Poster Abstracts for The 2012 Life Sciences Graduate Research Symposium

Posted by Bryan Olson on October 29, 2012

All of the Poster Abstracts for The Life Sciences Graduate Research Symposium, arranged alphabetically by last name.

Poster Title: Function and Evolution of Bacterial Microcompartments in Clostridia

Presenter: Farah Abdul-Rahman, Department of Microbiology

Abstract: Clostridia are a genetically diverse class of bacteria that are generally fermentative, endospore-forming, anaerobes with gram-positive cells walls.  They are present as commensals in the guts of many insects and animals, as soil saprophytes, and in agricultural and industrial effluent streams.  The Clostridia include potential bioremediation agents, important producers of biofuels, immune system stimulators and toxic producing pathogens.  Bacterial microcompartment (BMC) genes, which express organelles composed entirely of proteins and that carry out a specific metabolic reaction, have recently been reported in several Clostridia.   Using domain representations of the BMC genes we identified BMCs in genomes of over 50 Clostridia species, including human pathogens.  BMC genes frequently clustered at a single locus coding for a BMC with a distinctive metabolic role.  The Clostridia BMCs include functional types known to encode proteins for the metabolism of ethanolamine and propanediol, but novel classes of BMCs are present that contain genes suggesting putative functional roles.  In some species there are two or three BMC loci coding for different evolutionary and/or functional classes of BMCs.        Using Clostridium phytofermentans as a model, we demonstrate that the three BMC loci are differently expressed.  The distribution of BMC-containing species was mapped onto a phylogenetic tree constructed from 16S rRNA.  The presence of BMCs is sporadically distributed across the phylogenetic tree.  All families that contained species with BMCs also had species without BMCs.  Even within a species, BMC number varied indicative of frequent horizontal transfer and gene loss. Similarly, phylogenetic trees constructed from individual BMC genes indicates that gene transfer into/out of the Clostridia is a common occurrence.  Analysis of BMC distribution in the context of a Clostridia environmental attribute database allowed us to determine physiological and genomic characters that correlate with the presence of BMCs.  

 

Poster Title: Predicting population-level changes in ragweed (Ambrosia artemisiifolia L.) response to elevated carbon dioxide

Presenter: Jennifer M. Albertine, Stockbridge School of Agriculture

Abstract:

Background/Question/Methods

Assessing ecotypic variation in plant response to predicted levels of carbon dioxide (CO2) is a priority for understanding climate change effects on plant species, especially those that can affect human health. Common ragweed, a native annual North American plant, is a well-known allergenic weed that increases growth and reproduction in experimentally elevated CO2 conditions. However, it is not well known whether plants from environmentally distinct populations respond differently to elevated carbon dioxide. Ecotypic variation in CO2 response was tested here by exposing plants from 24 populations across a latitudinal gradient in the Northeastern US to three levels of CO2: 400 ppm, 600 ppm, and 800 ppm. The objective of the study was to test for differences among ecotypes in 1) changes in timing and duration of flowering, and 2) stimulatory effects on biomass and reproductive allocation. Wild-collected seeds from each population were planted in pots in outdoor growth chambers and evaluated weekly for phenological and growth data. Experimental design of 4 replications of each of the 3 carbon dioxide levels and 4 replications of the 24 populations within each chamber resulted in assessment of 1,152 plants. Plants were harvested and dried for biomass at the end of the growing season.

 

Results/Conclusions

Overall, northern populations showed the most stimulation while southern populations showed the least in response to elevated CO2. Preliminary results (n=300) indicate that plants flowered earlier and longer in elevated CO2 concentrations; this was especially evident in the northern most populations where the timing was earlier and longer than the mid- and low- latitudes. There was a significant increase in shoot and root biomass for all populations with elevated CO2; the greatest stimulation occurred in the northern populations. Northern populations invested the most mass in seed production and southern populations invested more mass in vegetative growth at 800ppm CO2 while mid-latitudes showed a switch from seed investment to vegetative investment with increasing CO2. The implications for male flower and pollen production are currently under study. It can be concluded from the current analysis that future CO2 concentrations may have the greatest effect on allergy season in northern parts of the study range due to the longer flowering season and enhanced reproductive effort.

 

Poster Title: Migratory birds in tropical agro-ecosystems: Assessing the influence of patch and landscape factors on habitat quality.

Presenter: Brett A. Bailey, Environmental Conservation Program

Abstract: Identification of the habitats that support non-breeding migrants and provide sufficient resources for spring migration is a critical research priority.  As agricultural development continues throughout the tropics, effective conservation planning requires an understanding of the role that local and landscape structure play in determining the quality of agricultural habitat for migratory birds.  Through a combination of point count, banding, and telemetry data collected from coffee farms and nearby forest fragments, we will model habitat quality across an agricultural region of northern Honduras.  Two species of high conservation concern, Wood Thrush and Golden-winged Warbler, are of particular interest.  This study addresses numerous research priorities by providing demographic information for species of high concern, by providing a robust local assessment of coffee habitat suitability for Neotropical migrants, and by quantifying the role of landscape structure in tropical agro-ecosystems.   We are working in collaboration with a local coffee cooperative, and within the context of an international education and research collaborative that includes universities in Massachusetts, Honduras, Nicaragua and Costa Rica.  Through these collaborations, this work will directly promote awareness of conservation issues and sustainable agricultural practices among coffee farmers, and will be widely disseminated throughout the coffee growing regions of Latin America.

 

Poster Title: Conservation genetics of brook trout (Salvelinus fontinalis) in Stanley Brook, Acadia National Park.

Presenter: Matthew Cembrola, Environmental Conservation Program

Abstract: Stanley Brook has been the site of a long-term, individual-based ecological study of brook trout (Salvelinus fontinalis) since 2006 through 2012.  Detailed demographic data have been collected over this time period, including abundance, survival rates, and individual growth rates.  Furthermore, fishing was stopped in the middle of this time period, in 2009.  This study therefore provides an opportunity to examine demographic and evolutionary responses to the cessation of size-selective harvest.  Here, we used genetic data from subsets of individuals distributed throughout the stream to estimate the effective number of breeders (Nb) for the 2006, 2008, 2009, 2010 and 2011 cohorts.  We then compared estimates of Nb to estimates of the number of adult (Na) brook trout present in the stream at the time of spawning.  Following the cessation of fishing, Na increased by approximately 123%, whereas Nb declined by about50%.  One possible explanation for this result is that skew in reproductive success has been greater since fishing stopped and the size of adults has increased. We performed a detailed analysis of reproductive skew for the 2008 cohort, prior to when fishing stopped. Based on the distribution of full-sibling family size, reproductive skew was low for that cohort, consistent with high Nb at this time period. An additional test of a later cohort would be required to test for the predicted increase in skew following the cessation of fishing.  The full sibling analysis allowed us to accomplish a secondary goal of examining the spatial distribution of spawning locations in Stanley Brook. We found distinct spatial clustering of families, suggesting that spawning and juvenile habitat is used throughout the stream. Our results lead to a counterintuitive result for management:  since the closure of fishing, population size has increased, but Nb, that is, the number of individuals successfully reproducing and transmitting genes to the next generation, has decreased. While an increase in population size bodes well for short-term persistence, a decrease in Nb may lower the likelihood of persistence over a longer time period.  Future genetic monitoring will be needed to determine if the trend in declining Nb continues.

 

Poster Title: Identifying WC1 Scavenger Receptor Cysteine-Rich “a1” Domains that Binds Leptospira spp.

Presenter: Rashalai Currington, Department of Veterinary and Animal Sciences

Abstract: WC1 molecules belong to the scavenger receptor cysteine-rich (SRCR) superfamily and are closely related to human CD163 genes (7, 8) SRCR domains are structurally highly conserved across evolutionary time, suggesting their functional importance (8).  WC1 molecules are a family 9of transmembrane glycoproteins exclusively expressed on cattle gamma delta Tcells (5). These WC1 molecules are grouped according to the recognition of their N-terminal SRCR a1 domains by the antibodies WC1.1 and WC1.2 (3). Only gamma delta Tcells expressing the WC1.1-type WC1 molecules, but not those expressing the WC1.2-type, respond to Leptospira spp. No SRCR domains from the WC1.2-type WC1-4 bind to Leptospira spp. In our study we hypothesize that only a subset of the WC1.1-type of WC1 molecules bind to Leptospira spp. The N-terminal a1 SRCR domains from WC1.1-type (WC-1, WC1-2, WC1-3, WC1-11) and from the WC1.2 –type WC1-9 were assessed for their binding to Leptospira spp. Preliminary data from a bacterial pull-down assay suggest that the N-terminal a1 SRCR domains from WC1.1-type WC1-1 and WC1-3 bind to Leptospira spp while the WC1.1-type WC1-2 and WC1-11 and WC1.2-type WC1-9 do not bind to bacteria. The further elucidation of which WC1 SRCR domains bind pathogens offers promise for the development of improved vaccines and other anti-bacterial agents.

 

Poster Title: Morphological and phonological traits affecting grain sorghum yield

Presenter: Fatemeh Etemadi, Sustainable Food and Farming

Abstract: Understanding the physiological and morphological aspects of sorghum may help

to improve grain yield through cultivation management and breeding strategies.

Correlation of phenology and morphology of sorghum varieties with grain yield,

were studied in an experiment conducted in 2009-2010. We found no positive correlation between plant height and grain yield. In fact the shortest genotype had the highest yield among all tested genotypes (9896 kg ha-1) and the lowest grain yield obtained from the tallest genotype (6348 kg ha-1). In this study we also found no distinctive correlation between biomass and final grain yield. The studied genotypes showed no GDD requirement differences until milk

stage. Significant differences were found in GDD requirement for milk stage as

well as dough stage. The most productive genotypes required greater GDD to reach

these two important growth stages. For example KGS5 which produced the highest

yield, required 1359 GDD to reach milking stage whereas KGS31 which was the

least productive genotype, reached milk stage after collecting only 1171 GDD.

Final sorghum grain yield determined primarily by average grain number per plant

followed by seed size. The top five high producing yield genotypes produced 12%

more grains compared to the bottom five genotypes. The difference in seed size of

high and low producing genotypes was only 4%.

 

 

Poster Title: An Assay to Assess Corticosterone in Rat Fur

Presenter: Christina Felder Gagliardi, Neuroscience and Behavior Program

Abstract: Corticosterone is the primary stress hormone released by rats during both acute and chronic stress.  While many methods exist for measuring acute stress in rats, there is currently no method for surveying chronic stress.  Assays have been developed to measure cortisol, the primary stress hormone in many other species, in the hair of humans, monkeys, dogs, and bears.  These assays can assess overall HPA activity over the span of one to three months.  Corticosterone has been effectively assayed in feathers, but never in fur.  Furthermore, rat fur differs greatly from other types of hair or fur and thus presents many challenges. We developed an assay which surmounts these challenges and can be used to consistently assess the concentration of corticosterone in rat fur.  The multistep process removes contaminants from the exterior of the hair shaft, extracts the corticosterone from the interior, and then purifies the extract.  The concentration of corticosterone in the purified extract can then be assessed using a commercially available corticosterone EIA kit. Ongoing work addresses the correlation between corticosterone concentration in the fur and changes in HPA activity.

 

Poster Title: Optimizing Bioremediation of Complex Organic Compounds using Hyperthermophiles

Presenter: Sarah Hensley, Department of Microbiology

Abstract: In the US, eutrophication causes $3 billion in losses each year through creating dead zones that kill aquatic macrofauna. Eutrophication can be caused by domestic and industrial waste streams, which are well-regulated to remove contaminants. However, complex organic compounds are difficult to remediate given their size. Since many waste streams are currently heat-treated, hyperthermophilic microorganisms (growth optimum above 80oC) can efficiently degrade complex organic compounds. However, these waste streams present a wide variety of environmental conditions, which may affect bioremediation rates. Pyrococcus furiosus represents an ideal study microorganism because of a: 1) capability to degrade many complex organic compounds, 2) characterization of enzymes in these degradation pathways 3) genomic sequence and 4) genetically tractable system. We are examining the change in growth rates, compound production and enzymatic expression in peptide and sugar degradation pathways of P. furiosus based on pH, acetate and H2 levels. Initially, we established protocols and values for 12 enzymatic assays in sugar or peptide-grown controls, which reflect previous findings. Also, we see a correlation between acetate presence and cell-specific H2 production rates, suggesting that enzymatic activities change with acetate presence. Finally, based on genomes analysis, P. furiosus could indicate how other hyperthermophiles respond to environmental changes. However, this remains to be examined, as well as the ability of P. furiosus to bioremediate agricultural and sewage waste products.

 

Poster Title: Air Pollution and Disadvantaged Populations in Southern California

Presenter: Megan Kierstead, Environmental Conservation Program

Abstract: Exposure to air pollution can lead to a number of health problems including lung conditions, heart attacks, cancer, and impaired childhood lung development. Underprivileged populations are particularly vulnerable to these types of environmental hazards because of regulations and decisions that can target these communities for the least desirable land uses. Southern California consistently ranks among the worst regions in the United States for air quality and has significant geographic disparities in economic privilege. Despite these risks, there have been no studies mapping the spatial coincidence of air pollution and economic disadvantage in Southern California to determine if disadvantaged communities are disproportionately affected by air pollution.

I use spatial analysis and statistical techniques to model Particulate Matter (PM10) dispersion and clusters of economically disadvantaged communities in six counties in Southern California that consistently fail to meet federal air quality standards. These techniques revealed spatial patterns positively associating economic disadvantage and increased air pollution exposure using multiple economic measures. I also found that the urban poor likely receive more intense air pollution exposure than the rural poor. Given the implications for public health and land use, more work should be done to understand the spatial relationships between air pollution and health risks.

 

Poster Title:  Emotional memory consolidation over mid-day sleep in early development

Presenter: Kurdziel, L.B.K., Neuroscience and Behavior Program

Abstract: Children transition to a monophasic sleep pattern (weaned from naps) between 4-6 years of age. A recent study, and decades of anecdotal evidence, suggests that naps play a role in emotional processing at this age.  In young adults, emotional memories are prioritized for consolidation over sleep. We hypothesized that naps benefit emotional regulation by consolidating recent emotional memories. To examine this, children (mean age = 51.7 +/- 6.7 months) were tested on their memory for faces described as either “mean,” or “nice.” Children were tested following a nap and an equivalent period of wake. All were tested in both conditions to control for differences in brain maturation and only children who napped at least 60 minutes were included (n = 28). Memory performance was not different immediately following a nap and wake period. However, the following day, a delayed benefit of the prior day’s nap was seen (F(1,22) = 4.22, p = 0.05). Nap-dependent consolidation was greatest for mean faces (t(22) = 1.68 p = 0.05).  Moreover, the total time spent napping for all children correlated with overall memory performance improvement (r = 0.33, p = 0.03). These results support a role of napping in emotional memory consolidation during development.

 

Poster Title: Phylogenetic Analysis of Cucurbita pepo Using Molecular Markers.

Presenter: Emad A. Mady, Stockbridge School of Agriculture

Abstract: Plant identification, classification, and genotyping within a germplasm collection are essential elements towards establishing a breeding program.  Breeding programs that make use of morphological and genetic diversity in selecting parental lines can enhance the probability of plants with desirable characteristics in the market place.  In this study, RAPD was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and hyperplasia.  A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77%) were polymorphic, indicating a large number of genotypes within the summer squash lines.  Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups.  Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program.

 

Poster Title: Can signaling between clonal strawberry ramets enhance resistance to insects?

Presenter: Evan Palmer-Young, Organismic & Evolutionary Biology Program

Abstract: Organisms in all kingdoms can benefit from the ability to anticipate and respond to threatening environmental conditions. In plants, constrained mobility makes anticipation of danger particularly important. The anticipation of herbivore presence is known as a "primed" state, in which a plant becomes more resistant to future attack than an "unprimed" control. Signals from damaged neighbor plants could provide reliable hints of nearby herbivores. Clonal plants, with genetically identical "sender" and "receiver" ramets, are probable systems in which to discover such signals. In beach strawberry, Fragaria chiloensis, "receiver" ramets could exploit three avenues of communication with damaged "sender" ramets to achieve a "primed" state: vascular signaling, in which "receivers" respond to cues that travel from "senders" through the aboveground stolons connecting ramets; volatile signaling, in which "receivers" respond to odors released from damaged "senders"; and rhizospheric signaling, in which "receivers" are primed by root exudates. I will manipulate "sender" herbivory together with vascular, volatile, and rhizospheric communication between ramets to determine the contributions of each of these communication channels to the "priming" of "receivers". Future work will evaluate whether these signals are genotype-specific. Results will suggest agricultural strategies to enhance insect resistance in monocultural crops without the use of pesticides.

 

Poster Title: Pre- and Post-Dredging Spartina alterniflora Productivity in a Threatened Salt Marsh

Presenter: Ellen Russell, Stockbridge School of Agriculture

Abstract: The tidal inlet of Ellisville Salt Marsh, Plymouth, Massachusetts (28 ha) has been dredged for fishing industry since 1770. In 1987, cessation of maintenance dredging led to tidal restriction, an apparent 3.5 ha loss of Spartina alterniflora over a 10 year period, and down-coast property erosion. A 2011 permit was obtained to alleviate constriction of tidal flow and restore Spartina alterniflora. Surface soil temperatures, obtained before and after dredging from each of 96 marsh monitoring plots, were translated to tidal hydroperiod estimates. Mean hydroperiod increased by 44% from pre- to post-dredge conditions and mean semi-diurnal tidal range increased by 0.4 m. A positive linear relationship between leaf height and hydroperiod (p<0.001, r2 =0.20, α = 0.05) for S. alterniflora was present. Plots with tall form S. alterniflora dominant (>55% cover) increased by 10% following dredging. Concentrations of NH4+ and PO43- in pore water significantly decreased after dredging (NPMANOVA, p<0.0001, α = 0.05). Stem density, salinity and pore water [S2-] were not significantly different post dredging. A parabolic relationship of the plant root-to-shoot ratio to hydroperiod, found an optimum range of 3000 to 6000 minutes inundation per month. These relationships will be considered during permit renewal in 2014.

 

Poster Title: Evaluating Switchgrass Varieties for Biomass Yield and Quality in Massachusetts

Presenter:  Amir Sadeghpour, Stockbridge School of Agriculture

Abstract: Currently there is little or no published data on switchgrass (Panicum virgatum L.) yield potential for Massachusetts. Our objective was to determine how cultivars perform in this northeastern United States climate and how time of harvest affected yield and quality of switchgrass.  Five upland varieties (Blackwell, Carthage, Cave-in-Rock-, Shawnee, and Shelter) were harvested at senescence (fall), kill frost (winter), and spring between 2009-2011. Measurements were taken for yield, ash, total nitrogen, and mineral content in the feedstock and non-structural carbohydrates in roots at each time of harvest. In the first year Carthage was the highest yielding variety, and harvesting at senescence in the fall consistently produced higher yields for all varieties than harvesting in winter or spring. Nutrients such as nitrogen, phosphorus, potassium, magnesium and ash all decreased in the feedstock when the harvest was delayed from fall to winter or spring. Soluble nonstructural carbohydrate concentrations in the roots were three times higher in the winter than in the fall. These levels decreased again in the spring. Results of this study recommend a winter harvest after a killing frost rather than a fall post-anthesis harvest.

 

Poster Title: PilA-independent mechanism of Fe(III) oxide reduction in Geobacter sulfurreducens strain KN400

Presenter: Jessica Smith, Department of Microbiology

Abstract: The type IV pili of Geobacter sulfurreducens are essential for Fe(III) oxide reduction and efficient electron transfer to electrodes. The pili microbial nanowires show electrical properties similar to that of organic metals which permit long range electron transport. The G. sulfurreducens pili are decorated with the multi heme c-type cytochrome OmcS, which is also required for Fe(III) oxide reduction. The deletion of pilA, the gene encoding the protein subunit of the pili filament, completely inhibits growth on Fe(III) oxides in both G. sulfurreducens and G. metallireducens. However, after several months the pilA deletion mutant was able to adapt to growth on Fe(III) oxide at a reduced rate in G. sulfurreducens KN400. Through continuous transfer the adapted strain became more proficient and started reducing insoluble Fe(III) oxide faster than the original KN400 strain. Microarray, proteomic, and deletion studies indicated that this adaptation was mostly due to the over-expression of a c-type cytochrome known as PgcA, which was previously identified to be involved in accelerated Fe(III) oxide reduction in G. sulfurreducens. Although this strain was a proficient Fe(III) oxide reducer, it was unable to produce current on the anode indicating this mechanism is not suited for long range electron transport. This study illustrates how microorganisms can activate a back-up plan for survival. Moreover, the decision of Geobacter species to initially use one mechanism of Fe(III) oxide reduction over the other indicates that the type IV pili-based mechanism is more robust and better suited for the environment than the c-type cytochrome only-based mechanism. 

 

Poster Title: The Purification of Bacterial Microcompartments from Clostridium Phytofermentans

Presenter: Megan Strough, Department of Microbiology

Abstract: Bacterial microcompartments, or BMCs, are 100-200nm, enzyme-encompassing organelles composed of interlocking proteins that form cyclical hexamers with a small central pore.  Clostridium phytofermentans or Cphy, is a Gram-positive, rod shaped, anaerobic soil microbe that has the ability to not only break down multiple polysaccharides simultaneously but also proceeds to ferment them into biofuels.   The genome of Cphy contains 3 BMC loci.  During growth on fucose and rhamnose, one of these loci is highly expressed and microcompartments can be viewed using TEM.  Under these growth conditions, three products, ethanol, propanol and propionate, which could potentially be highly useful in the biofuel and bioproducts industries, are produced.  The goal of this project is to harvest and purify BMCs from Cphy cultures in an effort to expand our understanding of the role that these structures play in the degradation of polysaccharides. We are currently developing methods to isolate BMCs. These BMCs will be analyzed by electrophoresis and subsequently submitted for proteomic analysis to determine their composition.  Furthering our understanding of these microcompartments and their constituents may allow for engineering higher levels of biofuel production and new products. 

 

Poster Title: Molecular detection and population genetics of Peronospora belbahrii from basil Presenter: Andrea L. Vu, Stockbridge School of Agriculture

Abstract: Downy mildew on basil is a destructive, emerging disease of basil (Ocimum basilicum) that was first reported in the U.S. in 2007. In 2011, 100% of commercial basil growers in Massachusetts reported crop loss due to this disease; with some growers estimating up to 100% loss. Downy mildew on basil is caused by Peronospora belbahrii, an obligate biotrophic oomycete that was formally described as a new species in 2009. Although the pathogen has been shown to spread long distances via seed, and locally by wind, the predominant mode of dispersal has yet to be determined. We are additionally interested to find out if hybridization is driving virulence. The incidence and prevalence of P. belbahrii on basil seed and seedlings were explored with a qPCR detection assay with specific primers. The pathogen was detected on seed that resulted in plants that did not show disease symptoms, and was also not detected on seed that resulted in plants that did become diseased; indicating that seedborne infection is not the sole mode of dispersal and “resistant” cultivars can be carriers. Population structure is being explored by analysis of rRNA, and preliminary results will be discussed.