Life Sciences Commons^™

Living With Coyotes, Owen H. Agnew

Capstones

Coyotes have been slowly moving into New York State from Canada since the 1930s. They reached Westchester County and the Bronx decades ago, and their numbers have been slowly rising. Sighting in Manhattan reached an all-time high last spring, and pet attacks in Westchester County have increased slightly in the last several years. But the slight increase in sightings and pet attacks in recent years has been amplified on social media in towns like Chappaqua, New York, where anxiety and fear about coyotes has pitted neighbors against neighbors.

Main character Frank Vincenti is a Long Island barber and a self-proclaimed …

The Sixty-Six Percent, Natalie Abruzzo

Capstones

The Sixty-Six Percent represent the percentage of women in the U.S. who are overweight. They are regarded as full-figured or “plus” size in the world of women’s apparel. Even though more than half of American women wear a “plus” size - size 14 and up - designs for these women account for a fraction of women’s apparel - Only 37% of women's wear is plus-size.

The Sixty-Six Percent is coming at an important time in a broader conversation about de-stigmatizing what it means to be a plus-size woman in America. Fat shaming has become taboo and mainstream media as well …

Special Muscles, Annamaria C. Scaccia

Capstones

Special Muscles is a documentary that explores living with Duchenne muscular dystrophy, a fatal degenerative disease that weakens the muscles at an aggressive rate. The film will give an uncensored look at how one family copes with inevitability of the disease and their journey chasing a promising experimental cure.

Special Muscles follows 7-year-old Pietro Scarso and his family as they face the challenges, complications and promise of treating Pietro’s progressive muscle disorder. The film travels from New York to Los Angeles to Philadelphia to document the Scarso family’s race against time as Pietro undergoes a 96-week clinical trial for Eteplirsen, …

Elimination Of Chromosomal Island Spycim1 From Streptococcus Pyogenes Strain Sf370 Reverses The Mutator Phenotype And Alters Global Transcription, Christina Hendrickson, Chad W. Euler, Scott V. Nguyen, Maliha Rahman, Kimberly A. Mccullor, Catherine J. King, Vincent A. Fischetti, W. Michael Mcshan

Publications and Research

Streptococcus pyogenes chromosomal island M1 (SpyCIM1) integrates by site-specific recombination into the 5’ end of DNA mismatch repair (MMR) gene mutL in strain SF370SmR, blocking transcription of it and the downstream operon genes. During exponential growth, SpyCIM1 excises from the chromosome and replicates as an episome, restoring mutL transcription. This process is reversed in stationary phase with SpyCIM1 re-integrating into mutL, returning the cells to a mutator phenotype. Here we show that elimination of SpyCIM1 relieves this mutator phenotype. The downstream MMR operon genes, multidrug efflux pump lmrP, Holliday junction resolution helicase ruvA, and DNA base excision …

Fungal Melanin: What Do We Know About Structure?, Joshua D. Nosanchuk, Ruth E. Stark, Arturo Casadevall

Publications and Research

The production of melanin significantly enhances the virulence of many important human pathogenic fungi. Despite fungal melanin’s importance in human disease, as well as melanin’s contribution to the ability of fungi to survive in diverse hostile environments, the structure of melanin remains unsolved. Nevertheless, ongoing research efforts have progressively revealed several notable structural characteristics of this enigmatic pigment, which will be the focus of this review. These compositional and organizational insights could further our ability to develop novel therapeutic approaches to combat fungal disease and enhance our understanding of how melanin is inserted into the cell wall.

Pvt1 Exon 9: A Potential Biomarker Of Aggressive Prostate Cancer?, Adeodat Ilboudo, Jyoti Chouhan, Brian K. Mcneil, Joseph R. Osborne, Olorunseun O. Ogunwobi

Publications and Research

Prostate cancer (PCa) is the most commonly diagnosed cancer as well as the greatest source of cancer-related mortality in males of African ancestry (MoAA). Interestingly, this has been shown to be associated with single nucleotide polymorphisms around regions 2 and 3 of the 8q24 human chromosomal region. The non-protein coding gene locus Plasmacytoma Variant Translocation 1 (PVT1) is located at 8q24 and is overexpressed in PCa and, therefore, is also a candidate biomarker to explain the well-known disparity in this group. PVT1 has at least 12 exons that make separate transcripts which may have different functions, all of which are …

The Smell Of Hopelessness, Juline Cariba Rachel Party

Capstones

Rafts of sargassum seaweed kilometers wide have been invading the Caribbean for more than five years, but 2015 was the worst. Tons of seaweed stretch from Texas south to Trinidad and Tobago, with the Lesser Antilles suffering the most damage. Residents near beaches are exposed to an insidious and pernicious danger, scientists say, from fumes that smell like rotten eggs, emitted by the decaying algae. The odor also drives tourists away from beaches and restaurants, and the tourism economy is collapsing.Amid the algae crisis, an elderly woman, Virginie Mark, is trying to survive. She struggles with her health, finances and …

Impact Of Executive Order 13211 On Environmental Regulation: An Empirical Study, Elizabeth Ann Glass Geltman

Publications and Research

A great deal has been written about the Energy Policy Act of 2005 exempting oil and gas operations using hydraulic fracturing from the purview of certain federal environmental laws. Far less attention has been paid to George W. Bush’s Executive Order 13211 (EO 13211), entitled “Actions Concerning Regulations that Significantly Affect Energy Supply, Distribution or Use.” The executive order requires federal agencies to evaluate the impact of federal regulations on “supply, distribution and use of energy.” This study examined the impact of EO 13211 on United States environmental and conservation regulations proposed and promulgated by federal agencies. The study found …

Parn Deadenylase Is Involved In Mirna-Dependent Degradation Of Tp53 Mrna In Mammalian Cells, Xiaokan Zhang, Emral Devany, Michael R. Murphy, Galina Glazman, Mirjana Persaud, Frida E. Kleiman

Publications and Research

mRNA deadenylation is under the control of cis-acting regulatory elements, which include AU-rich elements (AREs) and microRNA (miRNA) targeting sites, within the 3′ untranslated region (3′ UTRs) of eukaryotic mRNAs. Deadenylases promote miRNA-induced mRNA decay through their interaction with miRNA-induced silencing complex (miRISC). However, the role of poly(A) specific ribonuclease (PARN) deadenylase in miRNA-dependent mRNA degradation has not been elucidated. Here, we present evidence that not only ARE- but also miRNA-mediated pathways are involved in PARN-mediated regulation of the steady state levels of TP53 mRNA, which encodes the tumor suppressor p53. Supporting this, Argonaute-2 (Ago-2), the core component of miRISC, …

Chemo-Enzymatic Synthesis Of Site-Specific Isotopically Labeled Nucleotides For Use In Nmr Resonance Assignment, Dynamics And Structural Characterizations, Andrew P. Longhini, Regan M. Leblanc, Owen Becette, Carolina Salguero, Christoph H. Wunderlich, Bruce A. Johnson, Victoria M. D'Souza, Christoph Kreutz, T. Kwaku Dayle

Advanced Science Research Center

Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%.We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch …

Development And Evaluation Of A Multi-Year Fractional Surface Water Data Set Derived From Active/Passive Microwave Remote Sensing Data, Ronny Schroeder, Kyle C. Mcdonald, Bruce D. Chapman, Katherine Jensen, Erika Podest, Zachary D. Tessler, Theodore J. Bohn, Reiner Zimmermann

Publications and Research

The sensitivity of Earth’s wetlands to observed shifts in global precipitation and temperature patterns and their ability to produce large quantities of methane gas are key global change questions. We present a microwave satellite-based approach for mapping fractional surface water (FW) globally at 25-km resolution. The approach employs a land cover-supported, atmospherically-corrected dynamic mixture model applied to 20+ years (1992–2013) of combined, daily, passive/active microwave remote sensing data. The resulting product, known as Surface WAter Microwave Product Series (SWAMPS), shows strong microwave sensitivity to sub-grid scale open water and inundated wetlands comprising open plant canopies. SWAMPS’ FW compares favorably (R2 …

Training A New Trick Using No-Reward Markers: Effects On Dogs’ Performance And Stress Behaviors, Naomi Rotenberg

Theses and Dissertations

This study explored using no-reward markers (NRMs). Dogs were taught a novel trick. In the IG group dogs’ errors were ignored; in the NRM group they elicited a tone. Performance and stress were evaluated. IG dogs reached higher levels of performance, with no difference in the frequency of stress behaviors.

Biomechanical Performances Of Networked Polyethylene Glycol Diacrylate: Effect Of Photoinitiator Concentration, Temperature, And Incubation Time, Morshed Khandaker, Albert Orock, Stefano Tarantini, Jeremiah White, Ozlem Yasar

Publications and Research

Nutrient conduit networks can be introduced within the Polyethylene Glycol Diacrylate (PEGDA) tissue construct to enable cells to survive in the scaffold. Nutrient conduit networks can be created on PEGDA by macrochannel to nanochannel fabrication techniques. Such networks can influence the mechanical and cell activities of PEGDA scaffold. There is no study conducted to evaluate the effect of nutrient conduit networks on the maximum tensile stress and cell activities of the tissue scaffold.The study aimed to explore the influence of the network architecture on the maximum tensile stress of PEGDA scaffold and compared with the nonnetworked PEGDA scaffold. Our study …

The New York Head—A Precise Standardized Volume Conductor Model For Eeg Source Localization And Tes Targeting, Yu Huang, Lucas C. Parra, Stefan Haufe

Publications and Research

In source localization of electroencephalograpic (EEG) signals, as well as in targeted transcranial electric current stimulation (tES), a volume conductor model is required to describe the flow of electric currents in the head. Boundary element models (BEM) can be readily computed to representmajor tissue compartments, but cannot encode detailed anatomical information within compartments. Finite element models (FEM) can capture more tissue types and intricate anatomical structures, but with the higher precision also comes the need for semiautomated segmentation, and a higher computational cost. In either case, adjusting to the individual human anatomy requires costlymagnetic resonance imaging (MRI), and thus head …

Factors Influencing The Choice Of A Safe Haven For Offloading Illegally Caught Fish: A Comparative Analysis Of Developed And Developing Economies, Nerea Marteache, Julie S. Viollaz, Gohar A. Petrossian

Publications and Research

Using data from 72 countries, this study focuses on factors that affect illegal, unreported, and unregulated (IUU) fishing vessels’ choice of country to offload their catch, with a specific emphasis on the differences between developed and developing economies. The concept of choice-structuring properties is applied to analyze whether the following factors influence the selection of a country: concealability of vessels and illegally caught fish; convenience of the ports; strength of fisheries monitoring, control, and surveillance measures; effectiveness of country governance; and commitment to wildlife protection regulations. Results indicate that, rather than a country’s level of development, situational factors play a …

Cladribine Analogues Via O6-(Benzotriazolyl) Derivatives Of Guanine Nucleosides, Sakilam Satishkumar, Prasanna K. Vuram, Siva Subrahmanyam Relangi, Venkateshwarlu Gurram, Hong Zhou, Robert J. Kreitman, Michelle M. Martínez Montemayor, Lijia Yang, Muralidharan Kaliyaperumal, Somesh Sharma, Narender Pottabathini, Mahesh K. Lakshman

Publications and Research

Cladribine, 2-chloro-2′-deoxyadenosine, is a highly efficacious, clinically used nucleoside for the treatment of hairy cell leukemia. It is also being evaluated against other lymphoid malignancies and has been a molecule of interest for well over half a century. In continuation of our interest in the amide bond-activation in purine nucleosides via the use of (benzotriazol-1yl-oxy)tris(dimethylamino)phosphonium hexafluorophosphate, we have evaluated the use of O6-(benzotriazol-1-yl)-2′-deoxyguanosine as a potential precursor to cladribine and its analogues. These compounds, after appropriate deprotection, were assessed for their biological activities, and the data are presented herein. Against hairy cell leukemia (HCL), T-cell lymphoma (TCL) and chronic lymphocytic …

Two Distinct Modes Of Metal Ion Binding In The Nuclease Active Site Of A Viral Dna-Packaging Terminase: Insight Into The Two-Metal-Ion Catalytic Mechanism, Haiyan Zhao, Zihan Lin, Anna Y. Lynn, Brittany Varnado, John A. Beutler, Ryan P. Murelli, Stuart F.J. Le Grice, Liang Tang

Publications and Research

Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 A° . Such proximity of the two metal ions may play an essential role in catalysis by …

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 …

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 …

Mechanisms Of Vocal Coordination In Zebra Finches, Jonathan I. Benichov

Dissertations, Theses, and Capstone Projects

Social animals frequently emit communication calls. Although these calls are often innate in their acoustic structure, they can be used adaptably to coordinate behavior with other individuals. It is not known, however, what each animal needs to learn in order to achieve and maintain synchronized call patterns with others. To study this process, we have developed a vocal robot that can be programed to generate call patterns or to sense a bird's contact (short) calls and respond with precisely timed call answers. By varying the robot's vocal behavior, including call timing and rhythm, we tested how interacting zebra finches adapt …

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 …

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 …

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 …

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 …

The Insulin/Igf Signaling Regulator Cytohesin/Grp-1 Modulates Sensitivity To Excitotoxicity In C. Elegans, Nazila Tehrani

Dissertations, Theses, and Capstone Projects

Excitotoxicity is a form of neurodegeneration that serves as the main underlying cause of brain damage in stroke/brain ischemia, and a contributing factor in a range of neurological diseases such as Epilepsy, ALS, Alzheimer, and Huntington's disease. In excitotoxicity, over-activation of glutamate receptors causes necrotic neuronal cell death. In spite of intense study of excitotoxicity, the molecular mechanisms that lead from glutamate receptor activation to necrotic death remain a mystery. Aging neurons are known to be more vulnerable to excitotoxicity and less likely to recover, but the underlying reasons for the increased cellular vulnerability are unknown. To gain insight into …

The Ecology Of Winter Flounder From An Otolith Perspective, George William Jackman

Dissertations, Theses, and Capstone Projects

In this dissertation, sagittal otoliths were used as a lens to examine latent life history patterns in winter flounder (Pseudopleuronectes americanus) and also as a means of interpreting the species' relationship to their abiotic and biotic environment. Otoliths provide a unique and powerful perspective into the lives of the telost fishes, because they permanently record the spatial and temporal histories through sequential growth patterns from conception to capture. The patterns of growth and dormancy in the otolith are regulated by endogenous and exogenous rhythms, and as the otolith grows, trace elements are absorbed from the ambient environment and …

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 …

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 …

Explorations In Advancing Microalgae Productivity, Peter Neofotis

Dissertations, Theses, and Capstone Projects

This thesis is part of an effort to advance microalgae cultivation for biofuel and high value products. The first chapters describe a large scale screening effort in which novel strains that hold great promise in large outdoor cultivation systems were isolated. Among these are strains of Scenedesmus obliquus, Borodinellopsis texensis, Chlorella sorokiniana, Ankistrodesmus, Coelastrella, and a previously uncharacterized species in the Chlamydomonadales. These species are characterized in terms of their phylogenetic relationship, biomass productivity, and, for some, lipid and carotenoid profiles under growth and stress conditions. Also discussed in regards to growth metabolism and oil …