Category Archives: publications

Khakhalin lab: Intrinsic temporal tuning in the tectum

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.

Collins lab: Soil microbes and seed germination

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 feedbacksEcology and evolution9(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.

Keesing lab: Blood meal effects on tick microbiome

Ticks are parasites that ingest blood from their hosts. During their blood meals, they can also ingest microbes, such as bacteria, from their host’s blood, which could influence the microbial community, or “microbiome”, of the tick itself. Using high-throughput sequencing, Felicia Keesing and her colleagues sampled the microbiomes of ticks that had fed on individuals of five different host species — raccoons, Virginia opossums, striped skunks, red squirrels, and gray squirrels. They found that ticks that had fed on different host species had significantly different microbiomes. This is important because some of the microbes that ticks can acquire during their blood meals are pathogens of humans, including the bacterium that causes Lyme disease.

Publication link: https://www.sciencedirect.com/science/article/abs/pii/S1877959X18303297

Full citation:  Landesman, W. J., Mulder, K., Allan, B. F., Bashor, L. A., Keesing, F., LoGiudice, K., & Ostfeld, R. S. (2019). Potential effects of blood meal host on bacterial community composition in Ixodes scapularis nymphs. Ticks and tick-borne diseases.

Dueker lab: Fog in Urban Environments

The urban environment is complex and often highly contaminated. This paper from prof. Eli Dueker’s lab takes a close look at how this contamination influences bacteria in urban air.  The bacteria present in urban waterways were compared with the bacteria present in urban air, showing that there are many sources for atmospheric bacteria in an urban environment, including sewage contaminated waterways and polluted terrestrial areas. We also observed a ubiquitous distribution of sewage-associated bacteria, in water and air at several urban sites, highlighting the prevalence of of sewage contamination in crowded urban centers and underscoring the complexity of managing this form of pollution in water and air.  Surprisingly, we also found that, despite the absence of obvious ecological structures, the air harbored a much more diverse bacterial community than that found in urban waterways. This provides evidence for the possibility of an atmospheric “ecology” and is a step towards understanding the role of megacities in determining the quality of urban air.

Citation: Dueker, M. E., French, S., & O’Mullan, G. D. (2018). Comparison of Bacterial Diversity in Air and Water of a Major Urban Center. Frontiers in Microbiology9.

Link: https://www.frontiersin.org/articles/10.3389/fmicb.2018.02868/full

Keesing lab: livestock and wild animals can coexist

The savannas of East Africa are renowned for their abundant and diverse wildlife. But wildlife populations in this region are declining dramatically, in part because of conflicts with humans and their livestock. Felicia Keesing and her colleagues studied the ecological, economic, and social consequences that arise when livestock and wildlife co-occur versus when the two groups live separately. They found that when livestock, particularly cattle, are kept at moderate densities, they actually improve vegetation quality for wildlife, reduce the abundance of parasites, and provide economic and social benefits to people living in the area.

Keesing discussed the research, and its implications, with Scientific American.

Integrating livestock and wildlife

New paper from Felicia Keesing’s lab was published in Nature Sustainability. Globally, most wildlife live outside of protected areas, creating potential conflicts. Keesing et al. assess tradeoffs between management for wildlife and for livestock in an East African savanna (pictured), finding potential benefits from integrating the two.

Full citation and link: Keesing, F., Ostfeld, R. S., Okanga, S., Huckett, S., Bayles, B. R., Chaplin-Kramer, R., … & Warui, C. M. (2018). Consequences of integrating livestock and wildlife in an African savannaNature Sustainability1(10), 566.

Dueker lab: Biology of fog in Maine, and in Namib Desert

The lab of professor Eli Dueker published a new study on the microbial composition of fog in Maine and in the Namib Desert. Dr. Dueker and collaborators found that fog particles lift microorganisms off the surface of water, and deposit them inland, increasing the microbial diversity.

The study has made quite a splash in the press; look at these substantive and interesting reviews, one in The Atlantic, and this one on the Atlas Obscura website.

Professor Dueker was also invited for a radio interview at WAMC: you can listen to it here.

Full citation: Dueker, M. E. and S. Evans, R. Logan, and K. C. Weathers (2018). The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition. Science of the Total Environment 647: 1547-1556.

New paper from Perron lab: effects of arsenic on fish microbiome

We are our own zoos, harboring about 39 trillion bacteria symbionts, about as many as our cells. These bacteria, collectively called our microbiome, are indispensable for our health; they fight our infections, process our food, guide our behavior, and protect us from diseases. So, when our bacteria are disrupted so is our health.

The recent research article, written by Bard graduate Dylan Dahan ’15 and professor Gabriel Perron, in collaboration with professors Brooke Jude and Felicia Keesing, used zebrafish as a model to investigate how arsenic poisoning affects fish microbiomes. The researchers found that microbiomes were readily affected, with striking consequences such as loss of bacterial community members and potential increases in antibiotic resistance.

Arsenic poising in contaminated drinking water affects over 60 million people in Bangladesh and West Bengal. This research will inform how contaminated water may be altering peoples microbiomes and thus supports the case for cleaning contaminated water.

Full citation: Dahan, D., Jude, B. A., Lamendella, R., Keesing, F., & Perron, G. G. (2018). Exposure to arsenic alters the microbiome of larval zebrafishFrontiers in microbiology9.

On the photo: Dylan Dahan (class of 2015) presenting his data.

Nine genome announcements from Brooke Jude’s lab

This winter the lab of professor Brooke Jude published nine draft genomes of bacteria endemic to the Hudson Valley watershed. This work is a result of several senior projects performed in the Biology program, and three graduated biology students (Alexandra Bettina, Georgia Doing, and Kelsey O’Brien) are now first authors on three publications!

Bettina, A. M., Doing, G., O’Brien, K., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed. Genome announcements6(3), e01426-17.

Doing, G., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed. Genome announcements6(1), e01428-17.

O’Brien, K., Perron, G. G., & Jude, B. A. (2018). Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed. Genome announcements6(1), e01429-17.

New paper: Onshore Wind Speed and Microbial Aerosols at Urban Waterfronts

In this new paper, Bard professor Elias Dueker and collaborators study microbes that fly in the air, after small droplets of water get lifted from the ocean surface by the coastal wind. They found that depending on the wind speed, different amounts of microbes were picked up, and they were transported different distances into the city. They also described which types of microbes are more likely to get airborne, compared to those found below the water surface.

Citation: Dueker, M. E., O’Mullan, G. D., Martínez, J. M., Juhl, A. R., & Weathers, K. C. (2017). Onshore Wind Speed Modulates Microbial Aerosols along an Urban WaterfrontAtmosphere8(11), 215.