Life Sciences Commons^™

High Intralocus Variability And Interlocus Recombination Promote Immunological Diversity In A Minimal Major Histocompatibility System, Anthony B. Wilson, Camilla M. Whittington, Angela Bahr

Publications and Research

Background: The genes of the major histocompatibility complex (MHC/MH) have attracted considerable scientific interest due to their exceptional levels of variability and important function as part of the adaptive immune system. Despite a large number of studies on MH class II diversity of both model and non-model organisms, most research has focused on patterns of genetic variability at individual loci, failing to capture the functional diversity of the biologically active dimeric molecule. Here, we take a systematic approach to the study of MH variation, analyzing patterns of genetic variation at MH class IIα and IIβ loci of the seahorse, which …

Effects Of Extreme Climate Events On Tea (Camellia Sinensis) Functional Quality Validate Indigenous Farmer Knowledge And Sensory Preferences In Tropical China, Selena Ahmed, John Richard Stepp, Colin M. Orians, Timothy S. Griffin, Corene Matyas, Albert Robbat, Sean Cash, Dayuan Xue, Chunlin Long, Uchenna Unachukwu, Sarabeth Buckley, Edward J. Kennelly

Publications and Research

Climate change is impacting agro-ecosystems, crops, and farmer livelihoods in communities worldwide. While it is well understood that more frequent and intense climate events in many areas are resulting in a decline in crop yields, the impact on crop quality is less acknowledged, yet it is critical for food systems that benefit both farmers and consumers through high-quality products. This study examines tea (Camellia sinensis; Theaceae), the world’s most widely consumed beverage after water, as a study system to measure effects of seasonal precipitation variability on crop functional quality and associated farmer knowledge, preferences, and livelihoods. Sampling was conducted in …

Component Trees For The Exploration Of Macromolecular Structures In Biology, Lucas Oliveira

Dissertations, Theses, and Capstone Projects

Understanding the three-dimensional structure of a macromolecular complex is essential for understanding its function. A component tree is a topological and geometric image descriptor that captures information regarding the structure of an image based on the connected components determined by different grayness thresholds. This dissertation presents a novel interactive framework for visual exploration of component trees of the density maps of macromolecular complexes, with the purpose of improved understanding of their structure. The interactive exploration of component trees together with a robust simplification methodology provide new insights in the study of macromolecular structures. An underlying mathematical theory is introduced and …

Foraging Ecology Of Shorebirds At A Stopover Site: Niche Dynamics, Aggression And Resource Use In Delaware Bay, Ivana Novcic

Dissertations, Theses, and Capstone Projects

Classical ecological theory predicts that generally similar species ought to partition resources in order to minimize competition amongst themselves. This basic idea becomes complex when one is dealing with species that migrate over thousands of miles and forage in a broad diversity of habitats and geographical locations. I studied a suite of migratory sandpipers, and asked whether they partitioned niches at a major migratory stopover in Delaware Bay. During migration, shorebirds form large, usually mixed-species flocks, which forage on marshes, mudflats, beaches or similar two-dimensional habitats where all individuals are distributed on the same horizontal plane. These habitats are often …

Ecological Niches, Species Distributions, And Biogeographic Processes In Rodents On Neotropical Sky Islands, Mariano Soley

Dissertations, Theses, and Capstone Projects

This dissertation focused on the methodological and theoretical improvement of correlative ecological niche models (ENMs) to better understand the processes governing species distributions and associated evolutionary divergence in rodents inhabiting mesic conditions in the Neotropics. Focusing on a widespread rodent from northern South America (Heteromys anomalus), in the first chapter I proposed and tested a methodological approach to surmount the challenge of incorporating environmental information from the margins of species geographic ranges into ENMs. In so doing, I argue how populations that exist on the borders of species' local ranges (spatial margins) can lead to exaggerated estimates of their niches …

High Local Diversity Of Trypanosoma In A Common Bat Species, And Implications For The Biogeography And Taxonomy Of The T. Cruzi Clade, Veronika M. Cottontail, Elisabeth K. V. Kalko, Iain Cottontail, Nele Wellinghausen, Marco Tschapka, Susan L. Perkins, C. Miguel Pinto

Publications and Research

The Trypanosoma cruzi clade is a group of parasites that comprises T. cruzi sensu lato and its closest relatives. Although several species have been confirmed phylogenetically to belong to this clade, it is uncertain how many more species can be expected to belong into this group. Here, we present the results of a survey of trypanosome parasites of the bat Artibeus jamaicensis from the Panama´ Canal Zone, an important seed disperser. Using a genealogical species delimitation approach, the Poisson tree processes (PTP), we tentatively identified five species of trypanosomes – all belonging to the T. cruzi clade. A small monophyletic …

Long-Term Cre-Mediated Retrograde Tagging Of Neurons Using A Novel Recombinant Pseudorabies Virus, Hysell V. Oviedo, Hassasna K. Oyibo, Petr Znamenskiy, Lynn W. Enquist, Anthony M. Zador

Publications and Research

Brain regions contain diverse populations of neurons that project to different long-range targets. The study of these subpopulations in circuit function and behavior requires a toolkit to characterize and manipulate their activity in vivo. We have developed a novel set of reagents based on Pseudorabies Virus (PRV) for efficient and long-term genetic tagging of neurons based on their projection targets. By deleting IE180, the master transcriptional regulator in the PRV genome, we have produced a mutant virus capable of infection and transgene expression in neurons but unable to replicate in or spread from those neurons. IE180-null mutants showed no cytotoxicity, …

Review: Zinc’S Functional Significance In The Vertebrate Retina, Harris Ripps, Richard L. Chappell

Publications and Research

This review covers a broad range of topics related to the actions of zinc on the cells of the vertebrate retina. Much of this review relies on studies in which zinc was applied exogenously, and therefore the results, albeit highly suggestive, lack physiologic significance. This view stems from the fact that the concentrations of zinc used in these studies may not be encountered under the normal circumstances of life. This caveat is due to the lack of a zinc-specific probe with which to measure the concentrations of Zn2+ that may be released from neurons or act upon them. However, a …

Anthocyanin Characterization, Total Phenolic Quantification And Antioxidant Features Of Some Chilean Edible Berry Extracts, Anghel Brito, Carlos Areche, Beatriz Sepúlveda, Edward J. Kennelly, Mario J. Simirgiotis

Publications and Research

The anthocyanin composition and HPLC fingerprints of six small berries endemic of the VIII region of Chile were investigated using high resolution mass analysis for the first time (HR-ToF-ESI-MS). The antioxidant features of the six endemic species were compared, including a variety of blueberries which is one of the most commercially significant berry crops in Chile. The anthocyanin fingerprints obtained for the fruits were compared and correlated with the antioxidant features measured by the bleaching of the DPPH radical, the ferric reducing antioxidant power (FRAP), the superoxide anion scavenging activity assay (SA), and total content of phenolics, flavonoids and anthocyanins …

Collective Behaviour Without Collective Order In Wild Swarms Of Midges, Alessandro Attanasi, Andrea Cavagna, Lorenzo Del Castello, Irene Giardina, Stefania Melillo, Leonardo Parisi, Oliver Pohl, Bruno Rossaro, Edward Shen, Edmondo Silvestri, Massimilano Viale

Publications and Research

Collective behaviour is a widespread phenomenon in biology, cutting through a huge span of scales, from cell colonies up to bird flocks and fish schools. The most prominent trait of collective behaviour is the emergence of global order: individuals synchronize their states, giving the stunning impression that the group behaves as one. In many biological systems, though, it is unclear whether global order is present. A paradigmatic case is that of insect swarms, whose erratic movements seem to suggest that group formation is a mere epiphenomenon of the independent interaction of each individual with an external landmark. In these cases, …

Deriving High-Resolution Protein Backbone Structure Propensities From All Crystal Data Using The Information Maximization Device, Armando D. Solis

Publications and Research

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), …

Computational Analyses Of The Components Of Sinorhizobium Meliloti Exor-Exos/Chvi Pathway: The Exor And Exos Proteins, Eliza M. Wiech

Dissertations, Theses, and Capstone Projects

The Sinorhizobium meliloti periplasmic ExoR protein and the ExoS/ChvI two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. In the absence of crystal structures, understanding the molecular mechanism of interaction between ExoR and the ExoS sensor, which is thought to drive the key regulatory step in the invasion process, remains a major challenge. In this study, we present theoretical structural models of the active form of ExoR protein, ExoRm, as well as of the sensing domain of ExoS, ExoSp, generated using computational methods. Our model suggests that ExoRm possesses a super-helical fold comprising …

Comparative Phylogeography, Phylogenetics, And Population Genomics Of East African Montane Small Mammals, Terrence Constant Demos

Dissertations, Theses, and Capstone Projects

The Eastern Afromontane region of Africa is characterized by striking levels of endemism and species richness which rank it as a global biodiversity hotspot for diverse plants and animals including mammals, but has been poorly sampled and little studied to date. Using mtDNA and multi-locus nDNA sequence data, genome-wide RAD-Seq SNP data, and morphological data, I identify major cryptic biogeographic patterns within and between 11 co-distributed small mammal species/species groups across the Eastern Afromontane region. I focus on two endemic montane small mammal species complexes, Hylomyscus mice and Sylvisorex shrews, co-distributed across the Albertine Rift (AR) and Kenya Highlands (KH) …

Variation In Habitat Thresholds: An Analysis Of Minimum Habitat Requirements Of North American Breeding Birds, Yntze Van Der Hoek

Dissertations, Theses, and Capstone Projects

Many species show dramatic changes in population extinction or persistence probability at particular habitat amounts. These `extinction thresholds' could be translated to conservation targets, under the condition that we can derive generalities. I investigated the level of variation in landscape-level habitat thresholds for a suite of North American, forest-associated, breeding birds. Records from Breeding Bird Atlases and the availability of remotely-sensed land cover data allowed me to compare habitat thresholds for 25 species across the states of Massachusetts, Michigan, New York, Ohio, Pennsylvania, and Vermont. I show that variation in thresholds is considerable (Chapter II, III), as thresholds range from …

A Systematic Revision Of North American Tolypella A. Braun (Charophyceae, Charophyta), William Perez

Dissertations, Theses, and Capstone Projects

Charophyta comprises the algal classes Mesostigmatophyceae, Chlorokybophyceae, Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae and the land plants. However, the precise phylogenetic position of these algal classes with respect to land plants is unresolved as are the phylogenetic relationships among genera in Charophyceae (Characeae). Characeae contains two tribes with six genera: tribe Chareae (Chara, Lamprothamnium, Lychnothamnus and Nitellopsis) and tribe Nitelleae (Nitella and Tolypella). Tolypella was considered the third most species-rich genus but, in the most comprehensive taxonomic treatment of Characeae, 16 Tolypella species were consolidated into two species, T. nidifica and T. intricata in sections Rothia …

Role Of The Polyadenylation Factor Cstf-50 In Regulating The Brca1/Bard1 E3 Ubiquitin (Ub) Ligase Activity, Danae Fonseca

Dissertations, Theses, and Capstone Projects

The cellular response to DNA damage is an intricate mechanism that involves the interplay among several pathways. The studies presented in this dissertation focus on the determination and characterization of the role of mRNA processing factor CstF-50 and escort protein p97 in the regulation of the BRCA1/BARD1 E3 ubiquitin (Ub) ligase activity during the DNA damage response (DDR).

As part of the studies presented in Chapter II, I determined that the polyadenylation factor CstF plays a direct role in DDR, specifically in transcription-coupled repair (TCR), and that it localizes with RNA polymerase II (RNAP II) and BARD1 to sites of …

Association Between Symptomatic Vulvovaginal Candidiasis And Hiv Rna Levels In Plasma And Genital Secretions Among Women On Haart, Teke Apalata, William H. Carr, Benjamin Longo-Mbenza, Willem A. Sturm, P. Moodley

Publications and Research

Background. Genital tract (GT) inflammation plays a major role in HIV transmission. We aimed to determine the association between symptomatic vulvovaginal candidiasis (VVC) and HIV RNA levels in plasma and GTs of HIV-infected women on highly active antiretroviral therapy (HAART).

Method. Women with VVC on HAART were recruited from a primary healthcare clinic in KwaZulu-Natal Province, South Africa, between June 2011 and December 2011. VVC was diagnosed clinically, supported by Gram staining and culture of genital secretions. HIV RNA load was determined by reverse transcription polymerase chain reaction. CD4+ counts were obtained from patients’ medical records.

Results. Plasma HIV RNA …

Bioactivities Of Compounds From Elephantopus Scaber, An Ethnomedicinal Plant From Southwest China, Jianjun Wang, Ping Li, Basosai Li, Zhiyong Guo, Edward J. Kennelly, Chunlin Long

Publications and Research

Elephantopus scaber is an ethnomedicinal plant used by the Zhuang people in Southwest China to treat headaches, colds, diarrhea, hepatitis, and bronchitis. A new δ-truxinate derivative, ethyl, methyl 3,4,3′,4′-tetrahydroxy-δ-truxinate (1), was isolated from the ethyl acetate extract of the entire plant, along with 4 known compounds. The antioxidant activity of these 5 compounds was determined by ABTS radical scavenging assay. Compound 1 was also tested for its cytotoxicity effect against HepG2 by MTT assay (IC50 = 60 μM), and its potential anti-inflammatory, antibiotic, and antitumor bioactivities were predicted using target fishing method software.

Polymerase Alpha Components Associate With Telomeres To Mediate Overhang Processing, Raffaella Diotti

Dissertations, Theses, and Capstone Projects

Telomeres consist of TTAGGG repeats, which end with a 3' G-overhang and are bound by a six-protein complex, known as Shelterin. In humans, telomeres shorten at each cell division, unless telomerase is expressed and able to add telomeric repeats to the 3' G-overhang. However, for effective telomere maintenance, the DNA strand complementary to that made by telomerase must be synthesized. In this study, I focused on the Polα/primase complex, in particular the subunits p68 (POLA2, the regulatory subunit) and p180 (Polα, the catalytic subunit), and their potential roles at telomeres. I was able to detect p180, p68 and OBFC1, a …

The Interplay Of Visual Attention And Saccade Planning In Active Vision, Afsheen Khan

Dissertations, Theses, and Capstone Projects

Vision is a highly active process. When we view the world, we do not hold our eyes still, but constantly move them around in order to view the object or area of interest with the fovea (the region of the retina with the highest acuity). Saccades are the step-like movements that we most often employ for this purpose. In addition, our attention is constantly being covertly attracted or directed to points of interest. Combining these different aspects of viewing: visual processing, the orienting of attention, and eye movements can be referred to as `active vision'.

Most work on active vision …

Phylogeny, Taxonomy And Morphological Evolution In Conostegia (Melastomataceae: Miconieae), Ricardo Kriebel

Dissertations, Theses, and Capstone Projects

The genus Conostegia comprises 77 species of shrubs and trees ranging from Central America to northern South America and the Caribbean. They are ecologically important as they provide pollen for native bees and fruits for birds. One of the main questions of this study is if the genus Conostegia is actually monophyletic. I address this question for the first time by gathering genetic data from four chloroplast regions and two nuclear ribosomal regions of DNA. Phylogenetic analyses of these data revealed that Conostegia is not monophyletic and that a group of species in the genera Clidemia and Miconia fall within …

An Experimental Investigation Into The Mechanisms Of Bacterial Evolution, Zhenmao Wan

Dissertations, Theses, and Capstone Projects

This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation …

Identification And Characterization Of Protein Phopshatases Regulating The Sma/Mab Pathway In C. Elegans, Sheng Xiong

Dissertations, Theses, and Capstone Projects

TGF-beta signaling is a conserved signaling pathway among eukaryotes, which controls various normal cellular responses from cell proliferation to cell death. The mutations in its components are found in developmental disorders and cancer. Therefore, this signaling pathway is extensively investigated so that new therapeutic targets could be discovered and novel drugs could be developed. Previous studies suggested the involvement of phosphatases in regulation of TGF-beta signaling, but these studies were performed in cell culture rather than intact organisms. C. elegans is a tractable organism in which to study signaling in vivo. In C. elegans, growth is controled by a conserved …

Comparative Modeling And Functional Characterization Of Two Enzymes Of The Cyclooxygenase Pathway In Drosophila Melanogaster, Yan Qi

Dissertations, Theses, and Capstone Projects

Eicosanoids are biologically active molecules oxygenated from twenty carbon polyunsaturated fatty acids. Natural eicosanoids exert potent biological effects in humans, and a great deal of pharmaceutical research has led to the discovery of compounds for selective inhibition of specific enzymes in eicosanoid biosynthesis. Coupled with different receptors, eicosanoids mediate various physiological and pathophysiological processes, including fever generation, pain response, vasoconstriction, vasodilation, platelet aggregation, platelet declumping, body temperature maintenance and sleep-wake cycle regulation. In mammals, the eicosanoid biosynthesis has three pathways: the cyclooxygenase (COX) pathway, the lipoxygenase (LOX) pathway and the epoxygenase pathway. The COX pathway synthesizes prostanoids, which are important …

Testing Assumptions Of Coevolution In An Egg-Rejecting Brood Parasite Host: Uncovering Sensory, Cognitive, And Evolutionary Drivers Of Responses To Parasitism In American Robins (Turdus Migratorius), Rebecca Croston

Dissertations, Theses, and Capstone Projects

Hosts of brood parasitic birds face fitness costs associated with rearing unrelated offspring. In response, the recognition and rejection of parasitic eggs is a common host defense. Brown-headed cowbirds (Molothrus ater) challenge coevolutionary theory, because although they exploit over 200 host species, they lay non-mimetic eggs, and most hosts do not combat cowbird parasitism with egg rejection. American robins (Turdus migratorius) are one of a handful of cowbird hosts known to recognize and remove cowbird eggs from the nest. I addressed the mechanistic and evolutionary drivers of egg rejection in this host species, by disentangling the roles of spectral tuning …

How Important Is Land-Based Foraging To Polar Bears (Ursus Maritimus) During The Ice-Free Season In Western Hudson Bay? An Examination Of Dietary Shifts, Compositional Patterns, Behavioral Observations And Energetic Contributions, Linda J. Gormezano

Dissertations, Theses, and Capstone Projects

Trophic mismatches between predators and their prey are increasing as climate change causes decoupling of phenological relationships. Predators linked to the life histories of a particular prey will have a more difficult time persisting through environmental change unless they can alter their behavior to maintain the historical match or possess the ability to pursue alternate prey. Arctic predators typically possess flexible foraging strategies to survive in the labile environment, however, quantifying the limits of those strategies can be difficult when life history information is incomplete. In such cases, piecing together different aspects of a predator's foraging behavior, particularly when environmental …

Metabolic Checkpoints In Cancer Cell Cycle, Mahesh Saqcena

Dissertations, Theses, and Capstone Projects

Growth factors (GFs) as well as nutrient sufficiency regulate cell division in metazoans. The vast majority of mutations that contribute to cancer are in genes that regulate progression through the G1 phase of the cell cycle. A key regulatory site in G1 is the growth factor-dependent Restriction Point (R), where cells get permissive signals to divide. In the absence of GF instructions, cells enter the quiescent G0 state. Despite fundamental differences between GF signaling and nutrient sensing, they both have been confusingly referred to as R and therefore by definition considered to be a singular event in G1. Autonomy from …

Lipid Dependence In Ras-Driven Tumors, Darin Salloum

Dissertations, Theses, and Capstone Projects

Over past decade, metabolic alterations in cancer cells have received a substantial amount of interest. It had been established that cancer cells undergo a significant amount of metabolic alterations, and some of these alterations are similar to those in normal highly proliferative cells. However, it is becoming more apparent that many of the metabolic alterations are specific to particular oncogenic signaling pathways. Although altered metabolic machinery makes cancer cells more efficient at promoting growth when nutrients are supplied at the sufficient amounts, the dependency of cancer cells on particular metabolic reprogramming deems cancer cells susceptible to disruptions within metabolic network. …

Chytrid Loads, Pathogen Prevalence, And Contemporary Host Source-Sink Dynamics In Dry Vs. Wet Forests; Evaluating Refugia From Disease In Australian Torrent Frogs., Barbara Rizzo

Dissertations and Theses

No abstract provided.

The Impact Of Saccadic Eye Movement Training On Saccade Accuracy And Latency, Stephanie Montenegro

Dissertations and Theses

No abstract provided.