To minimize the impact of the Covid-19 pandemic, the faculty in the Bard Biology program are conducting classes remotely as of March 16, 2020. We are also running advising sessions by teleconference, and will handle moderations and senior projects remotely.
For those of you who have recently been admitted to begin studying at Bard in Fall 2020, congratulations! We know that this is a strange time, and that your decisions about college are especially challenging this year. We are happy to speak with you, to connect you with students, and to share some of our remote instruction if any of that would helpful to you in the coming weeks. We would love to have you join our community in the fall!
Please mail Biology Program chair, Felicia Keesing, at firstname.lastname@example.org to arrange a virtual visit, or contact any of us directly via email addresses on the Faculty and Staff page.
(Image sources: tapestry, style transform, virus)
Biology professor Felicia Keesing and her colleagues published a paper in Scientific Reports that describes a mathematical model that can be used to manage livestock on grazing lands around the world. While previous models to manage livestock grazing exist, they require a lot of data and those data are hard to collect, making the models less useful. Keesing’s team developed a model that requires very little data yet makes sophisticated predictions, including estimating how much grass would be left over to support wild grazers. The model successfully predicted grass abundance at the team’s field sites in Kenya.
Biology seminars are happening every Thursday, at 12 pm, in RKC 103 (the biggest auditorium, aka Bito auditorium)
The plan for this semester:
- 9/12 – Quanita Kendrick, ’17. In The Interim: Navigating the Field Post- Graduation
- 9/19 – Jeremy Kirchman, SUNY-Albany. The Evergreen archipelago: Ecology and Evolution of Birds at the Edge of the Boreal Forest
- 9/26 – Wyatt Shell, ’10, University of New Hampshire. Opportunities Beyond Undergrad: The Evolution of Research Potential
- 10/3 – Alexis Gambis, ’03. If Butterflies Could Speak!
- 10/10 – Michael Hood, Amherst College. Disease at the Edge of Species Distributions: Anther-smut Fungi of Wild Carnations
- 10/17 – Sonya Auer, Williams College. Energetic Mechanisms for Coping with Environmental Change
- 10/24 – Shari Wiseman, Associate Editor at Nature Neuroscience. Perspectives on Scientific Publishing
- 10/31 – Rick Relyea, RPI. The Jefferson Project: Integrating Science and Technology for Enduring Lake Protection
- 11/7 – Paula Checchi, Marist College. DNA Repair: Why Do We Care?
- 11/14 – Felicia Keesing, Bard College. How to Plan a Meaningful Summer
- 11/21 – Daryl Lamson, NY Dept. of Health. Special Case Investigations in Virology: Finding the Unexpected
- 12/5 – Senior Project Talks (tbc)
A new paper from the Khakhalin lab:
Intrinsic temporal tuning of neurons in the optic tectum is shaped by multisensory experience
Silas E. Busch and Arseny S. Khakhalin
5 SEP 2019 https://doi.org/10.1152/jn.00099.2019
(The published version is behind a paywall, but you can find a free version here: https://www.biorxiv.org/content/10.1101/540898v2)
In his senior project, which eventually became the foundation for the paper, Silas Busch ’16 asked whether different neurons in the optic tectum of Xenopus tadpoles are tuned to inputs of different duration. Now, there’s lots to unpack in this sentence! So let’s talk about it bit by bit. Silas worked with tadpoles: the larvae of Xenopus frogs (you might have seen these frogs: they look a bit like underwater rubber toys, and are popular as pets). Even though tadpoles are small, they still have a brain, and in this brain, they have a part called “the optic tectum”. This brain area helps tadpoles to navigate in the water. As everything else in the body, the brain is made of cells, and these cells, called neurons, are connected to each other in some meaningful fashion that, frankly, we still don’t completely understand. Neurons send electrochemical impulses to each other, and it is this dance of activation in the tectum that allows tadpoles to swim without running head-first into walls or other tadpoles.
The question that Silas asked in his paper, is whether tectal neurons are different from each other in one very specific way. He looked at whether they all respond similarly to fast and slow patterns of activation, arriving from other neurons, or whether some of them have a preference for either fast or slow activation profiles. Say, if a neuron receives signals from 3 other neurons at the same time, will it respond to them in the same way as it would respond if these signals were a tiny bit staggered? To answer this question, Silas used a fancy technique called the “Dynamic clamp” that allowed him to connect to neurons one by one with a tiny glass electrode, and then control electrical currents in each neuron with a computer, simulating different patterns of activation.
What Silas found is that most tectal neurons do have a preference for either short or long (synchronous or asynchronous) patterns of activation, and that this preference changes depending on what tadpoles see and hear. It means that the tadpole brain as a whole, and each individual neuron in this brain on its own, adjust to changes in the world around the animal; presumably, to give the tadpole an ability to better navigate and survive. This particular type of neuron-by-neuron temporal tuning was not described in the tectum before, and also nobody yet used the dynamic clamp technique to look for tuning of this type. We don’t yet know exactly what these findings could mean for our understanding of the brain, but it is very exciting to learn that there is one more aspect to brain develpoment, that was so far somewhat overlooked!
It is also curious to think that this paper would not have happened if Silas hadn’t returned to the lab to work for 4 extra days immediately after graduation, on a Sunday after his commencement ceremony! In April 2016, as he was writing his senior project, Silas realized that some of the data he recorded could not be used. Even though he was obviously tired, and excited to graduate and leave Bard, Silas still decided to spend four more (!) full days in a lab without windows (our lab just happens to not have windows), to finish the work. It is not that often that you can point at one seemingly minor decision and realize that it was a key for success, but for this paper, it is really true. Without these four extra days of work, we would not have had enough data, and this paper would have never happened.
New paper by a recent Bard graduate Liz Miller ’18, in collaboration between labs of Dr. Collins and Dr. Perron:
Miller, E. C., Perron, G. G., & Collins, C. D. (2019). Plant‐driven changes in soil microbial communities influence seed germination through negative feedbacks. Ecology and evolution, 9(16), 9298-9311.
As plants grow, fungal pathogens accumulate around the roots of plants. Negative plant-soil feedbacks occur when these pathogens reduce the success of individual plants belonging to the same species. As a consequence, pathogens regulate the density of their specific plant hosts, and plants tend to grow best when their neighbor is a different plant species.
While seedlings and adult plants are known to suffer from these negative feedbacks, much less is known about the effect of species-specific pathogens on seeds. We tested whether seeds of seven different species experienced higher mortality in soils “conditioned” by plants of their own species (soils where pathogens were allowed to accumulate over time around the plant roots), versus soils conditioned by a different species. We also used metagenomics tools to identify potential pathogens driving the feedbacks.
We discovered that seeds of several grassland plant species experience negative feedbacks, i.e., the die more in their own soil than in soil of neighboring species. We also found that the putative pathogens driving these feedbacks differed depending on which species conditioned the soil a seed was buried in. Our results suggest that negative feedbacks at the seed stage may play a role in population persistence and plant diversity, and that the role of particular pathogens for driving feedbacks may depend on which plant species are in the neighborhood.
We are excited to learn that the Tick Project, led by Bard professor Felicia Keesing, is now featured by The New Yorker magazine!
Check out this beautiful story by Micah Hauser:
Keesing said, “I don’t like ticks any more than the next person, but I do admire them. They are survivors. Those things live for two years and eat three times. They can survive ninety-five-degree, humid, horrible summers and twenty-below winters. If you are going to root for the little guy—”…
“And their saliva!” Ostfeld interrupted. “They have a pharmacopoeia in their saliva. How do you stay attached to an animal without being detected, shrugged off, squished, or broken in half, for up to a week or so?
Read more on the New Yorker website!
Ticks are vectors for several serious diseases (meaning that they can transmit these diseases to humans), including Lyme disease, babesiosis, and anaplasmosis. Melissa Yost-Bido ’19 studied something called Haller’s organs: chemosensory organs (essentially, a very special type of smell) that ticks have on their front legs, and that is thought to help them detect pheromones, carbon dioxide, and infrared radiation. As you can guess, all that ticks really care about, is how to find a host (such as a mouse, or a human), to attach to them, and feed on their blood. Being able to detect animal smells and heat would definitely help here!
Many methods of tick-borne disease prevention that are used now, harm not only ticks, but also other, good, beneficial organisms. If we learn more about the Haller’s organ, we can try to find new ways to fight ticks, by making sure that they cannot find new hosts. Melissa studied the ability of the Haller’s organ in blacklegged ticks (Ixodes scapularis; the nastiest ticks around here) to detect infrared light. She collected local ticks, separated them into groups, and then either left their Haller’s organs intact, or removed them. Then Melissa exposed each tick from each group to infrared light (heat), and recorded the distance that each tick moved towards the source of infrared radiation. She found that ticks with a Haller’s organ traveled farther towards the heat, compared to those that had their Haller’s organs removed. This suggests that Ixodes ticks can use Haller’s organs to detect warm bodies, which is something nobody had ever shown before!
We live in the era of antibiotic resistance: old, familiar antibiotics, that used to work so well in the past, are no longer guaranteed to kill harmful bacteria, as the bacteria evolve new ways to fight back and survive the treatment. Because of that, now, more than ever, it is important to study the fundamentals of gene regulation in bacteria, with a hope to find new ways to control them.
Riboswitches are a unique mechanism of gene regulation that is used by bacteria, fungi, and plants. A piece of RNA with a riboswitch changes its shape depending on what chemicals are present in the cell, which in turn changes what proteins are produced by the bacterium. Riboswitches were shown to be critical for the bacterial survival, which means that in the future, we can try to use them as targets for the development of new pharmaceuticals. With the guidance from Dr. Gabriel Perron and Dr. Swapan Jain, Rachael Mendoza ’19 used bioinformatic tools to identify and classify the riboswitches in thirty strains of a certain bacterial species (B. subtilis). She described the diversity of riboswitches in these strains, and put forth some interesting hypotheses about how this information can inform development of future medical treatments.
For her senior project, Lucy Christiana ’19 built a computer simulation of plant community dynamics. Lucy studied how plants would grow if they experience a phenomenon called “plant-soil negative feedback”. Despite a scary name, the idea of this effect is rather simple: imagine that every growing plant is attacked by some “bad stuff” living in the soil, such as pathogenic fungi that try to weaken or kill the plant. As a plant is growing , these fungal pathogens will multiply in the soil around it, making this patch of soil kind of hostile to this plant species. Any seed from this species, for example, will have a hard time surviving in this particular patch of soil, just because it is so rich with “bad fungi”. A different plant species, however, will have no problem living there, as it will be immune to pathogens (each plant species comes with its own list of enemies, so pathogens of one species don’t necessarily harm the other).
As you can imagine, this can really change how plants grow, and it would probably improve biodiversity: even if one plant species is a strong competitor, it will soon be weakened by local pathogens, allowing other species to grow in its place. Lucy was interested in how these negative feedbacks shape the emerging plant community, and she used over 30 years of historical vegetation data from a particular long-term field experiment in Lawrence, Kansas. Lucy built a cellular automata model for one of the species described in this experiment (Ambrosia artemisiifolia, aka common ragweed), and compared predictions of her model to real data. This study is a step towards a more integrated analysis of spatiotemporal patterns of plant community assembly dynamics, and it can help us to understand how plants interact with each other, and how these interactions shape the landscapes that surround us.