Physical Sciences and Mathematics Commons^™

Towards A New Role Of Mitochondrial Hydrogen Peroxide In Synaptic Function, Cliyahnelle Z. Alexander

Student Theses and Dissertations

Aerobic metabolism is known to generate damaging ROS, particularly hydrogen peroxide. Reactive oxygen species (ROS) are highly reactive molecules containing oxygen that have the potential to cause damage to cells and tissues in the body. ROS are highly reactive atoms or molecules that rapidly interact with other molecules within a cell. Intracellular accumulation can result in oxidative damage, dysfunction, and cell death. Due to the limitations of H₂O₂ (hydrogen peroxide) detectors, other impacts of ROS exposure may have been missed. HyPer7, a genetically encoded sensor, measures hydrogen peroxide emissions precisely and sensitively, even at sublethal levels, during …

Fine Characterization Of Leafing Phenology In The Brazilian Atlantic Forest By Optical And Microwave Remote Sensing, James B. Bell

Dissertations and Theses

Tropical forests provide important ecosystem functions in the global biosphere, but they remain among the most poorly understood elements of land surface models, especially with regard to their seasonal dynamics. For instance, in seasonally dry forests, the pattern of the annual green-up in their canopies closely follows annual patterns of rainfall. The same, however, does not occur in wet forest canopies which are dominated by evergreen trees. In the latter, water is not scarce enough to limit leaf photosynthetic function. Canopy leafing phenology in these forests is therefore poorly characterized by optical remote sensing methods which are not sensitive to …

The C. Neoformans Cell Wall: A Scaffold For Virulence, Christine Chrissian

Dissertations, Theses, and Capstone Projects

Cryptococcus neoformans is a globally distributed opportunistic fungal pathogen and the causative agent of life threatening cryptococcal meningoencephalitis in immunocompromised individuals, resulting in ~180,000 deaths each year worldwide. A primary virulence-associated trait of this organism is the production of melanin. Melanins are a class of diverse pigments produced via the oxidation and polymerization of aromatic ring compounds that have a characteristically complex, heterogenous, and amorphous structure. They are synthesized by representatives of all biological kingdoms and share a multitude of remarkable properties such as the ability to absorb ultraviolet (UV) light and protect against ionizing radiation. Melanin production in fungi …

Hydrophilic Porphyrins Based Chemosensors For First Transition Series Metal Ions [Chemistry], Sunaina Singh

Open Educational Resources

General Chemistry is a two-semester course (General Chemistry I, SCC 201 and General Chemistry II, SCC 202) required for majors in Biology and Environmental Sciences.

This lab experiment, aligned to LaGuardia Community College’s Inquiry and Problem Solving Core Competency and Written Communication Ability was designed for General Chemistry I (SCC 201 Honors) course. Honors courses in LaGuardia emphasize critical thinking, analytical writing, and introduce students to research. This lab experiment provides an opportunity for students to engage in hands-on laboratory work, to develop laboratory skills, and to conduct research in the classroom by using two water soluble porphyrins to detect …

Microwave Solventless Synthesis Of Meso-Tetrakis (Pentafluorophenyl)Poprphyrin (Tppf20) And Tris(Pentafluorophenyl))Corrole [Chemistry], Sunaina Singh

Open Educational Resources

Organic chemistry is a two-semester course (Organic Chemistry I, SCC 251 and Organic Chemistry II, SCC 252) required for majors in Biology. The SCC 251 course has been designated for the Integrative Learning Core Competency as well the Digital Communication Ability. This course emphasizes the synthesis, structure, reactivity, and mechanisms of reaction of organic compounds. Laboratory stresses various organic synthetic and analytic techniques (distillation, extraction, chromatography and spectroscopy).

This lab provided an opportunity for students to go deeper with the chemistry content by correlating to the concepts they learned in General Chemistry courses such as Valence shell electron pair repulsion …

Titration Of A Newtown Creek Environmental Water Sample To Determine The Amount Of Chloride Ions [Chemistry], Kevin Mark

Open Educational Resources

Main Course Learning Objectives:

The General Chemistry 1 (SCC 201) course has multiple course learning objectives, which articulate key introductory chemistry concepts that all STEM students should possess. In particular, the Newtown Creek titration experiment aligns with SCC 201 learning objectives of:

1. Demonstrate an appreciation of the role of chemistry in various aspects of life
2. Perform basic laboratory skills such as the proper execution of titration techniques
3. Describe and explain the fundamental chemistry concept of solution concentration
4. Analyze and represent experimental data in tables and graphs, interpret experimental results and write laboratory reports

In the SCC 201 laboratory, students are …

Digital Storytelling [Natural Sciences], Preethi Radhakrishnan

Open Educational Resources

A well-crafted and executed storytelling assignment can serve as an efficient and engaging learning activity which targets the three highest levels of Blooms’ taxonomy which are to Create, Evaluate and Analyze. This digital storytelling assignment is part of a signature assignment series (Stage 1) conducted in all courses of the First Year Seminar for Natural Sciences (NSF101). Students begin collecting pictures and videos for their assignment from the 3^rd week of the semester on a flash drive. During the fourth week of the semester, the instructor first describes the storytelling process and stages. This is followed by learning around …

Cooperative Standing-Horizontalstanding Reentrant Transition For Numerous Solid Particles Under External Vibration, Satoshi Takatori, Hikari Baba, Takatoshi Ichino, Chwen-Yang Shew, Kenichi Yoshikawa

Publications and Research

We report the collective behavior of numerous plastic bolt-like particles exhibiting one of two distinct states, either standing stationary or horizontal accompanied by tumbling motion, when placed on a horizontal plate undergoing sinusoidal vertical vibration. Experimentally, we prepared an initial state in which all of the particles were standing except for a single particle that was placed at the center of the plate. Under continuous vertical vibration, the initially horizontal particle triggers neighboring particles to fall over into a horizontal state through tumbling-induced collision, and this effect gradually spreads to all of the particles, i.e., the number of horizontal particles …

Walking As Ontological Shifter: Thoughts In The Key Of Life, Bibi (Silvina) Calderaro

Dissertations, Theses, and Capstone Projects

With walking as ontological shifter I pursue an alternative to the dominant modernist episteme that offers either/or onto-epistemologies of opposition and their reifying engagements. I propose this type of walking is an intentional turning towards a set of radical positions that, as integrative aesthetic and therapeutic practice, brings multiplicity and synchronicity to experience and being in an expanded sociality. This practice facilitates the conditions of possibility for recurring points of contact between the interiority perceived as ‘body’ and the exteriority perceived as ‘world.’ While making evident the self’s at once incoherence with it-self, it opens to a space beyond the …

Tumor Necrosis Factor Dynamically Regulates The Mrna Stabilome In Rheumatoid Arthritis Fibroblast-Like Synoviocytes, Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Christopher Sohn, Bethany Syracuse, Eugenia G. Giannopoulou, Sung Ho Park, Hyelim Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias

Publications and Research

During rheumatoid arthritis (RA), Tumor Necrosis Factor (TNF) activates fibroblast-like synoviocytes (FLS) inducing in a temporal order a constellation of genes, which perpetuate synovial inflammation. Although the molecular mechanisms regulating TNF-induced transcription are well characterized, little is known about the impact of mRNA stability on gene expression and the impact of TNF on decay rates of mRNA transcripts in FLS. To address these issues we performed RNA sequencing and genome-wide analysis of the mRNA stabilome in RA FLS. We found that TNF induces a biphasic gene expression program: initially, the inducible transcriptome consists primarily of unstable transcripts but progressively switches …

Species Identification Of Necrophagous Insect Eggs Based On Amino Acid Profile Differences Revealed By Direct Analysis In Real Time-High Resolution Mass Spectrometry, Justine E. Giffen, Jennifer Y. Rosati, Cameron M. Longo, Rabi A. Musah

Publications and Research

The colonization of decomposing remains by necrophagous insects such as blow flies is of forensic importance because the progression through the various stages of insect development can be correlated to time of death. The ability to infer this information hinges on accurate determination of the fly species that are associated with the entomological evidence collected. This evidence can include eggs, larvae, pupae, and puparial casings. Determination of the egg’s identity is particularly challenging because the eggs of multiple species are morphologically very similar. We report here that the species identity of fly eggs can be determined from their chemical fingerprint …

Bioremoval Of Phenol From Aqueous Solutions Using Native Caribbean Seaweed, Abel E. Navarro, Anibal Hernandez-Vega, Md Emran Masud, Loretta M. Roberson, Liz M. Diaz-Vázquez

Publications and Research

Among several Puerto Rican algae, Sargassum sp. (SG) and Chaetomorpha (CM) showed the highest phenol adsorption capacity from aqueous solutions and were used in optimized adsorption batch experiments at room temperature. The effects of pH, adsorbent dose, phenol concentration, salinity and presence of interfering substances were evaluated. Initial solution pH exhibited a strong effect, mainly on the phenol aqueous chemistry; showing the maximum adsorption at pH 10. Sorption isotherm results were modelled according to the Langmuir, Tempkin and Freundlich equations. Isotherm modelling indicated a maximum adsorption capacity (qmax) of 82.10 and 17.7 mg of phenol per gram of SG and …

A Mineralized Alga And Acritarch Dominated Microbiota From The Tully Formation (Givetian) Of Pennsylvania, Usa, John A. Chamberlain Jr., Rebecca B. Chamberlain, James O. Brown

Publications and Research

Sphaeromorphic algal cysts, most probably of the prasinophyte Tasmanites, and acanthomorphic acritarch vesicles, most probably Solisphaeridium, occur in a single 20 cm thick bed of micritic limestone in the lower part of the Middle Devonian (Givetian) Tully Formation near Lock Haven, Pennsylvania. Specimens are composed of authigenic calcite and pyrite crystals about 5–10 µm in length. Some specimens are completely calcitic; some contain both pyrite and calcite; and many are composed totally of pyrite. The microfossils are about 80 to 150 µm in diameter. Many show signs of originally containing a flexible wall composed of at least two layers. Some …

Computerized Classification Of Surface Spikes In Three-Dimensional Electron Microscopic Reconstructions Of Viruses, Younes Benkarroum

Dissertations, Theses, and Capstone Projects

The purpose of this research is to develop computer techniques for improved three-dimensional (3D) reconstruction of viruses from electron microscopic images of them and for the subsequent improved classification of the surface spikes in the resulting reconstruction. The broader impact of such work is the following.

Influenza is an infectious disease caused by rapidly-changing viruses that appear seasonally in the human population. New strains of influenza viruses appear every year, with the potential to cause a serious global pandemic. Two kinds of spikes – hemagglutinin (HA) and neuraminidase (NA) – decorate the surface of the virus particles and these proteins …

From Mollusks To Medicine: A Venomics Approach For The Discovery And Characterization Of Therapeutics From Terebridae Peptide Toxins, Aida Verdes, Prachi Anand, Juliette Gorson, Stephen Jannetti, Patrick Kelly, Abba Leffler, Danny Simpson, Girish Ramrattan, Mandë Holford

Publications and Research

Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, identifying bioactive venom peptides remains a significant challenge. In this review we describe our particular venomics strategy for the discovery, characterization, and optimization of Terebridae venom peptides, teretoxins. Our strategy reflects the scientific path from mollusks to medicine in an integrative sequential approach with the following steps: (1) delimitation of venomous Terebridae lineages through taxonomic and phylogenetic analyses; (2) identification and classification of putative teretoxins through omics …

Revised Distributional Estimates For The Recently Discovered Olinguito (Bassaricyon Neblina), Using Museum And Science Records, Beth E. Gerstner

Dissertations and Theses

In the context of global change, a necessary first step for the conservation of species is gaining a good understanding of their distributional limits. This is especially important for biodiversity hotspots with high endemism such as the Northern Andes. The olinguito (Procyonidae: Bassaricyon neblina) is a recently described, medium-sized carnivoran found in Northern Andean cloud forests. A preliminary distributional model was published along with the original description, and I here provide revised distributional estimates using updated locality records and more current ENM methods. I build ecological niche models in Maxent using occurrence data (georeferenced museum records and citizen science-derived photo-vouchers) …

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 …

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 …

Protein Sectors: Statistical Coupling Analysis Versus Conservation, Tiberiu Teşileanu, Lucy J. Colwell, Stanislas Leibler

Publications and Research

Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors”. The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be …

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 …

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 …

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 …

Group 11 Metal Compounds With Tripodal Bis(Imidazole) Thioether Ligands. Applications As Catalysts In The Oxidation Of Alkenes And As Antimicrobial Agents, Fangwei Liu, Reema Anis, Eunmi Hwang, Rafael Ovalle, Armando Varela-Ramírez, Renato J. Aguilera, María Contel

Publications and Research

New group 11 metal complexes have been prepared using the previously described tripodal bis(imidazole) thioether ligand (N-methyl-4,5-diphenyl-2- imidazolyl)2C(OMe)C(CH3)2S(tert-Bu) ({BITOMe,StBu}, 2). The pincer ligand offers a N2S donor atom set that can be used to coordinate the group 11 metals in different oxidation states [AuI , AuIII, AgI , CuI and CuII]. Thus the new compounds [Au{BITOMe,StBu}Cl][AuCl4]2 (3), [Au{BITOMe,StBu}Cl] (4), [Ag{BITOMe,StBu}X] (X = OSO2CF3 - 5, PF6 - 6) and [Cu{BITOMe,StBu}Cl2] (7) have been synthesized from reaction of 2 with the appropriate metal precursors, and characterized in solution. While attempting characterization in the solid state of 3, single crystals of the …

Polycationic Glycosides, Robert Engel, Ishrat Ghani, Diego Montenegro, Marie Thomas, Barbara Klaritch-Vrana, Alejandra Castaño, Laura Friedman, Jay Leb, Leah Rothman, Heidi Lee, Craig Capodiferro, Daniel Ambinder, Eve Cere, Christopher Awad, Faiza Sheikh, Jaimelee Rizzo, Lisa-Marie Nisbett, Erika Testani, Karin Melkonian

Publications and Research

Cationic lipids have long been known to serve as antibacterial and antifungal agents. Prior efforts with attachment of cationic lipids to carbohydrate-based surfaces have suggested the possibility that carbohydrate-attached cationic lipids might serve as antibacterial and antifungal pharmaceutical agents. Toward the understanding of this possibility, we have synthesized several series of cationic lipids attached to a variety of glycosides with the intent of generating antimicrobial agents that would meet the requirement for serving as a pharmaceutical agent, specifically that the agent be effective at a very low concentration as well as being biodegradable within the organism being treated. The initial …

Drug Off-Target Effects Predicted Using Structural Analysis In The Context Of A Metabolic Network Model, Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson

Publications and Research

Recent advances in structural bioinformatics have enabled the prediction of protein-drug off-targets based on their ligand binding sites. Concurrent developments in systems biology allow for prediction of the functional effects of system perturbations using large-scale network models. Integration of these two capabilities provides a framework for evaluating metabolic drug response phenotypes in silico. This combined approach was applied to investigate the hypertensive side effect of the cholesteryl ester transfer protein inhibitor torcetrapib in the context of human renal function. A metabolic kidney model was generated in which to simulate drug treatment. Causal drug off-targets were predicted that have previously been …

A Multidimensional Strategy To Detect Polypharmacological Targets In The Absence Of Structural And Sequence Homology, Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, J. Andrew Mccammon

Publications and Research

Conventional drug design embraces the ‘‘one gene, one drug, one disease’’ philosophy. Polypharmacology, which focuses on multi-target drugs, has emerged as a new paradigm in drug discovery. The rational design of drugs that act via polypharmacological mechanisms can produce compounds that exhibit increased therapeutic potency and against which resistance is less likely to develop. Additionally, identifying multiple protein targets is also critical for side-effect prediction. One third of potential therapeutic compounds fail in clinical trials or are later removed from the market due to unacceptable side effects often caused by off-target binding. In the current work, we introduce a multidimensional …