Life Sciences Commons^™

Musical Regularity And Rhythmic Patterns: A Quantitative Analysis Of Birdsong Structure, Eathan Ezra Janney

Dissertations, Theses, and Capstone Projects

Birdsong is a complex, learned behavior that, like music, has meaningful units at multiple timescales. Birds perform by constructing extended presentations of their phrase repertoire. Each bird's repertoire is built from small units, such as syllables, or groups of syllables with characteristic pitch, rhythm, and timbre. Like a musician each bird has its unique structure of performance that communicates its individual identity. Also contained within a bird's performance, is information about its group identity and species identity. Like a musician's performance, a bird's singing affects the behavioral state of listeners'birds perform to attract mates and defend territory.

Subjectively, many can …

The Role Of The Vta Nmda Receptors, Vta Da Cells And Vta Terminal Regions In Reward-Related Learning, Karen Kest

Dissertations, Theses, and Capstone Projects

Reward-related learning occurs when an initially neutral stimulus acquires the capacity to elicit responses similar to an unconditioned stimulus (US) with which it is associated, in which case the stimulus now functions as a conditioned stimulus (CS). The mechanisms whereby stimuli come to function as CSs are not fully understood and comprise the theme of this dissertation. We have previously proposed that coincident signals from an unconditioned and the eventual conditioned stimulus (US and CS) signals on dopamine (DA) cells of the ventral tegmental area (VTA) leads to strengthening of CS synapses, allowing the CS to acquire the ability to …

Regulation Of The Vacuolar Atpase Activity, Paulina Konarzewska

Dissertations, Theses, and Capstone Projects

In eukaryotes, V-ATPases play an essential role in cellular pH homeostasis as they transport hydrogen ions into the vacuoles. This assures an acidic vacuolar interior and normal physiological processes associated with this organelle. Studies show that mutations in any of the VMA genes encoding for subunits of the V-ATPase pump result in growth inhibition in the absence of inositol, suggesting that V-ATPases may play an important role in phospholipid biosynthesis or vice versa. It is not clear how VMA genes affect phospholipid biosynthesis and how the regulators of phospholipid biosynthetic genes may affect ATPase activity. Here, we employ biochemical and …

Molecular-Genetic And Behavioral Analysis Of The Functionality Of Patterning In The Trigeminal Neuraxis, Dana Bakalar

Dissertations, Theses, and Capstone Projects

A striking feature of the vibrissal representation in rodents is the presence; at brainstem (barrellettes), thalamic (barrelloids) and cortical levels (barrels) of a somatotopically organized pattern of neurons which is isomorphic, both morphologically and physiologically, to the pattern of vibrissae on the snout. The vibrissal system is required for several classes of behavior, including feeding and active vibrissal sensing, but the functional role of the patterning in these behaviors is unknown. We used two mutant animals lacking patterning in two areas of the vibrissal neuraxis to examine the functional role of patterning. We examined feeding behavior using a knockout of …

Diversity And Phylogeography Of Anurans Of The Highlands Of Ethiopia, Xenia Freilich

Dissertations, Theses, and Capstone Projects

Located in Eastern Africa, Ethiopia is a country of unique geological features, among them the largest continuous Afro-alpine zone in Africa and the Great Rift Valley (GRV). The GRV formation began ~20 mya; it is a fault system that splits the central Ethiopian dome in two separate highland systems (Baker et al., 1972, Chorowicz, 2005). In spite of the general assumption that the GRV has played a major role in shaping the biodiversity of the country, its influence has not been fully investigated, as only a handful of studies have addressed its impact on the phylogeographic and evolutionary history of …

Cultural Evolution In Natural Populations: A Quantitative Bioacoustic Analysis, Chenghui Ju

Dissertations, Theses, and Capstone Projects

Bird song is a powerful model system in behavioral biology, especially for learning and cultural evolution. Understanding the origins and maintenance of vocal diversity in nature is fundamentally important to acoustic biology. Here, we propose a large-scale, integrative population analysis of nearly 2000 songs of the house finch (Haemorhous mexicanus) (190 individuals) collected in western Long Island of New York during an interval of 37 years (between 1975 and 2012) to explore cultural change of bird songs. Generally, I have three aims in this study. In the chapter 1, to facilitate acoustic analysis for field recordings with ambient noise, of …

The Role Of Atp And Cleavage Factor Phosphorylation In Pre-Mrna 3' Cleavage Reaction, Asya Khleborodova

Dissertations, Theses, and Capstone Projects

The 3' end cleavage/polyadenylation (3' processing) is important in generating a functional messenger RNA (mRNA) transcript. It is long-known that ATP can significantly stimulate the in vitro cleavage of adenovirus type 2 L3 (Ad2L3) RNA substrate. Here, we used ATP analogs in structure-activity assays to show that the structural features of ATP and its analogs determine in vitro 3' cleavage efficiency. More specifically, we demonstrate that the structure of the nitrogenous base, the nucleotide sugar and the triphosphate group contribute to the efficiency of the nucleotide-stimulated in vitro 3' cleavage reaction.

It was found that AppNp, an analog of ATP …

Incipient Speciation In Freshwater Fish Species From Two Isolated Watersheds, Paula Gore Miller

Dissertations, Theses, and Capstone Projects

The process of speciation occurs as a result of restricted gene flow between segments of an interbreeding population occupying different geographic areas. This separation may result in isolated populations which undergo genetic and phenotypic changes. The Wisconsin glacial period, which ended approximately 17,500 years ago, dramatically altered the geography of North America. The glacier covered almost the entire North America as it advanced. Areas that were not covered with ice provided suitable habitats (refugia) for relict species that were previously widespread in the northern section of the continent. As the ice sheet retreated, animals and plants were able to return …

Biophysical Characterization Of A De Novo Elastin, Kelly Nicole Greenland

Dissertations, Theses, and Capstone Projects

Natural human elastin is found in tissue such as the lungs, arteries, and skin. This protein is formed at birth with no mechanism present to repair or supplement the initial quantity formed. As a result, the functionality and durability of elastin's elasticity is critically important. To date, the mechanics of this ability to stretch and recoil is not fully understood. This study utilizes de novo protein design to create a small library of simplistic versions of elastin-like proteins, demonstrate the elastin-like proteins, maintain elastin's functionality, and inquire into its structure using solution nuclear magnetic resonance (NMR).

Elastin is formed from …

Exploiting Cancer Cell Signaling And Metabolism: Implications For Therapeutic Approach, Suman Mukhopadhyay

Dissertations, Theses, and Capstone Projects

Over the last decade, metabolic dysregulation in cancer cells has stimulated a significant amount of interest in basic research. It has been established that cancer cells increase glucose uptake and alter the fate of glycolytic and tricarboxylic acid (TCA) cycle intermediates for the synthesis of biological molecules to accommodate high rates of cellular growth and proliferation. Moreover, it is more prominent that some metabolic dysregulations are specific to particular oncogenes. Exploiting the dysregulated metabolic dependency of cancer cells with therapeutic means could represent a novel approach for clinical aspect.

To meet the need of increased anabolic metabolism cancer cells engage …

Dna Methylation Dynamics Of Germinal Center B Cells Are Mediated By Aid, Pilar M. Dominguez, Matt Teater, Nyasha Chambwe, Matthias Kormaksson, David Redmon, Jennifer Ishii, Bao Vuong, Jayanta Chaudhuri, Ari Melnick, Aparna Vasanthakumar, Lucy A. Godley, F. Nina Papavasiliou, Oliver Elemento, Rita Shaknovich

Publications and Research

Changes in DNA methylation are required for the formation of germinal centers (GCs), but the mechanisms of such changes are poorly understood. Activation-induced cytidine deaminase (AID) has been recently implicated in DNA demethylation through its deaminase activity coupled with DNA repair. We investigated the epigenetic function of AID in vivo in germinal center B cells (GCBs) isolated from wild-type (WT) and AID-deficient (Aicda^−/−) mice. We determined that the transit of B cells through the GC is associated with marked locus-specific loss of methylation and increased methylation diversity, both of which are lost in Aicda^−/− animals. Differentially …

An Evolutionary Vaccination Game In The Modified Activity Driven Network By Considering The Closeness, Dun Han, Mei Sun

Publications and Research

In this paper, we explore an evolutionary vaccination game in the modified activity driven network by considering the closeness. We set a closeness parameter p which is used to describe the way of connection between two individuals. The simulation results show that the closeness p may have an active role in weakening both the spreading of epidemic and the vaccination. Besides, when vaccination is not allowed, the final recovered density increases with the value of the ratio of the infection rate to the recovery rate λ/μ. However, when vaccination is allowed the final density of recovered individual first increases and …

Homo Naledi, A New Species Of The Genus Homo From The Dinaledi Chamber, South Africa, Lee R. Berger, John Hawks, Darryl J. De Ruiter, Steven E. Churchill, Peter Schmid, Lucas K. Delezene, Tracy L. Kivell, Heather M. Garvin, Scott A. Williams, Jeremy M. Desilva, Matthew M. Skinner, Charles M. Musiba, Noel Cameron, Trenton W. Holliday, William Harcourt-Smith, Et Al.

Publications and Research

Homo naledi is a previously-unknown species of extinct hominin discovered within the Dinaledi Chamber of the Rising Star cave system, Cradle of Humankind, South Africa. This species is characterized by body mass and stature similar to small-bodied human populations but a small endocranial volume similar to australopiths. Cranial morphology of H. naledi is unique, but most similar to early Homo species including Homo erectus, Homo habilis or Homo rudolfensis. While primitive, the dentition is generally small and simple in occlusal morphology. H. naledi has humanlike manipulatory adaptations of the hand and wrist. It also exhibits a humanlike foot and lower …

A Generalist Brood Parasite Modifies Use Of A Host In Response To Reproductive Success, Matthew I M Louder, Wendy M. Schelsky, Amber N. Albores, Jeffrey P. Hoover

Publications and Research

Avian obligate brood parasites, which rely solely on hosts to raise their young, should choose the highest quality hosts to maximize reproductive output. Brown-headed cowbirds (Molothrus ater) are extreme host generalists, yet female cowbirds could use information based on past reproductive outcomes to make egg-laying decisions thus minimizing fitness costs associated with parasitizing low quality hosts. We use a long-term (21 years) nest box study of a single host, the prothonotary warbler (Protonotaria citrea), to show that local cowbird reproductive success, but not host reproductive success, was positively correlated with the probability of parasitism the following …

Short Peptides In Minimalistic Biocatalyst Design, Krystyna L. Duncan, Rein V. Ulijn

Publications and Research

We review recent developments in the use of short peptides in the design of minimalistic biocatalysts focusing on ester hydrolysis. A number of designed peptide nanostructures are shown to have (modest) catalytic activity. Five features are discussed and illustrated by literature examples, including primary peptide sequence, nanosurfaces/scaffolds, binding pockets, multivalency and the presence of metal ions. Some of these are derived from natural enzymes, but others, such as multivalency of active sites on designed nanofibers, may give rise to new features not found in natural enzymes. Remarkably, it is shown that each of these design features give rise to similar …

Suitability Of Great South Bay, New York To Blooms Of Pfiesteria Piscicida And P. Shumwayae Prior To Superstorm Sandy, October 29, 2012, Pawel Tomasz Zablocki

Theses and Dissertations

Pfiesteria piscicida and P. shumwayae are toxic dinoflagellates implicated in massive fish kills in North Carolina and Maryland during 1990s. A set of physical, chemica l, and biological factors influence population dynamics of these organisms. This study employs i nformation gathered from relevant literature on temperature, salinity, dissolved oxygen, pH, turbulent mixing, and dissolved nutrients, bacteria, algae, microzooplankton, mesozooplankton, bivalve m ollusks, finfish, and other toxic dinoflagellates, which influence Pfiesteria population dynamics. The research focused on whether conditions in the Great South Bay, Long Island, New York were suitable to blooms of Pfiesteria species prior to the passage of superstorm …

Geospatial Resolution Of Human And Bacterial Diversity With City-Scale Metagenomics, Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Amber Simmons, Timothy Nessel, Bharathi Sundaresh, Elizabeth Pereira, Ellen Jorgensen, Sergios-Orestis Kolokotronis, Nell Kirchberger, Isaac Garcia, David Gandara, Sean Dhanraj, Tanzina Nawrin, Yogesh Saletore, Noah Alexander, Priyanka Vijay, Elizabeth M. Hénaff, Paul Zumbo, Michael Walsh, Gregory D. O'Mullan, Scott Tighe, Joel T. Dudley, Anya Dunaif, Sean Ennis, Eoghan O'Halloran, Tiago R. Magalhaes, Braden Boone, Angela L. Jones, Theodore R. Muth, Katie Schneider Paolantonio, Elizabeth Alter, Eric E. Schadt, Jeanne Garbarino, Robert J. Prill, Jane M. Carlton, Shawn Levy, Christopher E. Mason

Publications and Research

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial …

Population Genetic Structure Of The Dwarf Seahorse (Hippocampus Zosterae) In Florida, Nathan Fedrizzi, Melanie L. J. Stiassny, J. T. Boehm, Eric R. Dougherty, George Amato, Martin Mendez

Publications and Research

The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as …

Common Cell Shape Evolution Of Two Nasopharyngeal Pathogens, Frédéric J. Veyrier, Nicolas Biais, Pablo Morales, Nouria Belkacem, Cyril Guilhen, Sylvia Ranjeva, Odile Sismeiro, Gérard Péhau-Arnaudet, Eduardo P. Rocha, Catherine Werts, Muhamed-Kheir Taha, Ivo G. Boneca

Publications and Research

Respiratory infectious diseases are the third cause of worldwide death. The nasopharynx is the portal of entry and the ecological niche of many microorganisms, of which some are pathogenic to humans, such as Neisseria meningitidis and Moraxella catarrhalis. These microbes possess several surface structures that interact with the actors of the innate immune system. In our attempt to understand the past evolution of these bacteria and their adaption to the nasopharynx, we first studied differences in cell wall structure, one of the strongest immune-modulators. We were able to show that a modification of peptidoglycan (PG) composition (increased proportion of pentapeptides) …

Nitric Oxide-Releasing Aspirin Suppresses Nf-Κb Signaling In Estrogen Receptor Negative Breast Cancer Cells In Vitro And In Vivo, Niharika Nath, Mitali Chattopadhyay, Deborah B. Rodes, Anna Nazarenko, Ravinder Kodela, Khosrow Kashfi

Publications and Research

Estrogen receptor negative (ER(−)) breast cancer is aggressive, responds poorly to current treatments and has a poor prognosis. The NF-κB signaling pathway is implicated in ER(−) tumorigenesis. Aspirin (ASA) is chemopreventive against ER(+) but not for ER(−) breast cancers. Nitric oxide-releasing aspirin (NO-ASA) is a safer ASA where ASA is linked to an NO-releasing moiety through a spacer. In vitro, we investigated anti-proliferation effects of NO-ASA (para- and meta-isomers) against ER(−) breast cancer cells MDA-MB-231 and SK-BR-23, effects on NF-κB signaling, and reactive oxygen species by standard techniques. In vivo, effects of NO-ASA were evaluated in a mouse xenograft model …

Mechanotransduction: Use The Force(S), Ewa K. Paluch, Celeste M. Nelson, Nicolas Biais, Ben Fabry, Jens Moeller, Beth L. Pruitt, Carina Wollnik, Galina Kudryasheva, Florian Rehfeldt, Walter Federle

Publications and Research

Mechanotransduction - how cells sense physical forces and translate them into biochemical and biological responses - is a vibrant and rapidly-progressing field, and is important for a broad range of biological phenomena. This forum explores the role of mechanotransduction in a variety of cellular activities and highlights intriguing questions that deserve further attention.

Rationale, Design And Respondent Characteristics Of The 2013–2014 New York City Health And Nutrition Examination Survey (Nyc Hanes 2013–2014), Lorna E. Thorpe, Carolyn Greene, Amy Freeman, Elisabeth Snell, Jesica S. Rodriguez-Lopez, Martin Frankel, Amado Punsalang Jr., Claudia Chernov, Elizabeth Lurie, Mark Friedman, Ram Koppaka, Sharon E. Perlman

Publications and Research

Purpose. Capacity to monitor non-communicable diseases (NCDs) at state or local levels is limited. Emerging approaches include using biomeasures and electronic health record (EHR) data. In 2004, New York City (NYC) performed a population-based health study on adult residents using biomeasures (NYC Health and Nutrition Examination Study, or NYC HANES), modeled after NHANES. A second NYC HANES was launched in 2013 to examine change over time, evaluate municipal policies, and validate a proposed EHR-based surveillance system. We describe the rationale and methods of NYC HANES 2013–2014.

Methods. NYC HANES was a population-based, cross-sectional survey of NYC adults using three-stage cluster …

Lesion-Specific Immune Response In Granulomas Of Patients With Pulmonary Tuberculosis: A Pilot Study, Selvakumar Subbian, Liana Tsenova, Mi-Jeong Kim, Helen C. Wainwright, Annalie Visser, Nirmalya Bandyopadhyay, Joel S. Bader, Petros C. Karakousis, Gabriele B. Murrmann, Linda-Gail Bekker, David G. Russell, Gilla Kaplan

Publications and Research

The formation and maintenance of granulomas is central to the host response to Mycobacterium tuberculosis (Mtb) infection. It is widely accepted that the lungs of patients with tuberculosis (TB) usually contain multiple infection foci, and that the granulomas evolve and differentiate independently, resulting in considerable heterogeneity. Although gene expression profiles of human blood cells have been proposed as biomarkers of Mtb infection and/or active disease, the immune profiles of discrete lesion types has not been studied extensively. Using histology, immunopathology and genome-wide transcriptome analysis, we explored the immunological profile of human lung TB granulomas. We show that although the different …

Monitoring The Progression Of Spontaneous Articular Cartilage Healing With Infrared Spectroscopy, Megan P. O'Brien, Madhuri Penmatsa, Uday Palukuru, Paul West, Xu Yang, Mathias P. G. Bostrom, Theresa Freeman, Nancy Pleshko

Publications and Research

Objective. Evaluation of early compositional changes in healing articular cartilage is critical for understanding tissue repair and for therapeutic decision-making. Fourier transform infrared imaging spectroscopy (FT-IRIS) can be used to assess the molecular composition of harvested repair tissue. Furthermore, use of an infrared fiber-optic probe (IFOP) has the potential for translation to a clinical setting to provide molecular information in situ. In the current study, we determined the feasibility of IFOP assessment of cartilage repair tissue in a rabbit model, and assessed correlations with gold-standard histology.

Design. Bilateral osteochondral defects were generated in mature white New Zealand rabbits, and …

Inhibition Of Cell Differentiation In Bacillus Subtilis By Pseudomonas Protegens, Matthew J. Powers, Edgardo Sanabria-Valentín, Albert A. Bowers, Elizabeth A. Shanka

Publications and Research

Interspecies interactions have been described for numerous bacterial systems, leading to the identification of chemical compounds that impact bacterial physiology and differentiation for processes such as biofilm formation. Here, we identified soil microbes that inhibit biofilm formation and sporulation in the common soil bacterium Bacillus subtilis. We did so by creating a reporter strain that fluoresces when the transcription of a biofilm-specific gene is repressed. Using this reporter in a coculture screen, we identified Pseudomonas putida and Pseudomonas protegens as bacteria that secrete compounds that inhibit biofilm gene expression in B. subtilis. The active compound produced by P. protegens was …

Use Of Rna Sequencing To Evaluate Rheumatic Disease Patients, Eugenia Giannopoulou, Olivier Elemento, Lionel B. Ivashkiv

Publications and Research

Studying the factors that control gene expression is of substantial importance for rheumatic diseases with poorly understood etiopathogenesis. In the past, gene expression microarrays have been used to measure transcript abundance on a genome-wide scale in a particular cell, tissue or organ. Microarray analysis has led to gene signatures that differentiate rheumatic diseases, and stages of a disease, as well as response to treatments. Nowadays, however, with the advent of next-generation sequencing methods, massive parallel sequencing of RNA tends to be the technology of choice for gene expression profiling, due to several advantages over microarrays, as well as for the …

Stably Stratified Canopy Flow In Complex Terrain, Xiyan Xu, Chuixiang Yi, Eric Kutter

Publications and Research

Stably stratified canopy flow in complex terrain has been considered a difficult condition for measuring net ecosystem–atmosphere exchanges of carbon, water vapor, and energy. A long-standing advection error in eddy-flux measurements is caused by stably stratified canopy flow. Such a condition with strong thermal gradient and less turbulent air is also difficult for modeling. To understand the challenging atmospheric condition for eddy-flux measurements, we use the renormalized group (RNG) k–ε turbulence model to investigate the main characteristics of stably stratified canopy flows in complex terrain. In this two-dimensional simulation, we imposed persistent constant heat flux at ground surface and linearly …

Interferon-Γ Regulates Cellular Metabolism And Mrna Translation To Potentiate Macrophage Activation, Xiaodi Su, Yingpu Yu, Yi Zhong, Eugenia Giannopoulou, Xiaoyu Hu, Hui Liu, Justin R. Cross, Gunnar Rätsch, Charles M. Rice, Lionel B. Ivashkiv

Publications and Research

Interferon-γ (IFN-γ) primes macrophages for enhanced inflammatory activation by Toll-like receptors (TLRs) and microbial killing, but little is known about the regulation of cell metabolism or mRNA translation during priming. We found that IFN-γ regulates human macrophage metabolism and translation by targeting the kinases mTORC1 and MNK that both converge on the selective regulator of translation initiation eIF4E. Physiological downregulation of mTORC1 by IFN-γ was associated with autophagy and translational suppression of repressors of inflammation such as HES1. Genome-wide ribosome profiling in TLR2-stimulated macrophages revealed that IFN-γ selectively modulates the macrophage translatome to promote inflammation, further reprogram metabolic pathways, and …

Cell Type Specificity Of Tissue Plasminogen Activator In The Mouse Barrel Cortex, Philip Chu, Eric Chen, Adesh Bajnath, Joshua C. Brumberg

Publications and Research

It has been suggested that tissue-type plasminogen activator (tPA), a serine protease, plays a key role in regulating the extracellular matrix core proteins, thereby impacting the structural plasticity in the cerebral cortex. Much is known about its role in regulating plasticity in the visual cortex. However, its permissive role has not been demonstrated to generalize to other cerebral cortical areas. By utilizing a combination of immunofluorescent histochemistry and confocal microscopy, we demonstrate that endogenous tPA is indeed present in the somatosensory cortex, and its expression is experience-dependent. Chronic sensory deprivation induced by whisker trimming from birth for one month leads …

Core And Shell Song Systems Unique To The Parrot Brain, Mukta Chakraborty, Solveig Walloe, Signe Nedergaard, Emma E. Fridel, Torben Dabelsteen, Bente Pakkenberg, Mads F. Bertelsen, Gerry M. Dorrestein, Steven E. Brauth, Sarah E. Durand, Erich D. Jarvis

Publications and Research

The ability to imitate complex sounds is rare, and among birds has been found only in parrots, songbirds, and hummingbirds. Parrots exhibit the most advanced vocal mimicry among non-human animals. A few studies have noted differences in connectivity, brain position and shape in the vocal learning systems of parrots relative to songbirds and hummingbirds. However, only one parrot species, the budgerigar, has been examined and no differences in the presence of song system structures were found with other avian vocal learners. Motivated by questions of whether there are important differences in the vocal systems of parrots relative to other vocal …