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Articles 1 - 29 of 29
Full-Text Articles in Life Sciences
Ecological Niches, Species Distributions, And Biogeographic Processes In Rodents On Neotropical Sky Islands, Mariano Soley
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 …
Foraging Ecology Of Shorebirds At A Stopover Site: Niche Dynamics, Aggression And Resource Use In Delaware Bay, Ivana Novcic
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 …
Component Trees For The Exploration Of Macromolecular Structures In Biology, Lucas Oliveira
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 …
Computational Analyses Of The Components Of Sinorhizobium Meliloti Exor-Exos/Chvi Pathway: The Exor And Exos Proteins, Eliza M. Wiech
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 …
A Systematic Revision Of North American Tolypella A. Braun (Charophyceae, Charophyta), William Perez
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 …
Variation In Habitat Thresholds: An Analysis Of Minimum Habitat Requirements Of North American Breeding Birds, Yntze Van Der Hoek
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 …
Comparative Phylogeography, Phylogenetics, And Population Genomics Of East African Montane Small Mammals, Terrence Constant Demos
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) …
Role Of The Polyadenylation Factor Cstf-50 In Regulating The Brca1/Bard1 E3 Ubiquitin (Ub) Ligase Activity, Danae Fonseca
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 …
Phylogeny, Taxonomy And Morphological Evolution In Conostegia (Melastomataceae: Miconieae), Ricardo Kriebel
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 …
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 …
Polymerase Alpha Components Associate With Telomeres To Mediate Overhang Processing, Raffaella Diotti
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 …
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 …
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 …
Lipid Dependence In Ras-Driven Tumors, Darin Salloum
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. …
Metabolic Checkpoints In Cancer Cell Cycle, Mahesh Saqcena
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 …
An Experimental Investigation Into The Mechanisms Of Bacterial Evolution, Zhenmao Wan
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
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 …
The Interplay Of Visual Attention And Saccade Planning In Active Vision, Afsheen Khan
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 …
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
The Impact Of Saccadic Eye Movement Training On Saccade Accuracy And Latency, Stephanie Montenegro
Dissertations and Theses
No abstract provided.
Kos Modulation Of Mitochondrial Fission And Fusion, Herman Kucharavy
Kos Modulation Of Mitochondrial Fission And Fusion, Herman Kucharavy
Dissertations and Theses
No abstract provided.
Structure-Function Analysis Of Zapc, An Ftsz-Ring Stabilizer, In Escherichia Coli Cytokinesis, Lukasz Tchorzewski
Structure-Function Analysis Of Zapc, An Ftsz-Ring Stabilizer, In Escherichia Coli Cytokinesis, Lukasz Tchorzewski
Dissertations and Theses
In Escherichia coli, cell division is defined by the polymerization and constriction of a cytokinetic ring (Z ring) formed by FtsZ, a tubulin-like GTPase, at midcell. Division also involves the formation of a multi-protein complex at midcell known as the divisome. Several divisome proteins promote the assembly/disassembly processes of FtsZ, thereby exercising spatiotemporal control over division. Among FtsZ regulatory proteins are the FtsZ ringassociated proteins (Zap), which either directly or indirectly stabilize the Z-ring by increasing lateral interactions amongst FtsZ protofilaments in the Z-ring. ZapA-D are recruited during early cytokinesis and have overlapping functions in stabilizing FtsZ at midcell, but …
Investigating Innate Immune Signaling Cross-Talk In A Drosophila Tumor-Inflammation Model, Rebecca Moore
Investigating Innate Immune Signaling Cross-Talk In A Drosophila Tumor-Inflammation Model, Rebecca Moore
Dissertations and Theses
No abstract provided.
Methodological Advancements For Improving Performance And Generating Ensemble Ecological Niche Models, Robert Boria
Methodological Advancements For Improving Performance And Generating Ensemble Ecological Niche Models, Robert Boria
Dissertations and Theses
This study employs spatial filtering of occurrence data with the aim of reducing overfitting to sampling bias in ecological niche models (ENMs). Sampling bias in geographic space leads to localities that may also be biased in environmental space. If so, the model can overfit to those biases. As a preliminary test addressing this issue, we used Maxent, bioclimatic variables, and occurrence localities of a broadly distributed Malagasy tenrec, Microgale cowani (Family Tenrecidae: Subfamily Oryzorictinae). We modeled the abiotically suitable area of this species using three distinct datasets: unfiltered, spatially filtered, and rarefied unfiltered localities. To quantify overfitting and model performance, …
Screen For Suppressors And Enhancers Of Excitotoxic Neurodegeneration, Anthony Omorodion Edokpolo
Screen For Suppressors And Enhancers Of Excitotoxic Neurodegeneration, Anthony Omorodion Edokpolo
Dissertations and Theses
Excitotoxicity is an important and frequently observed neurodegenerative process. Excitotoxicity mediates brain damage in a range of diseases and conditions including stroke, and is triggered by excessive stimulation of glutamatergic synapses. In spite of extensive studies, the molecular mechanisms involved in excitotoxicity following the over-activation of postsynaptic glutamate receptors are not well understood, and clinical trials based on our partial understanding of the process ended with disappointment. Genetic screens in simple animal models offer a powerful alternative approach, since screens are unbiased, analysis is facilitated by strong research tools, and cellular mechanisms are highly conserved through evolution. We produced a …
Caffeine's Attenuation Of Cocaine-Induced Deficiency In Acoustic Startle Response By Inhibition Of Adenosine In A Sex And Dose Dependent Manner, Lauren B. Malave
Caffeine's Attenuation Of Cocaine-Induced Deficiency In Acoustic Startle Response By Inhibition Of Adenosine In A Sex And Dose Dependent Manner, Lauren B. Malave
Dissertations and Theses
No abstract provided.
Synaptic Physiology Of Glutamate Clearance In The Nematode Caenorhabditis Elegans, Jenny (Chan Ying) Wong
Synaptic Physiology Of Glutamate Clearance In The Nematode Caenorhabditis Elegans, Jenny (Chan Ying) Wong
Dissertations and Theses
No abstract provided.
A Phylogeographic Study Of Two Neotropical Bird Species, The Red-Headed Manakin (Pipna Rubrocapilla) And The White-Crowned Manakin (Dixiphia Pipra)., Ivandy Castro-Astor
A Phylogeographic Study Of Two Neotropical Bird Species, The Red-Headed Manakin (Pipna Rubrocapilla) And The White-Crowned Manakin (Dixiphia Pipra)., Ivandy Castro-Astor
Dissertations and Theses
No abstract provided.
Experimental Studies Of Rctb- Initiator Of Vibrio Cholerae Chromosome Ii Replication: Genetic Engineering, Protein Purification, And Protein Crystals, Olha Ivashkiv
Dissertations and Theses
Vibrio cholerae, a member of the Vibrionaceae family, is notorious as the causative agent of acute gastrointestinal disease known as cholera. Genetic information in members of the Vibrionaceae family is distributed between two chromosomes that are distinctively maintained. In V. cholerae, the initiation of DNA replication in each chromosome involves distinct processes. While the initiation of replication of chromosome I is carried by DnaA, the initiation of chromosome II replication is controlled by RctB, a DNA-binding protein that is an exclusive attribute of all Vibrio species. RctB has no homologs among other members of bacteria proteins and can serve as …