhaps self-conscious emotions like shame. By better understanding these relationships, more healthful ways of coping with stress can be developed, which is particularly important given that for many, stress has become an unavoidable part of daily life.


Chromosome Tethering in Yeast

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.

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