Talk Abstracts for The 2012 Life Sciences Graduate Research Symposium

All of the Life Sciences Graduate Research Symposium talk abstracts, arranged alphabetically by last name.

Talk Title: Demographic response of a shrubland bird to habitat creation, succession, and disturbance in a ‘shifting mosaic’ landscape

Speaker: Michael E. Akresh, Environmental Conservation Program

Abstract: Due to suppression of natural disturbances, most shrubland habitat currently consists of habitat created and maintained in various forms by management: newly created shrubland habitat that matures over time (e.g., clearcuts), habitat that is persistent but disturbed on a continual basis (e.g., scrub oak barrens), or habitat that is persistent yet minimally disturbed through time (e.g., power line corridors). As shrubland bird populations decline, there is a critical need to understand the effects of habitat creation, succession, and disturbance, and to acquire knowledge of basic demographic parameters that are keys to shrubland bird conservation. We studied a population of color-banded prairie warblers (Setophaga discolor) between 2008-2011 in a shifting mosaic landscape within a Massachusetts inland, pitch pine-scrub oak barren. We present data showing that the abundance and population structure at this site appears to be a function of colonization of newly created habitat by second-year birds, which are likely excluded from mature early-successional habitat by site-faithful older birds. Breeding season fecundity did not differ significantly between newly-created and mature habitats. Birds displaced by mowing or fire dispersed to nearby suitable habitat the following year, had relatively similar reproductive success, and did not negatively affect pairing or reproductive success in adjacent areas. Our findings are novel and show that the effects of shrubland management on shrubland birds are beneficial in the short- and long-term.


Talk Title: Learning and memory, a molecular perspective

Speaker: Rosamund Combs-Bachmann, Neuroscience and Behavior Program

Abstract: One of the primary goals of the Chambers lab is to develop a more complete understanding of the molecular processes underlying memory formation. Long term potentiation (LTP) at synapses is thought to be one of the key processes underlying the formation of new memories, and the controlled movement of glutamate receptors into and out of the post-synaptic membrane plays a critical role. Understanding how glutamate receptors are trafficked and stabilized in the neuron is fundamental to understanding dynamic excitatory synaptic communication and will enable elaboration of the molecular mechanisms behind this complex process.

One approach we have taken to investigate synaptic and extrasynaptic glutamate receptor activity is the development of a novel photochemical tool to probe glutamate receptor location and movement. A secondary approach we have used to study the importance of certain auxiliary proteins (TARPS) that anchor glutamate receptors at the synapse is to compare the memory formation and consolidation of wild type C. elegans in behavioral memory tasks to memory formation and consolidation in strains lacking these TARPS.


Talk Title: Developmental and genetic basis of a morphological novelty in East African cichlids

Speaker: Concannon, M.R., Organismic & Evolutionary Biology Program

The production of novel phenotypic variation provides new traits on which selection can act and is often associated with expanded ecological opportunity. We aim to understand the developmental and genetic basis of phenotypic novelty by utilizing the massive adaptive radiation of East African Cichlids, where craniofacial variation is a major axis of divergence. A species at the far end of the phenotypic spectrum, Labeotropheus fuelleborni (LF), is characterized by a fleshy elongated snout (‘flap’) that rests on the upper jaw and is absent from any other cichlid, including a phenotypically similar ecological competitor, Tropheops red cheek (TRC). We analyzed flap development in both species and found that it begins to diverge relatively late in development when fry are about 1.4 cm in standard length, at which point the flap continues to grow isometrically in LF and plateaus in TRC. Using an F2 hybrid mapping population, we identified three significant loci that influence the development of this trait. Given these data and the tractability of this system, we are poised to identify the specific genetic loci and developmental mode of action involved in the evolution of this phenotypic novelty as well as a foundation for its ecological and biological significance.


Talk Title: The Evolution of Three Hybrid Sterility Loci in US Weedy Red Rice

Speaker: Stephanie Craig, Plant Biology Graduate Program

Abstract: Plant outbreeding enables hybrid vigor and enhanced offspring.  However, some plants, when outcrossed, do not display these improved familial qualities and in contrast, experience sterility or lethality.  The inability of plants to experience heterosis is due to underlying genetic mating barriers that occur either pre- or post-zygotically.  These genes are regarded as large contributors to the speciation process, as they can cause reproductive isolation between diverging populations.  Three post-zygotic speciation genes have been recently cloned in Oryza sativa, Sa, s5, and DPL; these genes explain, in part, the limited hybridization that occurs between the domesticated cultivated rice varieties, O. sativa spp. japonica and O. sativa spp. indica.  In the United States, cultivated fields of japonica rice are often invaded by conspecific weeds that have been shown to be of indica origin. Crop-weed hybrids have been identified in crop fields, but at low frequencies.  This study aims to examine the role of these known hybrid incompatibility loci in the interaction between cultivated and weedy rice, and further assess the evolutionary processes acting at these loci. Analysis of the population structure of these genes between cultivated and weedy groups will help elucidate the forces responsible for the evolution of incompatible substitutions, and the possible impact on weed management in the US rice agroecosystem.


Talk Title: Metric Strength Modulates Early Auditory Processing

Speaker:  Ahren Fitzroy, Neuroscience and Behavior Program

Abstract: Selectively attending to portions of an incoming sensory stream based on certain distinguishing aspects can help us make sense of what would otherwise be overwhelming amounts of information.  Previous research on selective attention has largely focused on the use of spatial selection, but recent evidence demonstrates that people also use time of stimulus presentation as an attentional selection criterion.  Event-related brain potential (ERP) research has shown that temporally selective attention affects early perceptual processing as indexed by the amplitude of the first negative peak 100 ms after sound onset (N1) in a manner similar to that observed for spatially selective attention.  Furthermore, this effect is larger when the time of stimulus presentation is cued by an exogenously presented isochronous pulse than when cued by explicit instruction alone.  These findings are consistent with the predictions of Dynamic Attending Theory (DAT).  Multiple oscillator variants of DAT predict that hierarchically organized exogenous rhythms will induce a hierarchical distribution of attention across time; the present studies employ stimulus-inherent and subject-initiated hierarchical rhythmic structures to test this hypothesis. Auditory evoked potentials elicited by physically identical stimuli presented at times of relative strength and weakness in these metric hierarchies were compared. Sounds presented at points of metric strength elicited larger amplitude N1s than the same sounds presented at points of metric weakness. This result suggests that attention is allocated preferentially to points of metric strength and provides electrophysiological support for DAT.


Talk Title: Impact of Land Cover Changes on Ecosystem Services in the Orinoco Basin – Colombia and Venezuela

Speaker: Luisa F. Galindo, Environmental Conservation Program

Abstract: The effects of the land cover changes have an impact in ecosystem services especially in the maintenance of hydrologic dynamics, avoidance of soil loss and availability of habitats. The future development of the basin will impact these services but little is known about the direction and extent of these effects in the Orinoco basin. In this study, we use a 1km MODIS NDVI composite data, precipitation data series, land uses, coverage and topography to assess and quantify changes in ecosystem services. The Orinoco basin originates from the Andes and flows into the Atlantic and passes to Colombia and Venezuela. It is one of the most biologically and hydrologically diverse areas of the world. General observation is that ecosystem services vary over space and have cumulative benefits at a watershed scale. Our findings provide new insight into the relationship between vegetation, precipitation, soil loss and habitat provision, which are critical for the management of terrestrial and aquatic ecosystems. Adaptation strategies should thus focus on site-specific conservation while account for watershed-wide enhancement of ecosystem services. The results develop new methods and baseline assessments in sustaining ecosystem services of watershed systems. The methods are transferable to other watersheds for developing adaptive management plans.


Talk Title: Evolving Color: Analysis of Carotenoid Synthesis Genes in Wild Tomatoes

Speaker: Ian Gillis, Plant Biology Graduate Program

Abstract: Fleshy fruits are an excellent source of energy and nutrition for animals. Humans actively select fruits for these properties, but in wild populations, these traits would need to experience sufficient selective pressures to go to fixation, most likely by animals in their native habitats. To determine if fruit color, which is caused by carotenoid accumulation, was under positive selection in wild tomatoes, I examined several colored-species for color variation, expression of carotenoid genes, and accumulation of carotenoids. Genes were selected based on relevance to color differences in fruit color. These genes were sequenced and analyzed for signs of selection. The Cyc-B gene is involved with the transition of red lycopene to orange beta-carotene. The promoter of Cyc-B was found to be under selection, though the coding region was not. Cyc-B shows signs that the allele found in red-fruited S. pimpinellifolium had been under selection and gone to fixation before the other color-fruited species, S. cheesmaniae and S. galapagense, diverged. These species have orange fruits and show no selection for any of the gene sequence, which could indicate that on the Galapagos Islands the selective pressures needed to maintain this costly trait may not be present.


Talk Title: BdMYB48 directly controls the accumulation of biomass in the model grass Brachypodium distachyon

Speaker: Pubudu P Handakumbura, Plant Biology Graduate Program

Abstract: MYB proteins comprise one of the largest multi-functional plant transcription factor families. They are involved in a variety of developmental processes and defense responses. Several MYBs are well characterized in the model dicot Arabidopsis thaliana and few in rice, maize and switchgrass. Increasing interest in utilizing plant biomass for the production of biofuels has created a need to better understand the molecular switches governing biomass accumulation. Brachypodium distachyon servers as a suitable model for energy crop research due to its close phylogenetic resemblance to species such as switchgrass and miscanthus. In addition, it has many model organism attributes including a completely sequenced genome, self-compatible rapid life cycle and genetic transformation. Within the B. distachyon MYB family, BdMYB48 is highly expressed in stem, tissue that accounts for a majority of above ground biomass. A reverse genetics approach was used to generate loss-of-function mutants by constitutively over-expressing the coding region fused to a dominant repressor. Mutants exhibited a significant reduction in plant height, above ground biomass, increase in flag leaf angle, and a significant reduction in stem lignification. Collectively the data suggests a role for BdMYB48 in growth and biomass accumulation and its potential to be used in future energy crop improvement.


Talk Title: Escalation of aggressive signals in black-throated blue warblers: a sequential playback study

Speaker: David Hof, Organismic & Evolutionary Biology Program

Abstract: Rival conspecifics often produce stereotyped sequences of signaling behaviors as agonistic interactions escalate.  Successive signals in a sequence have been hypothesized to convey increasingly pronounced levels of aggressive motivation.  Here, we propose and test a model of aggressive escalation in black-throated blue warblers, by presenting subjects with two sequential and increasingly elevated levels of threat. One speaker initiated an interaction from outside the territorial boundary, and a second speaker, accompanied by a taxidermic mount, subsequently simulated a territorial intrusion.  We predicted that signaling behaviours produced in response to playback from the boundary speaker (low threat level) should predict signaling patterns to the within-territory speaker (escalated threat level), and that signaling behaviours at each stage should be increasingly reliable predictors of ultimate attack.  We found that use of specific song types (type II songs) in response to boundary playback predicted use of low-amplitude “soft” song in response to within-territory playback.  Soft song, in turn, predicted attack of the mount.  Use of type II song during either stage of playback, by contrast, did not predict attack.  These results support the hypothesis that vocal signaling behaviours in songbirds can follow a progressive sequence where successive signals convey increasing levels of threat.


Talk Title: Adaptor dependence of an essential AAA+ protease

Speaker: Joanne Lau, Department of Microbiology

Abstract: Regulated proteolysis by the energy-dependent protease ClpXP governs cell cycle in Caulobacter crescentus, and a response regulator protein CpdR couples ClpXP activity to a periodic cell cycle phosphorelay. CpdR had been shown to direct ClpX to subcellular locations during cell cycle, thus indirectly acting as an adaptor for causing degradation of cell cycle substrates. Interestingly, CpdR is directly required as an adaptor for proteolysis of a cell cycle phosphodiesterase governing cellular levels of the ubiquitous second messenger cyclic-di-GMP. Here, we present an integrated mechanistic study of how CpdR acts as an adaptor to control proteolytic activity directly and indirectly. Using purified proteins, we reveal surface residues in the output face of the adaptor CpdR that are important for the phosphodiesterase degradation in vitro. We find that cells expressing these CpdR mutants cannot support wildtype cell morphology, motility, or regulated proteolysis of cell cycle factors. Through microscopy, interaction assays, and kinetic studies, we discover that these mutations are key to modulating the protease ClpXP. Together our work establishes a mechanistic framework for understanding how a small response regulator protein modulates proteolysis of cell cycle factors in the cell through a protease essential for cell division.


Talk Title: Chemical defenses and rare resistance to herbivory in Eastern Hemlock

Speaker: Elizabeth McKenzie, Plant Biology Graduate Program

Abstract: Hemlock woolly adelgid (Adelges tsugae, abbreviated HWA) is an invasive insect from Japan causing heavy damage and mortality to eastern and Carolina hemlock trees (Tsuga canadensis and T. caroliniana) in the eastern US.  However, recent efforts have identified a small number of eastern hemlocks showing relative resistance to HWA.  The terpene class of plant semiochemicals is expected to participate in any mechanism of resistance to herbivory, so this study compares terpenoid levels in resistant and susceptible hemlocks.  Compounds extracted from foliage and twigs are identified by mass spectrometry and quantified by gas chromatography.  Samples are being taken seasonally to better describe the profile and mechanism of HWA resistance.


Talk Title: Investigating HDAC6ʼs role in enhancing Alzheimerʼs disease tau pathology

Speaker: Kathryne A. Medeiros

Abstract: Alzheimer disease (AD) is a devastating neurodegenerative disease that currently affects millions of people worldwide and has no cure. Extracellular amyloid plaques and intracellular neurofibrillary tangles, the two hallmark lesions in a typical AD brain, are comprised of aggregated beta-amyloid (Aβ) and hyperphosphorylated tau (p-tau), respectively. The accumulation of oligomers of Aβ and p-tau correlate with disease progression and deficits in learning and memory. Accumulation of these proteins, are associated with disrupted synaptic function and neuronal death. Here we focus on understanding the underlying molecular mechanisms leading to the accumulation of aggregated Aβ and p-tau. We investigate the role of a histone deacetylase (HDAC), which has been shown to have increased protein levels in the neural tissue of patients who have succumbed to the disease. Our experiments have focused on characterizing the biochemical interaction between this HDAC and Protein Phosphatase 1 (PP1), a protein that is known to play a key role in regulating tau pathology. By using standard biochemical techniques in a heterologous expression system, as well as confocal imaging using dissociated neurons, we have found that overexpression of this HDAC causes an increase in the amount of phosphorylated tau. Of particular interest is the enhanced level of p-tau in the soma of these neurons. This data suggest that this HDAC is an underlying molecular factor mediating tau pathology.


Talk Title: Bioenergetics of the sulfate reducing bacteria Desulfobacter postgatei 2ac9 growing under nutrient-limiting conditions

Speaker: Roberto Orellana, Department of Microbiology

Abstract: The addition of acetate to groundwater at the U(VI) bioremediation study site in Rifle, CO, produced two phases: an initial Fe(III) and U(VI) reducing phase, in which Geobacter species predominated, and a second phase in which sulfate reducing bacteria (SRB) predominated and U(VI) reduction was poor. The main player among the SRB community is the acetate-oxidizing, Desulfobacter postgatei. In order to study its physiology, a chemostat system for culturing D. postgatei was developed under electron donor-limiting (EDL) and electron acceptor-limiting (EAL) conditions with acetate as the electron donor and either sulfate or thiosulfate as the electron acceptor. Under both conditions, biomass concentration remained constant and the biomass productivity was linear at dilution rates of 0.014–0.032 h-1, consistent with classical Monod-type growth. Calculations of the specific respiration rate under EDL, evidence that D. postgatei is more efficient that Geobacter sulfurreducens in the use of energy at low growth rates, implying that has lower energy maintenance requirements. This results provide insights into growth of D.postgatei in subsurface and provide data for developing in silico model reconstruction.


Talk Title: Characterizing the molecular pathogenesis of acute equine laminitis: yes, someone pays us to do this, and no, we can’t use a mouse model.

Speaker: Erica Pawlak, Department of Veterinary and Animal Sciences

Abstract: Equine laminitis is a devastating disease in which the digital laminae, two layers of tissue responsible for suspending the skeleton within the hoof capsule, detach, resulting in rotation and sinking of the pedal bone.  While there are many pathophysiological conditions associated with this disease, to date there have been few studies of molecular mechanism.  Our group has found that failure of this tissue is likely to be mediated by dysregulation of the laminar basal epithelial cells (LBECs) of the secondary epidermal lamellae, resulting in aberrant metalloprotease production and down regulation of the canonical wnt signaling pathway.  This leads to detachment of these LBECs from each other and their basement membrane, as well as reorganization of the surrounding extracellular matrix.  By characterizing the expression of these proteins throughout disease, our group has defined the molecular pathology of acute, carbohydrate-induced laminitis, and identified several targets for therapeutic intervention.


Talk Title: ECM Stiffness and Modulus as Independent Controllers of Cancer Metastasis

Speaker: Dannielle Ryman, Molecular and Cellular Biology Program

Abstract: Twenty to thirty percent of breast cancer cases will have metastases, which is the process by which individual cells leave the primary tumor site and colonize distant organs. Our objective is to study metastatic breast cancer at an early developmental stage, and to examine how the extracellular matrix (ECM) influences cell invasion at the primary tumor site. The ECM has been shown to affect cell motility via ligand-receptor interactions, and physical cues, such as matrix stiffness. Given that the primary tumor site considerably stiffens during disease progression, it seems likely that the ability of cells to sense and respond to these matrix features is relevant to cancer cell invasion.  It is now widely accepted that mechanical properties of the ECM can regulate cell migration. However, up to now, tissue modulus and stiffness have been used as interchangeable terms, and it is not clear if cell responses are sensitive to bulk tissue modulus, or, rather, tissue stiffness on the geometric length scale of the cell.  We have adapted two experimental systems to quantify the independent effects of ECM stiffness and modulus on the migration of breast cancer cells.

First, we have a polymer microlens system that contains a PDMS base, which has a patterned array of cylindrical wells, coated with a thin, spuncoated film of polystyrene (PS). Cells only directly interact with the PS layer, but by controlling the geometry of both the PS and the PDMS, we can independently tune the stiffness and modulus that the cells experience. The inherent polymer architecture of the PDMS and PS controls the geometry-independent modulus, while the PDMS well diameter and thickness of the PS independently control the geometric stiffness. The completed microlenses consist of “compliant” regions of a thin film of PS (1.5N/m), and “stiff” regions where the PS film is supported by the PDMS (12 and 37N/m). Our second model system consists of poly(ethylene glycol) (PEG)-based hydrogels, wherein we can control the hydrogel thickness (on the order of tens of microns), independently of crosslinker concentration. The crosslinker content controls the hydrogel modulus, whereas the thickness of the gel overlaying a rigid glass coverslip controls the stiffness. Both the microlenses and the PEG hydrogels were coated with varying concentrations of collagen, and we quantified the migration of the metastatic breast cancer cell lines MDA-MB-231. Thus far, our results show that the highly metastatic MDA-MB-231 are stiffness sensitive: cells achieve maximum cell speeds at high concentrations of collagen I on the polymer microlenses and show a biphasic response dependent on stiffness on PEG-PC hydrogels. We are currently investigating what role integrin-binding proteins play in controlling mechanosensing across these geometric length scales, and if we can control mechanosensing via force transduction signaling pathways. By determining the appropriate length-scale by which mechanical properties regulate cancer metastasis, we hope to eventually uncover novel therapeutics to block cell invasion. 


Talk Title: "Hybrid-push" model- a common mechanism in all RNA polymerases.

Speaker: Satamita Samanta, Chemistry Graduate Program

Abstract: The molecular machine RNA polymerase carries out this highly regulated and essential process in each of our cells. The well-studied RNA polymerases fall into two distinct and apparently unrelated classes: the “single subunit” family, and the multi-subunit bacterial and eukaryotic enzyme family. Although the structural details of initiation complexes from single subunit (T7 RNA polymerase) and from multi-subunit (bacterial and eukaryotic Pol II) RNA polymerases are known, the energetic and mechanistic details of abortive cycling (the premature release of short RNA products from initially transcribing complexes) and promoter escape remain puzzling. To test global mechanistic hypotheses, we study the role of the RNA-DNA hybrid, sigma factor and transcription bubble collapse in abortive cycling and backtracking in initially transcribing complexes of E. coli RNA polymerase to show that the fundamental mechanism of abortive cycling is common in all polymerases. We have engineered nicks, gaps and mismatch sequences in DNA templates to understand the role of the collapse of the transcriptional bubble in abortive initiation. We demonstrate clearly that DNA “scrunching” is not the primary driving force of abortive instability. Instead, our results argue for a “hybrid-push” model that links the requirement of timed promoter release to hybrid instability. My studies with a mutant sigma factor support this model and present clear parallels in both prokaryotic and eukaryotic DNA dependent RNA polymerases.


Talk Title: A conundrum of covariation: The effects of missing data on disparity analysis

Speaker: Andrew Smith, Organismic & Evolutionary Biology Program

Abstract: Disparity, or morphological diversity, is a metric of biodiversity used to analyze evolutionary trends in form over geological timescales. Although missing data are common in fossil datasets, we do not fully understand how sensitive disparity metrics are to missing data. We wished to simulate the non-random removal of characters from a phylogenetic data matrix to explore how data loss affects disparity output. First we calculated covariation in character loss from extinct taxa in the matrix, and then used that covariance structure to remove characters from a data-rich matrix of extant taxa. We then sequentially removed characters in every taxon from the extant matrix such that the average character loss across taxa represented 0% to 75% loss. At each character loss step, we calculated morphospace range and variance (average spread and dissimilarity among taxa respectively) with and without character covariation. With covariation, range and variance metrics exhibited steady declines in disparity as character loss increased. Without covariation, range and variance metrics displayed more rapid declines in disparity with significantly steeper slopes. Results show that character covariation has important consequences for disparity metrics, and should be taken into consideration in future disparity studies when comparing groups with different amounts of loss.


Talk Title: The Rising Cost of Living: Growth Energies in Hydrothermal Vent Systems

Speaker: Lucy Stewart, Department of Microbiology

Abstract: Deep-sea hydrothermal vent sites are considered a good model for potential sites of extraterrestrial life, due to their extreme conditions and chemosynthesis-based ecosystems. Efforts have been made to model microbial distribution at these sites based on the differing energy availability from various forms of chemosynthesis, to help predict habitability at extraterrestrial sites. However, the accuracy of these models is restricted by a lack of experimentally derived data for the minimum energy requirements of anaerobic, chemosynthetic microorganisms, especially at thermophilic temperatures. Our study experimentally measured growth energies of the methanogenic archaea Methanocaldococcus jannaschii (optimum 82°C) and Methanothermococcus thermolithotrophicus (optimum 65°C) across a range of temperatures and bio-available nitrogen concentrations. We found that their growth energies rose with temperature but were comparable between the two organisms, even with optimal growth temperatures and ranges approximately 20°C apart. In contrast, nitrogen availability had no impact on their growth energies. This suggests that current models, which assume that organisms’ growth energies rise with optimal growth temperature, may be overestimating minimum growth energies for methanogenic archaea at these sites.


Talk Title: Genetic diversity and structure of Bangladeshi jackfruit

(Artocarpus heterophyllus, Moraceae)

Speaker: Colby Witherup, Plant Biology Graduate Program

Abstract: Jackfruit (Artocarpus heterophyllus, Moraceae) is an important fruit crop throughout Asia, including in Bangladesh, where deforestation has resulted in the loss of most natural areas. Little is known about its origins or levels of diversity throughout its range. Bangladesh could be a prime source of jackfruit genetic material due to the presence of diverse phenotypes and its proximity to the possible area of origin. My research seeks to measure a baseline of current diversity, identify patterns of genetic structure to shed light on the evolution and domestication history of the crop, measure changes in diversity, and identify causes of possible diversity loss. Thirteen microsatellite markers were used to analyze 394 jackfruit individuals from throughout Bangladesh. Diversity levels were spread relatively equally among 8 geographic districts of Bangladesh. Weak correlation was found between genetic differentiation and geographic districts through pairwise comparison of Fst and Structure analysis. In Bangladesh, jackfruit is traditionally propagated through the direct planting of seeds, but nursery-raised, seed-propagated saplings have increased in popularity since the 1980s. My results identify a trend of diversity loss over time. However, my results suggest that the change from direct-seed to sapling propagation is not influencing the loss of diversity.

Posted by Bryan Olson on October 29, 2012