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Parp Pet Imaging Agents, Brandon Carney

Dissertations, Theses, and Capstone Projects

The poly (adenosine-diphosphate (ADP) ribose) polymerase (PARP) family of enzymes has been of interest to researchers and clinicians for over fifty years, especially the first member of the family, PARP1. This enzyme has become a target for cancer therapeutics due the reliance of highly proliferating cells on PARP1 for genomic maintenance. In the coming age of individualized medicine, however, highly specific therapeutic agents like PARP inhibitors are in need of similarly highly specific companion diagnostic agents. These kind of agents have been made possible with the quickly progressing field of molecular imaging. Specifically, positron emission tomography (PET) has enabled the …

Discovery And Development Of A Three-Component Oxidopyrylium Cycloaddition And Its Application Towards Alpha-Hydroxytropolone Synthesis, Michael P. D'Erasmo

Dissertations, Theses, and Capstone Projects

Historically, natural products have provided unique research opportunities and challenges for organic synthesis, chemical biology, and medicinal chemistry due to their molecular complexity and effects on physiological systems. The total synthesis of natural products has not only produced novel reaction methods and strategies capable of efficiently generating complex structural motifs but also granted access to sufficient quantities of otherwise scarce natural product material for clinical evaluation. These synthetic efforts have facilitated the formation of a transdisciplinary partnership between chemistry, biology, and medicine that has been paramount in elucidating the chemical and pharmaceutical utility of natural products. Chapter I of this …

Synthesis Of 1,4-Triazolyl Combretacoumarins As Potential Anticancer Agents, Tashrique A. Khandaker

Dissertations and Theses

Coumarins are natural compounds that have various physiological and therapeutic properties, making them pharmacologically important. Combretastatin A-4 (CA-4) is a microtubule-binding agent that has potent cytotoxic effects against human cell lines. In CA-4 the trimethoxyarene moiety plays a crucial role in its carcinopreventive effect. Thus, we decided to synthesize novel, potential anti-cancer agents called 1,4-triazolyl combretacoumarins, by coupling different coumarins and the functionally relevant group of CA-4 i.e, the trimethoxyarene moiety, via a 1,2,3-triazolyl ring using a copper-catalyzed [3 + 2] azide-alkyne cycloaddition (CuAAC) reaction, which is a very atom-economical reaction. The coupling partners, 4-azidocoumarins, required for making these …

Gene Coexpression Network Analysis Of Fruit Transcriptomes Uncovers A Possible Mechanistically Distinct Class Of Sugar/Acid Ratio-Associated Genes In Sweet Orange, Liang Qiao, Minghao Cao, Jian Zheng, Yihong Zhao, Zhi-Liang Zheng

Publications and Research

Background: The ratio of sugars to organic acids, two of the major metabolites in fleshy fruits, has been considered the most important contributor to fruit sweetness. Although accumulation of sugars and acids have been extensively studied, whether plants evolve a mechanism to maintain, sense or respond to the fruit sugar/acid ratio remains a mystery. In a prior study, we used an integrated systems biology tool to identify a group of 39 acid-associated genes from the fruit transcriptomes in four sweet orange varieties (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal …

Lichen Conservation In Eastern North America: Population Genomics, Climate Change, And Translocations, Jessica Allen

Dissertations, Theses, and Capstone Projects

Conservation biology is a scientific discipline that draws on methods from diverse fields to address specific conservation concerns and inform conservation actions. This field is overwhelmingly focused on charismatic animals and vascular plants, often ignoring other diverse and ecologically important groups. This trend is slowly changing in some ways; for example, increasing number of fungal species are being added to the IUCN Red-List. However, a strong taxonomic bias still exists. Here I contribute four research chapters to further the conservation of lichens, one group of frequently overlooked organisms. I address specific conservation concerns in eastern North America using modern methods. …

Rseqrep: Rna-Seq Reports, An Open-Source Cloud-Enabled Framework For Reproducible Rna-Seq Data Processing, Analysis, And Result Reporting, Travis L. Jensen, Michael Frasketi, Kevin Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes B. Goll

Publications and Research

RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated to identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise to reveal insights into molecular mechanisms of treatment effects, identify biomarkers, and realize personalized medicine. RNA-Seq Reports (RSEQREP) is a new open-source cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis on a preconfigured RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS or on their own Ubuntu Linux machine. The framework works with unstranded, stranded, and paired-end sequence FASTQ files stored locally, on Amazon Simple Storage …

Review Of The Algal Biology Program Within The National Alliance For Advanced Biofuels And Bioproducts, Clifford J. Unkefer, Richard T. Sayre, Jon K. Magnuson, Daniel B. Anderson, Ivan Baxter, Ian K. Balby, Judith K. Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P. Devarenne, C. Meghan Downes, Susan K. Dutcher, David T. Fox, Ursula Goodenough, Jan Jaworski, Jonathan E. Holladay, David M. Kramer, Andrew T. Koppisch, Mary S. Lipton, Babetta L. Marrone, Margaret Mccormick, István Molnár, John B. Mott, Kimberly L. Ogden, Ellen A. Panisko, Matteo Pellegrini, Juergen Polle, James W. Richardson, Martin Sabarsky, Shawn R. Starkenburg, Gary D. Stormo, Munehiro Teshima, Scott N. Twary, Pat J. Unkefer, Joshua S. Yuan, José A. Olivares

Publications and Research

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome …

Role Of Humor In Emotion Regulation: Differential Effects Of Adaptive And Maladaptive Forms Of Humor, Lindsay Mathews

Dissertations, Theses, and Capstone Projects

Humor is widely believed to be an adaptive method of regulating emotions; however, the empirical literature remains inconclusive. One potential explanation for inconsistent results is that humor may be a multidimensional construct. Correlational research suggests that “adaptive” humor styles (Self-Enhancing and Affiliative) are more beneficial than “maladaptive” humor styles (Self-Defeating and Aggressive). The current study examined the effects of humor styles on positive and negative emotion in a sample of 146 young adults. In Part I of the study, participants were 1) randomly assigned to three conditions (adaptive humor, maladaptive humor, and distraction), 2) instructed to write about life events …

College Senate Minutes May 12, 2016, Bronx Community College Senate

BCC Governance Archives

Minutes for the meeting of the College Senate on May 12, 2016.

Integrated Systems Biology Analysis Of Transcriptomes Reveals Candidate Genes For Acidity Control In Developing Fruits Of Sweet Orange (Citrus Sinensis L. Osbeck), Dingquang Huang, Yihong Zhao, Minghao Cao, Liang Qiao, Zhi-Liang Zheng

Publications and Research

Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid …

Hydrodynamic Loading In Concomitance With Exogenous Cytokine Stimulation Modulates Differentiation Of Bovine Mesenchymal Stem Cells Towards Osteochondral Lineages, Stephen M. Goldman, Gilda A. Barabino

Publications and Research

Background: Mesenchymal stem cells (MSCs) are viewed as a having significant potential for tissue engineering and regenerative medicine therapies. Clinical implementation of MSCs, however, demands that their preparation be stable and reproducible. Given that environmental and bioprocessing parameters such as substrate stiffness, seeding densities, culture medium composition, and mechanical loading can result in undirected differentiation of the MSC population, the objective of this study was to systematically investigate how hydrodynamic loading influences the differentiation of bone marrow-derived mesenchymal stem cells (MSCs) towards the osteochondral lineages both in the presence and absence of exogenous, inductive factors.

Methods: Expanded bovine MSCs were …

The Conflicts Of Coexistence: Contested Meanings Of Carnivore Management And Conservation In The Greater Yellowstone Ecosystem, Hannah F. Jaicks

Dissertations, Theses, and Capstone Projects

The Greater Yellowstone Ecosystem (GYE) encompasses urbanizing areas adjacent to essential conservation habitat with an inimitable capacity to support carnivore populations, including grizzly bears, wolves, and cougars. This geography has resulted in divisive social conflicts about these animals’ management as well as physical conflicts when they come into contact with people over the course of daily life in the region. Employing a qualitative methodology with semi-structured interviews, participant observation, wilderness treks, and archival work, this study examines the context, social processes, and decision-making processes that underlie the predator conflicts and produce management challenges in the GYE. This approach integrates theory …

The Clustered Protocadherin Endolysosomal Trafficking Motif Mediates Cytoplasmic Association, Adam Shonubi, Chantelle Roman, Greg R. Phillips

Publications and Research

Background Clustered protocadherins (Pcdhs) are a large family of neural cadherin-like proteins encoded by individual exons located within three gene clusters. Each exon codes an extracellular, transmembrane, and proximal cytoplasmic domain. These “variable” regions may be spliced to a constant cytoplasmic moiety encoded at the end of a cluster. Pcdh extracellular domains mediate homophilic cell-cell binding but their cytoplasmic domains cause intracellular retention and may negatively regulate Pcdh cell-cell binding. Pcdhs can be found at the cell surface in neurons and other cells but are also, unlike classical cadherins, prominently trafficked to the endolysosome system. It was previously found that …

In Vitro And In Vivo Evaluation Of Water-Soluble Iminophosphorane Ruthenium(Ii) Compounds. A Potential Chemotherapeutic Agent For Triple Negative Breast Cancer, Malgorzata Frik, Alberto Martínez, Benelita T. Elie, Oscar Gonzalo, Daniel Ramírez De Mingo, Mercedes Sanaú, Roberto Sánchez-Delgado, Tanmoy Sadhukha, Swayam Prabha, Joe W. Ramos, Isabel Marzo, María Contel

Publications and Research

A series of organometallic ruthenium(II) complexes containing iminophosphorane ligands have been synthesized and characterized. Cationic compounds with chloride as counterion are soluble in water (70–100 mg/mL). Most compounds (especially highly water-soluble 2) are more cytotoxic to a number of human cancer cell lines than cisplatin. Initial mechanistic studies indicate that the cell death type for these compounds is mainly through canonical or caspase-dependent apoptosis, nondependent on p53, and that the compounds do not interact with DNA or inhibit protease cathepsin B. In vivo experiments of 2 on MDA-MB-231 xenografts in NOD.CB17-Prkdc SCID/J mice showed an impressive tumor reduction (shrinkage) of …

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 …

Cyclometalated Iminophosphorane Gold(Iii) And Platinum(Ii) Complexes. A Highly Permeable Cationic Platinum(Ii) Compound With Promising Anticancer Properties, Malgorzata Frik, Jacob Fernández-Gallardo, Oscar Gonzalo, Víctor Mangas-Sanjuan, Marta González-Alvarez, Alfonso Serrano Del Valle, Chunhua Hu, Isabel González-Alvarez, Marival Bermejo, Isabel Marzo, María Contel

Publications and Research

New organometallic gold(III) and platinum(II) complexes containing iminophosphorane ligands are described. Most of them are more cytotoxic to a number of human cancer cell lines than cisplatin. Cationic Pt(II) derivatives 4 and 5, which differ only in the anion, Hg2Cl62– or PF6– respectively, display almost identical IC50 values in the sub-micromolar range (25–335-fold more active than cisplatin on these cell lines). The gold compounds induced mainly caspase-independent cell death, as previously reported for related cycloaurated compounds containing IM ligands. Cycloplatinated compounds 3, 4, and 5 can also activate alternative caspase-independent mechanisms of death. However, at short incubation times cell death …

Climate Change And Phenology: Empoasca Fabae (Hemiptera: Cicadellidae) Migration And Severity Of Impact, Mitchell B. Baker, P. Dilip Venugopal, William O. Lamp

Publications and Research

Climate change can benefit individual species, but when pest species are enhanced by warmer temperatures agricultural productivity may be placed at greater risk. We analyzed the effects of temperature anomaly on arrival date and infestation severity of potato leafhopper, Empoasca fabae Harris, a classic new world long distance migrant, and a significant pest in several agricultural crops. We compiled E. fabae arrival dates and infestation severity data at different states in USA from existing literature reviews and agricultural extension records from 1951–2012, and examined the influence of temperature anomalies at each target state or overwintering range on the date of …

A Reproducible Approach To High-Throughput Biological Data Acquisition And Integration, Daniela Börnigen, Yo Sup Moon, Gholamali Rahnavard, Levi Waldron, Lauren Mciver, Afrah Shafquat, Eric A. Franzosa, Larissa Miropolsky, Christopher Sweeney, Xochitl C. Morgan, Wendy S. Garrett, Curtis Huttenhower

Publications and Research

Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, …

Chemotaxis Of Central Nervous System-Derived Tumor Cells Within Controlled Microenvironments, Jennifer Rico Varela

Dissertations and Theses

Medulloblastoma (MB) is a malignant pediatric brain tumor known for its aggressive metastatic potential. Despite the well-documented migration of MB cells to other parts of the brain and spinal column, MB chemotaxis is poorly understood. Herein, we examined the in vitro migratory and cellular responses of MB-derived cells to external signaling of Epidermal Growth Factor (EGF), hepatocyte growth factor (HGF), platelet-derived growth factor (PDGF-BB), and the stromal cell-derived factors 1-alpha (SDF-1). Experiments utilized transwell assays and immunocytochemistry to identify receptor activation in MB migration, and used a microfluidic platform to examine directionality, trajectory, and gradient- dependence of motile cells. Data …

The Phytotronist And The Phenotype: Plant Physiology, Big Science, And A Cold War Biology Of The Whole Plant., David Munns

Publications and Research

This paper describes how, from the early twentieth century, and especially in the early Cold War era, the plant physiologists considered their discipline ideally suited among all the plant sciences to study and explain biological functions and processes, and ranked their discipline among the dominant forms of the biological sciences. At their apex in the late-1960s, the plant physiologists laid claim to having discovered nothing less than the “basic laws of physiology.” This paper unwraps that claim, showing that it emerged from the construction of monumental big science laboratories known as phytotrons that gave control over the growing environment. Control …

Synthesis And Evaluation Of Sensitizer Drug Photorelease Chemistry: Micro-Optic Method Applied To Singlet Oxygen Generation And Drug Delivery, Goutam Ghosh

Dissertations, Theses, and Capstone Projects

This thesis summarizes a new micro-optic method for singlet oxygen generation and sensitizer drug delivery, which include i) synthesis and evaluation of a first generation device for drug delivery from native and fluorinated silica probe tips, ii) synthesis of PEG conjugated sensitizers to study phototoxicity in ovarian cancer cells, and iii) synthesis and evaluation of tris-PEGylated chlorin conjugated fluorinated silica for its future integration into the device to use as a 2nd generation device. A first generation micro-optic device was developed that works by sparging O2 gas and light generating cytotoxic singlet oxygen that cleaves the covalently attached drug (sensitizer) …

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 …

Chronic Corticosterone Exposure Persistently Elevates The Expression Of Memory-Related Genes In The Lateral Amygdala And Enhances The Consolidation Of A Pavlovian Fear Memory, Melissa S. Monsey, Lara M. Boyle, Melinda L. Zhang, Caroline P. Nguyen, Hope G. Kronman, Kristie T. Ota, Ronald S. Duman, Jane R. Taylor, Glenn E. Schafe

Publications and Research

Chronic exposure to stress has been widely implicated in the development of anxiety disorders, yet relatively little is known about the long-term effects of chronic stress on amygdala-dependent memory formation. Here, we examined the effects of a history of chronic exposure to the stress-associated adrenal steroid corticosterone (CORT) on the consolidation of a fear memory and the expression of memory-related immediate early genes (IEGs) in the lateral nucleus of the amygdala (LA). Rats received chronic exposure to CORT (50 μg/ml) in their drinking water for 2 weeks and were then titrated off the CORT for an additional 6 days followed …

An Ethnobotanical, Ecological And Lc-Ms-Based Chemometric Investigation Of Phaleria Nisidai, A Traditional Adaptogen Containing Diterpene Esters From Palau, Micronesia, Daniel Kulakowski

Dissertations, Theses, and Capstone Projects

An ethnobotanical, ecological and LC-MS-based chemometric investigation of Phaleria nisidai, a traditional adaptogen containing diterpene esters from Palau, Micronesia

Palau is a country with a rich heritage of traditional medicine still being practiced. One of the most popular and respected remedies in Palau is a tea made from fresh leaves of Phaleria nisidai Kaneh. (Thymelaeaceae). Interviews conducted to determine the use of this plant revealed that it is employed non-specifically to treat a variety of general health concerns. Its use as a prophylactic to keep away sickness, as a 'system cleaner', as well as for strength and energy indicate …

Create Cornerstone: Introduction To Scientific Thinking, A New Course For Stem-Interested Freshmen, Demystifies Scientific Thinking Through Analysis Of Scientific Literature, Alan J. Gottesman, Sally G. Hoskins

Publications and Research

The Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment (CREATE) strategy for teaching and learning uses intensive analysis of primary literature to improve students’ critical-thinking and content integration abilities, as well as their self-rated science attitudes, understanding, and confidence. CREATE also supports maturation of undergraduates’ epistemological beliefs about science. This approach, originally tested with upper-level students, has been adapted in Introduction to Scientific Thinking, a new course for freshmen. Results fromthis course’s initial semesters indicate that freshmen in a one-semester introductory course that uses a narrowly focused set of readings to promote development of analytical …

College Senate Minutes March 21, 2013, Bronx Community College Senate

BCC Governance Archives

Minutes for the meeting of the College Senate on March 21, 2013.

College Senate Minutes February 21, 2013, Bronx Community College Senate

BCC Governance Archives

Minutes for the meeting of the College Senate on February 21, 2013.

Yousef Studies The Physics Of Life And Health, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

When Whales Became Mammals: The Scientific Journey Of Cetaceans From Fish To Mammals In The History Of Science, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Morphological And Neuroanatomical Changes Associated With The Induction Of Neurodegeneration And Life Span Reduction In Drosophila Melanogaster By Glia Targeted Expression Of Cdh1/Rap/Fzr, An Activator Of The Anaphase Promoting Complex, Israel Nnah

Dissertations and Theses

"The retina aberrant in pattern (rap) gene encodes the Fizzy-related protein (Fzr), an activator of the E3 ubiquitin ligase complex: the Anaphase Promoting Complex/Cyclosome (APC/C). APC/C facilitates the cell cycle stage-specific degradation of cyclins and other mitotic regulators, resulting in the inactivation of Cdk (Cyclin Dependent Kinase) complexes, thus promoting completion of mitosis. Previous studies from our laboratory have shown that Rap/Fzr (the Drosophila homolog of the mammalian Cdh1) regulates glia differentiation and promotes neuron formation. Recent studies have shown that the glia specific over expression of Rap/Fzr causes progressive neurodegeneration and life span reduction preceded by temperature sensitive paralysis, …