Faculty and Student Presentations
MAKI INADA gave a poster presentation, “Serine Phosphorylation in the C-Terminal Domain of RNA Polymerase II Modulates Gene Expression in Sub-telomeric Regions of Schizosaccharomyces pombe via Chromatin States”. Eukaryotic mRNA Processing Meeting. Cold Spring Harbor Laboratory, NY. August 2015.
Ben Jung '16. Poster presentation.” Investigating the regulation of splicing of RPS30 paralogs that arose form genome duplication in S. cerevisiae”. Northeast Regional Meeting of American Chemical Society. Ithaca College. June 2015. Ben also won a poster award. Advisor: Maki Inada
MAKI INADA presented, "Linking the C-Terminal Domain Code of RNA Polymerase II to Modulating Chromatin States in Schizosaccharomyces pombe", RNA Society Meeting. Madison, WI, May 2015.
Erika Bucior '16. Poster presentation. "Plant habit and morphological characters are more important than rates of photosynthesis in determining species dominance of an introduced (Scaevola taccada) compared to a native (S. plumieri) species measured on the island of Culebra, Puerto Rico." Northeast Regional American Society of Plant Biologist Conference. Northeastern University. Boston, MA. April 2015. This presentation was on their research work conducted in Puerto Rico.
Authors: Erika Bucior and Peter Melcher
Maki Inada presented, "To Splice or Not to Splice: an Ultraconserved Mode of Gene Regulation," and guest lectured in an Advanced Biochemistry Course on the Molecular Biology of Cancer titled, "My very own lung cancer case study: targeted therapies" in the Chemistry and Biochemistry Department at Washington and Lee University. November 2014.
Queen's University Biological Station. Summer 2014.
Bruce Smith had a display on the diversity of water mites and their pathogens and Kit Muma presented a poster entitled "Tick Talk". Open House.
Bruce P. Smith and Kit E. Muma presented, "Kiwis and Kokakos: Wildlife Conservation in New Zealand". Queen's University Biological Station Wednesday Night Seminar Series. .
NCUR student presentations. University of Kentucky. April 2014
- Belko, N. ’14 (advisor, Ed Cluett). "The use of ONO-RS-082 a phospholipase A2 inhibitor, to investigate the localization of amyloid precursor protein"
- Benn, R. ’15 (advisor, Maki Inada). " Investigating the Role of Carboxy-Terminal Domain of RNA Polymerase II in Chromatin Remodeling and Gene Expression in Schizosaccharomyces pombe”
- Coleman, H. (Ian Woods). "The Role of CART in arousal behaviors in larval zebrafish"
- Falcone, E. (Leann Kanda). "The brave little hamster"
- Linton, A. (Jean Hardwick). “Galanin localization and actions in the guinea pig cardiac plexus”
- Moore, A. (Leann Kanda). "To forage or not to forage: the perception of fear in Phodopus sungorus"
- Rabice, S. (Andy Smith). “Interactions among carbohydrates and proteins that could determine performance of terrestrial slug glue"
- Sarah Boyle (Ed Cluett). “The effect of PLA2 Inhibitors on the endosomal network and the processing of amyloid precursor protein
- Holly Garbacz (Andy Smith). "Reduction Effects on Mechanical Strength of Defensive Glue Secreted by Arion subfuscus"
- Alex Wilks (Andy Smith). "Polysaccharides and Proteins Intertwined: Testing the Double Network Hypothesis for Tough Glue"
Alex won the award for best presentation in his category.
Peter Melcher presented, "A new approach to measure hydraulic resistance in plants". American Society of Plant Biology Northeastern sectional meeting in Rhode Island, March 30th, 2014.
Dave Gondek presented, “Using a Student Response System in Biology Courses to Engage Students”, Faculty Show and Share, Ithaca College. March 2014.
Emily Powers (Biochemistry ’15) and Alisha Linton (Biology ‘14) presented, "Galanin localization and actions in the guinea pig cardiac plexus". Society for Neuroscience conference. Funding support was provided by the Jack and Flo Bernard Family Undergraduate Research Fund and an EGI Grant. (Faculty Advisor: Jean Hardwick).
Robert Nichols (Biochemistry ’14) presented, "Linking the C Terminal Domain Code of RNA Polymerase II to Modulating Chromatin States in Schizosaccharomyces pombe”. 2013 Finger Lakes RNA Meeting. October. 2013. (Faculty Advisor: Maki Inada).
Kanda, L.L., B. Donnelly, and B. Hayes. (2013) The road less travelled: even recreational trails affect wildlife movement. Poster. International Mammalogical Congress, Belfast, Ireland.
Peter Melcher. Invited Speaker. Do Plants Defy Physical Laws? How plants move water against the forces of gravity and hydraulic resistance without using a heart-like pump. r. Ithaca College.Physics Department Seminar Series. Fall 2013.
Maki Inada. Poster Presentation. "Linking the C-Terminal Domain Code of RNA Polymerase II to Modulating Chromatin States in fission yeast Schizosaccharomyces pombe”. Cold Spring Harbor Laboratory Eukaryotic mRNA Processing Meeting. Cold Spring Harbor, NY. August 2013. Co-authored with Robert Nichols (Biochemistry ’14), Beate Schwer (Cornell Weill Medical College) and Jeff Pleiss (Cornell University).
Joshua Messinger (Biochemistry '14). Poster Presentation. "I can grow there too: A survey of Chlamydia growth across species boundaries". Chlamydia Basic Research Society Meeting. San Antonio, TX. March 19-22, 2013. Research supervised by Dave Gondek.
Maya Patel presented with my colleague, Dr. Daniel Kjar of Elmira College. "Learning Inquiry and the Nature of Science through and Open Investigation in a Field Biology Course". National Association for Research in Science Teaching's International Conference, Puerto Rico. June 2013.
Nancy Jacobson presented, “Flipping the Classroom to Correct Student Misconceptions”. International Institute for SoTL Scholars and Mentors. Los Angles, CA. Summer 2013.
Adrienne Antonson, Biology ’13 (Bruce Smith), “Is there preferential orientation to vertically or horizontally polarized light by Bosmina spp. cladocerans and calanoid copepods?”
Pamela Millan, Biology ’13 (Bruce Smith), “Stretched to the limit: body contortion in Limnochares americana (Hydrachnidia: Limnocharidae)”
Sarah Rabice, Biochemisty ’13 (Andy Smith), “Glue from the Slug Arion subfuscus”.
- Won a best presentation award for the Biochemistry section.
Caitlyn Ludington, Biology ’13 (Leann Kanda), “The Cowardly Hamster: Evaluating Aggression and Boldness in Dwarf Hamsters, Phodupus sungorus”.
- Won best presentation in her section, Organismic Biology.
Botanical Society of America Meeting, New Orleans, LO. 2013.
- Robert Griffin-Nolan* and Peter Melcher. "The physiological responses of moss to green light."
- *Winner of the Physiological Section "BEST POSTER AWARD"
The goal of this study was to determine if moss could use green light to power photosynthesis. Measurements were made on three species of moss (Dichodontium pellucidum (Schimp.),Amblystegium serpens (Schimp.), and Leucobryum albidum (Bird. ex P. Beauv)) collected from field sites that varied in their light conditions. We found that moss collected from the field could use green light to drive photosynthesis at rates similar to when exposed to red, blue, or full spectrum light (all measured at 100 umol m-1s-2). Mosses were also collected from the field and grown for three weeks under three light conditions: low and slightly higher full-spectrum light at 30 and 100 umol m-1s-2, respectively; and green light at 30 umol m-1s-2. We measured photosynthetic electron transport efficiency (ETR) using a LICOR 6400 leaf chamber Fluorometer. We found that mosses grown under only green light had similar ETR compared to plants grown under full spectrum light. From carbon and nitrogen isotope analysis, we found that moss exhibit resource allocation plasticity when exposed to different light environments. These data support our hypothesis that moss can use green light to power photosynthesis but the degree to which they use green light to overcome respiratory demands depends on their light environment (e.g. sun vs. shade). The mechanism by which plants use green light to photosynthesize is unclear. However, the fact that mosses are able use green light for photosynthesis suggests that the mechanism evolved early on in land plant history.
- Yongqian, Zhang (Poster). "The effects of herbivory on leaf-level photosynthesis measured on wild tobacco plants." Co-authored with Robert Griffin-Nolan, Leanne Donahue, Michael Guidi, Jason Hamilton, and Peter Melcher.
A broad range of effects of herbivory on photosynthesis as the plant’s main primary metabolic process has been reported. Pioneering studies of herbivore-induced changes in photosynthesis found that the majority of defoliating herbivores cause an increase in photosynthetic activity, whereas mesophyll and phloem feeders, stem borers and gall formers mainly decreased photosynthesis in the remaining plant tissue. Plants also have indirect defenses, such as the production of volatile organic compounds that can facilitate top-down control of herbivore populations by increasing the foraging success of herbivore predators and parasitoids. Abiotic and biotic induced plant responses are not restricted to secondary metabolism, but include changes in various primary metabolic pathways. To investigate these plant-animal interactions, we are measuring leaf-level photosynthetic responses of wild tobacco plants collected from field sites in Arizona and Utah in response to various phytochemicals. Previously, our group showed that these wild tobacco plants respond to herbivory attack with increased photosynthesis from myriad bug herbivory and decreased photosynthesis from Manduca hornworm herbivory. Since these leaf-level photosynthetic measurements take an enormous amount of time, we developed a rapid screening method that allows one to measure variation in PSII electron efficiency in response to chemical treatments on many (up to 96) samples simultaneously using a CF Fluorescence Imaging system (Technologia, UK). We were successful to measure changes in electron efficiency in the leaves of tobacco using two phytochemicals Jasmonic acid (JA) and Salicylic Acid (SA) compared to deionized water and an electron blocker (3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). Future work will involve measurements of chemicals extracted and isolated from wild myrid bug and manduca hornworm salivary glands on leaf-level electron transport efficiency and results from these studies will be presented.
Animals modulate arousal state to ensure that their sensory responsiveness and locomotor activity match environmental demands. Neuropeptides have been implicated in arousal, but studies of their roles in vertebrates have been constrained by the vast array of neuropeptides, their pleiotropic effects, and behavioral complexity. To overcome these limitations, we systematically dissected the neuropeptidergic modulation of arousal in larval zebrafish. We genetically overexpressed evolutionarily-conserved neuropeptides (adcyap1b, cart, cck, cgrp, galanin, hcrt, and pnoc) and quantified spontaneous and stimulus-evoked locomotor behaviors. Our study reveals that arousal behaviors are dissociable. For example, neuropeptide expression uncoupled spontaneous locomotor activity, a measure of endogenous arousal, from responsiveness to sensory stimuli, a measure of exogenous arousal. Both endogenous and exogenous arousal behaviors could be further partitioned into discrete parameters, including modality-specific changes in sensory responsiveness and distinct characteristics of voluntary locomotion. Principal components analysis and phenotypic clustering revealed both shared and divergent features of neuropeptidergic functions: hcrt and cgrp stimulated voluntary locomotion, whereas galanin and pnoc attenuated these behaviors. In contrast, cart and adcyap1b increased sensory responsiveness yet had minimal impacts on voluntary locomotor activity, while cck expression induced the opposite effects. Furthermore, hcrt and pnoc induced modality-specific differences in responsiveness to changes in illumination. Our study provides the first systematic high-throughput analysis of neuropeptidergic modulation of arousal, demonstrates that arousal is partitioned into independent behavioral components, and indicates ancestral and conserved functions of neuropeptides in regulating arousal.
NCUR: University of Wisconsin-La Crosse. April 2013.
Michael Armstrong (Leann Kanda) Oral Presentation. HAMSTER HOME DECOR: AN EXAMINATION OF NEST MANIPULATION IN SIBERIAN DWARF HAMSTERS (PHODOPUS SUNGORUS)
Behavioral syndromes are suites of correlated personality traits, and have been observed in many animals. To see if behavioral syndromes exist in Siberian Dwarf Hamsters (Phodopus sungorus) we tested individual hamsters in two types of mazes and scored their nesting habits every seven days. Previous research has shown the tunnel maze is a reliable measure of activity and boldness; the novel test is designed to test exploratory tendencies; nesting habits were evaluated for manipulation of food and nesting box. We analyzed the results for individual reliability across time in each test. Activity in the tunnel maze and food bowl and nest box manipulation were consistent over time, but boldness in the tunnel maze was not. Repeatability of the novel test could not be evaluated. Correlations between the behaviors from each test were examined by Spearman correlations. Analysis of the data revealed a partial behavioral syndrome between activity in the tunnel maze and nest box manipulation. This conclusion mirrors that of Ned Dochterman and Stephen Jenkins’s 2007 study on Merriam’s Kangaroo Rat, where a partial behavioral syndrome was found in a different study animal.
Abigail E Finley (Bruce Smith). Oral Presentation. AN EXTENSIVE SURVEY OF INFECTION BY POTENTIAL SEX RATIO DISTORTING PATHOGENS AMONG SPECIES OF ARRENURUS WATER MITES.
Many organisms produce a sex ratio distortion where the progeny of an individual female is primarily male or female. This has been observed in some Acari, as well as many other arthropods, and even a few vertebrate species. There are adaptive mechanisms that cause a sex bias in offspring including haploidiploidy, parahaploidy, thelytoky, and temperature-induced sex determination. However, various pathogens are also known to cause sex ratio distortion, which is adaptive for the pathogen but is typically not adaptive for the host. Types of pathogens known to cause a biased progeny include Wolbachia, Spiroplasma, Rickettsia, Cardinium, and Microsporidia. In previous research, it was determined that Arrenurus manubriator from Lake Opinicon in Canada have both sex ratio distorting pathogens Rickettsia and Cardinium. However, these infections did not directly correlate to the sex ratio distortion observed in this species of mite. In North America, species of the genus Arrenurus represent about ¼ of the total water mite diversity. I am currently conducting a survey of Cardinium infection among approximately 60 species from South Eastern Ontario, Canada. I also plan to test these species of mites for other known sex-distorting pathogens including Wolbachia, Spiroplasma, Microsporidia, and Rickettsia. To diagnose an infection, molecular techniques are used including extracting DNA, amplifying pathogen-specific sequences through PCR, and screening for the presence of amplified DNA through gel electrophoresis. The extent of pathogen infection is important to study because endosymbiotic bacteria play important roles in arthropod evolution and ecology. Thus far, I have identified three Cardinium infections in 60 individual hosts, which consisted of males and females from six different species.
Robert Nichols (Jeffrey Pleiss, Beate Schwer & Maki Inada) Oral Presentation. LINKING THE CARBOXY-TERMINAL DOMAIN CODE OF RNA POLYMERASE II TO MODULATING CHROMATIN STATE
Regulation of gene expression is essential for all living organisms. One critical step in regulating gene expression is altering the ability of the transcriptional enzyme, RNA Polymerase II (RNAPII), to access DNA by manipulating chromatin states. Eukaryotic DNA is kept in tightly packed chromatin wrapped around proteins called histones. The carboxy-terminal domain (CTD) of RNAPII, is believed to play a critical role in chromatin remodeling through its recruitment of factors that modify the histones. Conserved throughout evolution, the CTD contains a repeated YSPTSPS heptapeptide sequence that undergoes dynamic posttranslational modifications. The capability of each serine within the sequence to undergo phosphorylation and dephosphorylation allows for 8^n CTD isoforms where ‘n’ is the number of heptapeptide repeats. These combinatorial CTD states are thought to create a readable ‘code’ that recruits multiple factors that can determine when processes, such as chromatin remodeling occur. In order to characterize how specific phosphorylation marks in the CTD affect gene expression, mutants of fission yeast Schizosacchromyces pombe were rendered defective for phosphorylation by substituting a nonphosphorylatable alanine in place of each serine in position 2 in the heptad sequence (S2A), each position 7 serine (S7A), or all serines in position 2 and position 7 in combination (S2A, S7A). In addition, a fourth mutant was created in which the position 7 serines were substituted for the phosphomimetic glutamic acid (S7E). We have performed microarray experiments with these mutants to study the genome-wide effects of eliminating and altering these phosphorylation events. Strikingly, analysis of these microarray data revealed an upregulation of positionally related clusters of genes, specifically in telomeric regions in our mutants. Further quantitative PCR analysis of genes in these telomeric regions confirmed the significant upregulation of genes in the telomeric regions spanning 50kb for our mutants. Our microarray analyses and subsequent qPCR validation suggest a role for the dynamic phosphorylation and dephosphrylation of serines within the CTD code in modulating the chromatin states in large telomeric regions
Keyla C Tumas (Andrew Smith) Oral Presentation. THE NATURE OF CROSS-LINKS IN A BIOLOGICAL GLUE: WHY DOES INCREASED TEMPERATURE WEAKEN SLUG GLUE?
Our lab studies the glue produced by the slug Arion subfuscus with the goal of developing a biomimetic adhesive. Our current research looks to understand how interactions between proteins and carbohydrates make this glue elastic and stiff despite consisting of roughly 97% water. Dynamic rheometry experiments showed that the glue becomes markedly less stiff when heated from 20°C to 50°C. The purpose of these experiments was to establish the cause of this unexpected decrease in stiffness. This may tell us more about the nature of the cross-links that strengthen the glue. We have evidence that calcium ions directly cross-link the glue, as do imine bonds. Thus, we hypothesize that heating decreases glue stiffness by breaking these reversible bonds. Alternatively, there may be enzymatic degradation of proteins and/or carbohydrates. To test the loss of cross-links, we compared the decrease in glue stiffness with the calcium content after heating. Calcium was measured by atomic absorption spectroscopy. We also compared the decrease in stiffness to the imine bond content, which was measured biochemically after sodium borohydride treatment. We found that calcium loss and imine bond breakage were not responsible for glue weakening. Furthermore, SDS-PAGE showed no protein degradation with heating. Inhibiting protease activity did not block the loss of stiffness. Similar experiments will determine if there is any carbohydrate degradation. At present, there does not appear to be enzymatic degradation, and the loss of stiffness is not correlated with loss of any of the known cross-links. Because the extent of cross-linking is observable as large aggregates in non-denaturing gel electrophoresis, we will use this technique to confirm if heating impacts cross-linking in any way. If the loss of stiffness is not due to changes in cross-linking, we will investigate whether there are structural changes in the polymers of the glue using circular dichroism spectroscopy. Finding the cause of this weakening effect will help advance the understanding of how this glue works, which can then be applied to developing a strong biomimetic gel useful for the medical field to replace band aids and stitches.
Longwich, Adam (Condon, Marty and Susan Swensen) Oral Presentation. MOLECULAR PHYLOGENETIC RECONSTRUCTION OF THE NEOTROPICAL CUCUMBER GENUS GURANIA BASED ON THE SERINE/ THREONINE PHOSPHATASE LOW-COPY NUCLEAR MARKER
Gurania are a genus of monoecious flowering Neotropical vines that are found in Central and South America. They are classified in the economically important family Cucurbitaceae that include melons, squashes, pumpkins, and cucumbers. Gurania serve as hosts to fruit flies in the genus Blepharoneura where as many as seven different species of flies may parasitize a single species of Gurania (Condon et al. 2008). Currently, there is no clear picture of host plant phylogeny. Taxonomic revision based on morphology of hosts has been attempted, but geographical variation within species has led to difficulties in species definitions and no phylogenetic analysis has been completed. As a result, phylogenetic reconstructions require the analysis of multiple, rapidly evolving gene regions. However, our preliminary analysis of eight chloroplast intergenic spacer regions and the low-copy nuclear marker, serine/ threonine phosphatase (s/t phos) has offered 1.06% and 18.43% phylogenetic utility, respectively. The primary goal of the proposed project is: construct a molecular phylogeny based on the highly informative s/t phos nuclear marker and address whether specific morphological characteristics observed in the genus Gurania that are currently used to differentiate the species are in fact reflected in the molecular based phylogenies. To achieve a resolved phylogeny new species will be added in order to address evolutionary questions regarding the species in the genus Gurania. Parsimony and maximum likelihood-based phylogenetic analysis of the low-copy nuclear maker with analysis of specific morphological characters will be presented.
Andy Smith. Presented, “Double network gels and biological glues: a powerful new toughening mechanism”. Society for Integrative and Comparative Biology, San Francisco, California, January 2013.
Limpets, marsh periwinkles and some terrestrial slugs produce remarkable glues that are gels. A key question has been how they can achieve tenacities on the order of several hundred kilopascals using only a dilute gel that is a modified lubricating mucus. Previous work has shown that the essential change is the addition of relatively small, cross-linked proteins. Nevertheless, highly cross-linked gels are typically brittle and fail easily. Molluscs may avoid this through the use of a “double network”. Recent work in materials science has found that combining two highly dissimilar, interpenetrating gel networks can increase gel strength by a factor of 100 to 1000 over the strength of the two gels separately. A prototypical double network gel combines a deformable network of very large polymers and a highly cross-linked network of much smaller polymers. Initial fracture occurs in the stiffer, highly cross-linked network. Fracturing the soft network as well, though, requires extensive deformation. This deformation damages the rigid network in a large volume surrounding the crack. This can increase the energy required to propagate the crack by several orders of magnitude. Such a mechanism is likely at play in molluscan adhesive gels given their structure. In fact, any biological gel containing proteoglycans or similarly large polymers in combination with smaller cross-linked proteins has the potential to operate this way. This talk will outline the structural and mechanical criteria for double network gels and consider the applicability of this mechanism to different biological materials.
For the past 24 years the Mind and Life Institute has been hosting dialogues between His Holiness the Dalai Lama and Western scientists on a variety of topics, exploring the similarities and differences in views of Buddhism and Western science. Over the past decade these conferences have become open for the public to attend and now many of the conference talks are posted online for open viewing. To further these dialogues, Namgyal Monastery is sponsoring a series of discussions on topics presented during selected Mind and Life conference sessions. This discussion series will focus on dialogues held during Mind and Life XVIII: “Attention, Memory and Mind”. These talks focus on discussions of Western Neuroscience and Buddhist views of attention, memory and consciousness. Participants will view segments of presentations together along with a panel of two neuroscientists, neuropsychologist and scholar of Buddhist philosophy from local universities. Participants will have an opportunity to ask questions to clarify their understanding on topics covered in the Mind and Life talks as well as gain related information from other resources. The spirit of these sessions is intended to deepen learning, understanding and dialogue on these topics, rather than foment debate or critique of different views.
Panel members: Bruce Johnson, PhD: Senior Research Associate, Neurobiology and Behavior, Cornell University, Kit Muma, MSc: Instructor, Biology Department, Ithaca College, Charles Goodman, PhD: Associate Professor, Philosophy Department, Binghamton University. Moderator: Deana Bodnar, PhD LMSW