Publications: A model of tadpole brain detects impeding collisions

In the paper published in “Frontiers Neural Circuits”, Bard professor Arseny Khakhalin shows that a realistic artificial neural network, modeled after tadpole brain, can detect impeding collisions.  In this study the network was not specifically designed or tuned for any particular task, but rather it was made to incorporate as much information about the tuning of actual neurons in real biological tadpole tecta as possible. After this realistic model was created, the team studied its properties in ways that would be hard to do in a real tadpole, and found that the network is uniquely suited to solve one of the key problems animals are facing: it naturally detects looming stimuli, and can help spatial navigation and predator detection.

Citation: Jang, E. V., Ramirez-Vizcarrondo, C., Aizenman, C. D., & Khakhalin, A. S. (2016). Emergence of selectivity to looming stimuli in a spiking network model of the optic tectum. Frontiers in Neural Circuits, 10.

Full text link: http://journal.frontiersin.org/article/10.3389/fncir.2016.00095/full

Publications: No effect of transformation on the evolution of phage resistance

In this paper, professor Gabriel Perron and the team tested a particular hypothesis about the mechanisms of bacterial evolution, and found that the data did not support this hypothesis. It is a really nice example of a publication that faithfully presents important negative results, when an attractive, logical, and perfectly plausible hypothesis has to be rejected based on experimental evidence.

Citation: McLeman, A., Sierocinski, P., Hesse, E., Buckling, A., Perron, G., Hülter, N., … & Vos, M. (2016). No effect of natural transformation on the evolution of resistance to bacteriophages in the Acinetobacter baylyi model system. Scientific Reports, 6.

Link to full text: http://www.nature.com/articles/srep37144

Featured student project: Shailab Shrestha

Shailab Shrestha studied how bacteria develop resistance against antimicrobial agents, such as antimicrobial peptides. Together with prof. Gabriel Perron, Shailab sequenced genomes of several experimentally evolved Pseudomonas fluorescens populations resistant to high concentrations of a certain synthetically modified antimicrobial peptide named pexiganan, and compared these genomes to each other. The results of his original studies were not quite clear due to possible  contamination, but Shailab followed up on them during BSRI 2016, and the project has high chances of being eventually published as research paper.

 

Featured student project: Katherine Moccia

In her senior project, Katherine Moccia  studied potential effects hydraulic fracturing (aka fracking) can have on microbial communities in streams near fracking sites. Under supervision of prof. Brooke Jude, Katherine tried to understand whether the presence of bacteria that produce purple pigments, such as species of Janthinobacterium, can be used as an indicator for the overall “health” of a natural water stream. She used microbial isolates from a local creek, and added a commonly used hydraulic fracturing material called glutaraldehyde to simulated microbial communities, to quantify the effects glutaraldehyde would have on the number of purple colonies. The results of this project were not quite clear, but are promising methodologically.

The Science Literacy website has launched!

What should all students know about science by the time they graduate from college? A great deal of attention has been paid to the training of future scientists, but the education of students who will not pursue the study of science is an equally important challenge. These students might take just a single science course in college. What do we as a society think they should know or be able to do?

The “Science Literacy Project” was supported by a generous grant to Bard College from the Howard Hughes Medical Institute. Our goal was to develop and implement a plan for science literacy for undergraduates.

Read more on the project web site:
http://scienceliteracy.bard.edu/

Biology Seminar: Fall 2016

The bio seminars happen every Thursday at noon, in RKC 103 (large auditorium). The list of speakers and talks this semester:

  • 1-Sep; Information session
  • 8-Sep: Alexandra Bettina; Univesity of Virginia. Macrophage-colony stimulating factor promotes the survival of mononuclear phagocytes and controls secondary liver damage during Klebsiella pneumonia
  • 15-Sep: Peter Lipke; CUNY Brooklyn. Using the Force with Amyloids for Good and Evil: Ale, Biofilms, Commensalism, and Disease
  • 22-Sep: Chris Solomon; Cary Institute. Why We Turned a Lake Brown and What We Learned
  • 29-Sep: Jozsef Meszaros; Columbia. Two Diverging Roads Differing in Risk and Reward
  • 6-Oct: Paul Turner; Yale. Virus Adaptation (or not) to Environmental Change
  • 13-Oct: Arseny Khakhalin, Bard
  • 20-Oct: Petko Bogdanov; SUNY Albany. Mining processes in biological networks
  • 27-Oct: Ayse Aydemir; BHSEC Manhattan. Remodeling Under Pressure: Bone cell differentiation in response to mechanical stimulation
  • 3-Nov: Heather Bennett; Philadelphia Children’s Hospital. Using C. elegans to Investigate How Animals Survive in Low Oxygen Conditions
  • 10-Nov: Wendy E. Nack-Lawlor; Taconic Biosciences. Title to be confirmed (industry, biotechnology)
  • 17-Nov: Ludmilla Aristilde; Cornell. Using Molecular Biology Tools to Understand Molecular Environmental Chemistry: My Interdisciplinary Journey in Academia
  • 24-Nov: Thanksgiving, no seminar
  • 1-Dec: Annalisa Scimemi; SUNY Albany. A novel role for astrocytes in hemorrhagic brain stroke
  • 8-Dec: Student talks

Featured student project: Theo Black

Many aquatic insects use polarized light to find water surfaces on which they reproduce, and where their larvae live and grow.  Manmade objects and structures can sometimes mimic these water surfaces by polarizing light. Moreover, in some cases they can be more attractive to aquatic insects than water itself. This effect causes “ecological traps” that can lead aquatic insects to population decline or even extinction.

Previous studies have shown that the attractiveness of polarizing synthetic surfaces can be reduced if grids of non-polarizing lines are strategically placed on them. In his senior project, Theodore Black measured the effect of line thickness on the attractiveness of polarizing non-water surfaces. Early in the morning he would install his polarizing traps near the water stream, and late at night he would collect them. Then, for days and days, he would sort and identify insects trapped in oil under the microscope, classifying them into such poetically named groups as non-biting midges (Chironomidae), black flies (Simulliidea), caddisflies (Trichoptera), and mayflies (Ephemeroptera). This work allowed Theo to analyze and describe the effect of non-polarizing line thickness on the attractiveness of traps, which will help to protect aquatic insects from human interference. Using this new information, engineers will be able to design solar panels that are efficient, yet don’t trick aquatic insects into laying eggs on it, helping them to avoid an evolutionary trap.

The Tick Project: a Large-Scale Study Aimed at Reducing Ticks and Lyme Disease

The Steven & Alexandra Cohen Foundation has awarded a $5 million dollar leadership grant to support a scientific study that seeks to reduce Lyme disease in neighborhoods. If successful, the project will revolutionize Lyme disease prevention.

Bard College biologist Felicia Keesing and Cary Institute disease ecologist Richard Ostfeld will direct the scientifically rigorous five-year study. It will take place in Dutchess County, New York, which is home to one of the nation’s highest Lyme disease infection rates. Residents of 24 neighborhoods will be recruited from Lyme disease hotspots identified by the researchers and their partners at the Dutchess County Department of Health.

Link to the project web-page:
http://www.tickproject.org/

Full press-release from Bard.