All posts by khakhalin

Biology Seminar: Spring 2017

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

  • 2-Feb: Information session
  • 9-Feb: Cancelled because of a snowstorm
  • 16-Feb: Emma Rosi; Cary Institute; Our Rivers on Drugs
  • 23-Feb: Kirk Haltaufderhyde; University of RI; Characterization of Human T cell Response to Dengue
  • 2-Mar: Paolo Forni; SUNY Albany; Terminal differentiation of vomeronasal sensory neurons and GnRH-1 neuronal migration, from new models to new stories
  • 9-Mar: Jordan Ruybal; U Scranton; The influence of climate change and evolution on mosquito life history traits and pathogen transmission
  • 16-Mar: Cathy Collins, on the ecology of plant-fungal interactions
  • 23-Mar: Spring Recess
  • 30-Mar: Sarita Lagalwar; Skidmore; Ataxin1-pS776: Single site phosphorylation and its impact on neurodegenerative disease
  • 6-Apr: Chris Elphick; U Connecticut; Canaries in the saltmarsh: tidal marsh conservation in the face of sea level rise
  • 13-Apr: Allison Appleton; SUNY Albany; Psychosocial adversity: the epigenetic origins of health disparities
  • 20-Apr: Sarah Bowden; Cary Institute; The ecology of West Nile virus in the United States
  • 27-Apr: Charvann Bailey; Vassar; Molecular mechanisms of SLUG-induced chemotherapeutic resistance in triple-negative breast cancer (TNBC)
  • 4-May: Alexander Petroff; Rockefeller; tbc (mathematical dynamics of microbial cooperation)
  • 11-May: Michelle Hersh; Sarah Lawrence; tbc (ecology of fungal-plant interactions)
  • 18-May: Student talks

Illustration: Scholars at an Abbasid library, House of Wisdom, Baghdad. A miniature by Yahyá al-Wasiti, 1237, from the Maqamat of al-Hariri manuscript.

Publications: Ecology of Sacred Groves

For centuries followers of the Ethiopian Orthodox Church have conserved patches of native trees around church buildings as sacred sanctuaries for church communities. Today there are as many as 20 000 church forests in northern Ethiopia’s Amhara Peoples National Regional State – these unique social-ecological systems offer an opportunity to study multiple natural forest patches across a large multipurpose landscape, including in many places where little or no other natural forest remains. This image is a satellite photo of Robit Bata church, located 15 km north of the city of Bahir Dar, and three km upstream of Lake Tana (the largest lake in Ethiopia). The natural forest at Robit Bata church hosts some of the only mature indigenous trees in the local landscape. In her recent paper, Bard professor Cathy Collins and colleagues illustrate how understanding patterns in the tree species composition of church forests requires consideration of the complex interplay between ecological gradients and anthropogenic influences over time. This publication also made a cover page of the January issue of “Ecography” journal.

Citation: Reynolds, T. W., Collins, C. D., Wassie, A., Liang, J., Briggs, W., Lowman, M., … & Adamu, E. (2017). Sacred natural sites as mensurative fragmentation experiments in long‐inhabited multifunctional landscapes. Ecography, 40(1), 144-157.

Featured student project: Martie Stothoff

For her senior project Martie studied the behavioural response in captive common marmosets (Callithrix jacchus – the second smallest primate in the world) to the introduction of a novel foraging-enrichment device. In captivity, animals often become bored, depressed, or stressed, and enrichment is a way in which caretakers can improve the lives of captive animals. Compared to many other animals, monkeys are very smart, and therefore need even more stimulation to keep them physically and psychologically active. Knowing how to keep animals happy and healthy in captivity is a highly important aspect of conservation biology.

In the wild, marmosets don’t just collect fruits and insects like many other monkeys do, but gouge trees with their teeth and suck out the sap. In captivity however, most monkeys are fed fruits and vegetables from stationary bowls, which provides enough nutrition, but gives no practice in natural ways foraging, and makes the marmosets lose their ability to gouge trees. With the help of Bard professor Felicia Keesing, Martie designed a novel enrichment device for captive marmosets living in captivity in Costa Rica. The device was made of a small wooden log with holes drilled all around it, that Martie filled with honey and hang up vertically in the cages. This study was the first ever to try honey as a sap substitute for common marmosets, and Marite found that this simple device increased positive foraging behaviours and decreased inactivity, significantly improving the well-being of captive monkeys.

Publications: Solar panels and aquatic insects

Professor Bruce Robertson had two new publications in the fall 2016: one review on the theory of evolutionary traps, and an experimental study, in which he and his colleagues from Hungary looked at the polarizing properties of solar panels, and the effects this light polarization may have on the life cycle of aquatic insects. This line work was since continued by Bard students, and will undoubtedly bring more senior projects next year.

Citations:

Száz, D., Mihályi, D., Farkas, A., Egri, Á., Barta, A., Kriska, G., … & Horváth, G. (2016). Polarized light pollution of matte solar panels: anti-reflective photovoltaics reduce polarized light pollution but benefit only some aquatic insects. Journal of Insect Conservation, 20(4), 663-675.

Robertson, B. A., & Chalfoun, A. D. (2016). Evolutionary traps as keys to understanding behavioral maladapation. Current Opinion in Behavioral Sciences, 12, 12-17.

Self-published books teach schoolchildren about biology

Last fall, students in the non-major level Conservation Biology class, taught by professor Cathy Collins, researched and wrote children’s books about the ecology and conservation of Hudson Valley ecosystems. They first consulted with first- and second-graders in October to find out what they knew, and worked in groups to write and illustrate books. In December, 2016 Bard students visited the JFK Elementary school in Kingston again, this time to read their stories to the children. They then donated their books to each classroom, and a story to each child.

This project was supported by the Center for Civic Engagement at Bard.

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/