Digital Commons Network^™

Harnessing Redox Regulation Of Ptp1b: A Novel Path To Therapeutic Design, Ioana Rus Rus

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Protein tyrosine phosphatase 1B (PTP1B) is an important negative regulator of signaling by the insulin and leptin receptors. PTP1B-null mice are sensitized to insulin and resistant to diet-induced obesity, making PTP1B a prized target in the pharmaceutical industry for therapeutic intervention in type two diabetes and obesity. Efforts to develop inhibitors of PTP1B focused on the active site pocket; however, those efforts have been hindered by poor oral bioavailability of the compounds. Our lab has exploited the conformational changes associated with redox regulation of PTP1B to devise an alternative method of inhibiting the enzyme. Reactive oxygen species, generated in response …

An Investigation Of Pelagophyte Ecology, Yoonja Kang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Pelagophytes are important picoplankton in the open ocean and in coastal waters where Aureococcus anophagefferens and Aureoumbra lagunensis form ecosystem-disruptive brown tides. Despite decades of research, factors facilitating brown tides are not completely understood. This dissertation is a comparative study of pelagophytes assessing processes facilitating brown tides and transcriptional similarities among open ocean and coastal pelagophytes. During my dissertation, top-down (e.g. grazing) and bottom-up (e.g. nutrients) processes shaping phytoplankton communities were examined during brown tides in the Indian River Lagoon, Florida, USA. While moderate levels of ammonium promoted Aureoumbra growth over picoprokaryotes, grazing pressure on Aureoumbra was near absent permitting …

Cosmogenic Silicon €“ 32 Reveals Extensive Authigenic Clay Formation In Deltaic Systems And Constrains The Marine Silica Budget | Cosmogenic Silicon – 32 Reveals Extensive Authigenic Clay Formation In Deltaic Systems And Constrains The Marine Silica Budget, Shaily Rahman

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Silica is an essential nutrient and an important control on primary production, the biological pump, and carbon cycling in the ocean. In our current understanding of the marine silica cycle, the known sources outweigh the sinks, by as much as 35%. The quantity of biogenic silica stored in lithogenic sediments along continental margins is poorly constrained. Cosmogenic 32Si (t1/2 ~ 140 yrs) was used in a novel way to constrain the quantity of reactive Si storage and early diagenetic reactions of Si in the highly mobile deltaic sediments along the coast of French Guiana, representative of deposits along the ~1600 …

The Role Of The Transcription Machinery In The Remodeling Of The Promoter-Proximal Nucleosomes In Saccharomyces Cerevisiae, Michael Charles Tramantano

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Approximately 147 base pairs of DNA wraps almost two turns around a protein core comprised of two copies of each H2A, H2B, H3 and H4 histones to form a nucleosome—the fundamental packaging unit of chromatin. In Saccharomyces cerevisiae, nucleosomes are organized along the genome in a closely spaced and non-random manner. This compact structure blocks assembly of the transcription machinery and thus is refractory to gene expression. Surrounding the promoters of most genes, a wider nucleosome depleted region (NDR), maintained in part by the activities of chromatin remodelers, serves as the platform for assembly of the transcription preinitiation complex (PIC). …

The Role Of Dna Polymerase Lambda In The Repair Of Oxidative Dna Damage, Matthew John Burak

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

8-oxo-7,8-dihydro-2′-deoxyguanosine is a major oxidative product present in cells and can arise in either DNA (8-oxo-dG) or the nucleotide pool (8-oxo-dGTP). Both 8-oxo-dG and 8-oxo-dGTP exhibit dual-coding potential and can pair with cytosine or adenine. Accordingly, these lesions interfere with replication by DNA polymerases, lead to mutation and ultimately drive diseases such as cancer. Interestingly, DNA polymerase lambda (Pol λ) is uniquely capable of facilitating the error-free bypass of 8-oxo-dG-containing DNA and has thus been implicated in its repair. As such, I have utilized structural techniques (X-ray crystallography), complemented with biochemical experiments (steady-state kinetics), to gain insight into the mechanism …

Investigations In The Crystal Growth And Neutron Scattering Of Superconductors And A Relaxor Ferroelectric, John Schneeloch

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this dissertation, I present research on four materials with properties that are not well understood, and illustrate the many roles inhomogeneity and disorder may play in material properties. First, we investigated materials synthesis and annealing conditions of the proposed topological superconductor CuxBi2Se3, finding that quenching above a minimum temperature was essential for superconductivity. Due to the inhomogeneity of CuxBi2Se3, we suggest that a metastable secondary phase may be responsible for the superconductivity. Second, we performed neutron scattering measurements on samples in the Fe1+yTe1−xSex family of iron-based superconductors, focusing on the anomalous phonon mode recently discovered near Bragg peaks forbidden …

Transverse Movements Of The Components Of The Lipid Bilayer, Jamie Lebarron

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Cell membranes are a complex mixture often composed of approximately equal parts lipid and protein molecules. Lipids are amphipathic, having polar headgroups that prefer to associate with water and hydrophobic tails that self-associate away from water. As a result, the lipids in cell membranes exist in the form of a lipid bilayer, with lipid polar headgroups facing outwards towards water and tails grouped together in the middle. Proteins embedded in this bilayer facilitate the movement of molecules across this barrier. The molecules that form the membrane have an asymmetric distribution, with different lipids being preferentially found on one side of …

The Integration Of Mathematics In Middle School Science: Student And Teacher Impacts Related To Science Achievement And Attitudes Towards Integration, Luisa Mchugh

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Contemporary research has suggested that in order for students to compete globally in the 21st century workplace, pedagogy must shift to include the integration of science and mathematics, where teachers effectively incorporate the two disciplines seamlessly. Mathematics facilitates a deeper understanding of science concepts and has been linked to improved student perception of the integration of science and mathematics. Although there is adequate literature to substantiate students’ positive responses to integration in terms of attitudes, there has been little empirical data to support significant academic improvement when both disciplines are taught in an integrated method. This research study, conducted at …

Increasing College Students’ Interest And Engagement In Stem: A Comparison Of Strategies For Challenging Stem Stereotypes | Increasing College Students’ Interest And Engagement In Stem: A Comparison Of Strategies For Challenging Stem Stereotypes, Jiyun Elizabeth Shin

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Increasing science, technology, engineering, and mathematics (STEM) graduates has become an important part of the education agenda in the U.S. in recent years. Stereotypes about STEM (i.e. | belief that STEM abilities are innate, and that European American men are best suited for STEM) have been identified as one of the critical factors that may contribute to low recruitment and retention of STEM students. Drawing from the literatures on biological essentialism and role models, this study compared different strategies for challenging STEM stereotypes among undergraduate students in STEM and non-STEM fields. STEM stereotypes were challenged directly with research articles that …

Multi-Objective Clustering Analysis, Tingjun Ruan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Cluster analysis is an important tool for unsupervised learning. It is commonly used for pattern recognition and dimension reduction. Traditional clustering algorithms include hierarchical clustering and k-means clustering, as well as model based approach such as the group trajectory analysis. A major draw-back of the traditional clustering analysis is that it considers only a single objective (dissimilarity measurement) whilst in reality, one usually holds several criteria for the classification. Therefore, in this thesis, we strive to develop novel multiple-objective clustering methods – with a focus on the more approachable dual-objective ones. This thesis consists of two parts. In the first …

Introduction Of Biosimilar Therapeutics Into Nephrology Practice In The United States: Report Of A Scientific Workshop Sponsored By The National Kidney Foundation, Jay B. Wish, Chaim Charytan, Glenn M. Chertow, Kamyar Kalantar-Zadeh, Alan S. Kliger, Robert J. Rubin, Jerry Yee, Steven Fishbane

Nephrology Articles

Biosimilars are biologic medicines highly similar to the reference product with no meaningful clinical differences in terms of safety, purity, and potency. All biologic medicines are produced by living cells, resulting in an inherent heterogeneity in their higher order structures and post-translational modifications. In 2010, the US Congress enacted legislation to streamline the approval process for biosimilars of products losing patent protection, with the goal of decreasing costs and improving patient access to therapeutically important but expensive biologic agents. In 2015, the US Food and Drug Administration approved the first biosimilar agent through this pathway. Approval of additional biosimilar agents …

Annual Forage Cropping-Systems For Midwestern Ruminant Livestock Production, John Ernest Mcmillan

Open Access Dissertations

Annual forage cropping systems are a vital aspect of livestock forage production. One area where this production system can be enhanced is the integration of novel annual forages into conventional cropping systems. Two separate projects were conducted to investigate alternative forage options in annual forage production. In the first discussed research trial, two sets of crops were sown following soft red winter wheat (Triticum aestivum L.) grain harvest, at two nitrogen application rates 56 and 112 kg ha-1 . The first set of crops were C4 summer annuals seeded within two weeks of wheat grain harvest and included, brown …

Non-Invasive Lifestyle Modifications That Mitigate The Non-Modifiable Risks Of Breast Cancer In Potential High Risk Patients, Angelica Rosinski

Honors Capstones

Breast cancer is most common invasive cancer occurring in US women. The standard treatment for breast cancer includes surgery, systemic therapy (e.g., chemotherapy, biotherapy, targeted therapy) and radiotherapy. The Healthy People 2020 initiative promotes education and prevention instead of treatment. Therefore, non-invasive lifestyle modifications should be developed to decrease the risk of developing breast cancer among women at population risk and those who carry a genetic mutation conferring increased breast cancer risk. Diet, weight management, and exercise as methods to reduce breast cancer are examined within this literature review. These lifestyle adjustments should be introduced to individuals who are at …

Identification Of The Plateau Of Cadmium Extraction From Aqueous Solution By Invasive Macrophyte: Eichhornia Crassipes, Micalah Spenrath

2016 Fall Honors Capstone Projects - Archive

Cadmium is an extremely deleterious heavy metal characterized by high toxicity, environmental disruptiveness and difficult removal. Utilizing an aquatic macrophyte, Eichhornia crassipes, as a phytoremediant of cadmium has been shown to be experimentally viable and less environmentally degrading than conventional methods of heavy metal remediation. To further understand the time required to optimize cadmium uptake and minimize the rerelease of contaminants, E. crassipes was studied to identify the plateau of cadmium extraction. The experimental plants were housed in aquatic environments with cadmium concentrations of 5 ppm for 144 hours. Water samples were analyzed in atmosphere in a Shimadzu EDX- 7000 …

The Role Of Wnt3a In Bone-Muscle Biochemical Crosstalk And Promoting Myoblast Differentiation Among Mouse Primary Muscle Cells, Sarah Daggs

2016 Fall Honors Capstone Projects - Archive

Bone and muscle crosstalk is a newly emerging field that focuses on the ability of bone cells and muscle cells to communicate with each other through mechanical and biochemical mechanisms. Until recently, the secretory function of both bone and muscle cells has largely been unexplored. My thesis focuses on continuing my faculty mentor’s current research on bone-muscle crosstalk by analyzing the effects of WNT3a, an important bone-secreted factor of the Wnt/β-catenin pathway, on myogenesis. Myogenesis is the process of producing muscle cells from stem cells in the embryonic stages of development and the regeneration of muscle tissue after cell injury …

Nanoscale Solutions To Tailor Fiber Architectures For Realizing Composites With Triumvirate Properties, Vishnu Priya Ramineni

All Theses

The paramount need for the development of multifunctional, smart and adaptive material systems for application in industries like automobile, aeronautical and aerospace is undeniable. Polymer composites are fast becoming the primary material options to this demand in light of their superior mechanical properties, low density, high corrosion resistance and easy manufacturability. The design flexibility offered in terms of achieving higher specific properties and light weighting is the key reason behind their success. Among all the properties that composites possess, it is the stiffness, strength and toughness that most applications mandate. These properties however, provide complimentary and contrasting characteristics for composites …

Effect Of Manures On Food Waste Degradation In Biocell, Md Nur Basit Zaman

Civil Engineering Theses - Archive

Proper disposal of food waste is a challenge due to adverse effect on the environment through generation of excessive leachate and greenhouse gas (CH4). After food loss through the food supply chain, the food waste ends up mostly in landfills. A study by EPA showed food waste to be the second largest component found in landfill. However, food waste imposes major cost on landfill management, and demands a potential alternative disposal solution that can negate the adverse effects. Though anaerobic digester and composting are possible solutions for food waste disposal, the former is highly expensive while in later solution, a …

F420 H2:Nadp+ Oxidoreductase Hydride Transfer Rates: Kinetic Analysis Of Thr09 Mutant, Katie Kang

McNair Scholars Research Journal

No abstract provided.

Intracellular Biochemical Targets Of Ruthenium Polypyridyl Complexes In Multiple Cancer Cell Models, Adam S. Dayoub

Chemistry & Biochemistry Dissertations - Archive

The ruthenium (II) polypyridyl complexes [(phen)2Ru(tatpp)Ru(phen)2]4+, RPC4 and [(phen)2Ru(tatpp)]2+, RPC3 are promising anticancer candidates due to their observed cytotoxic effect against multiple cancer cell lines. These complexes contain a reactive oxygen species (ROS) creating redox-active tetraazatetrapyridopentacene (tatpp) bridge inducing cytotoxic activity against multiple cancer lines and types. Also, they have shown a selectivity towards malignant and normal cell tissue types that are of interest in cellular biological systems and treatment care. They exhibit the ability to regress tumor growth in mouse models, cleave DNA in gel assays and exhibit efficacies in a hypoxic environment similar to that of tumors in …

Integrative Approaches For Large-Scale Biomedical Data Analysis, Ashis Kumer Biswas

Computer Science and Engineering Dissertations - Archive

Advancement of the Next Generation Sequencing (NGS), also known as the High Throughput Sequencing (HTS) technologies allow researchers investigate genome, transcriptome, or epigenome of any organism from any perspective, thereby contributing to the enrichment of the biomedical data repositories for many of the lesser known phenomena. The regulatory activities inside genome by the non-coding RNAs (ncRNAs), the transcribed product of the long-neglected "junk DNA" molecules is one such phenomenon. While large-scale data about the ncRNAs are becoming publicly available, the computational challenges are being imposed to the bioinformaticians for efficient mining to get reliable answers to few subtle questions. Given …

Tracing The Dawn Of The Elapidae Through The Molecular Systematics And Historical Biogeography Of Old World Coralsnakes, Utpal Smart

Biology Dissertations - Archive

Much debated since the early 20th century, the evolutionary history and origin of the clinically important family Elapidae is of enormous interest. A persistent lack of higher-level phylogenetic resolution however, has impeded a clear understanding of the biogeography of this charismatic group of snakes. The traditional limiting factor in studies on higher-level elapid relationships has been the availability of samples from Old World coralsnakes (genera Sinomicrurus and Calliophis). Usually small, shy and fossorial, these animals are amongst the rarest Oriental snakes and their sampling in molecular studies has been sparse. Herein, primarily using molecular data, I work out the systematic …

Phylogeography Of The American Green Treefrog Species Group, Paul Nathaniel Pasichnyk

Biology Dissertations - Archive

The southeastern United States is an important temperate biodiversity hotspot, housing a multitude of endemic species and multiple large rivers fragmenting their ranges. To determine if the Riverine Barriers Hypothesis explains population divergence in this region, this study utilizes of a combination of phylogeographic methods and ecological niche modeling to investigate the role of rivers in genetic dispersal. Intra-and interspecific phylogenies for the hylid treefrogs Dryophytes cinereus, D. gratiosus and D. squirellus were estimated using nuclear and mitochondrial DNA sequences to identify relationships and genetic variation within these species and test for population structure, especially with respect to potential riverine …

Response Of Microbial Networks And Microbiomes To The Forest-To-Pasture Conversion In Amazon Soils, Md Abdul Wadad Khan

Biology Dissertations - Archive

The Amazon rainforest is the largest tropical rainforest ecosystem in the world, and an extremely important region ecologically. Due to the growing human needs mainly for cattle ranching and cultivation, the rainforest has been in the process of clearing since 1970s losing an average of 25,000 km annually. This ecosystem conversion has a substantially adverse impact on biological diversities, in which the response of microbial diversity has not been studied until recently. Several studies showed that the conversion severely altered microbial diversities, with an increased alpha and decreased beta diversities. Given that microorganisms are closely associated with soil-associated functions, where …

Recipients Of Major Scientific Awards A Descriptive And Predictive Analysis, Andrew Calvin Barbee

Educational Leadership & Policy Studies Dissertations - Archive

Recent trends demonstrate an increase of women in leadership roles, STEM fields, and participating in higher education including graduate and doctoral programs, which is a result of Title IX. This quantitative study considered major scientific awards awarded to females and examines demographic characteristics of awardees from the Nobel, National Academy of Sciences (NAS), and National Science Foundation (NSF). More specifically, the following awards were examined the Nobel Prize in Chemistry, the NAS Public Welfare Medal, and the NSF National Medal of Science within the discipline of Physical Science. Also, this study focused on equality to determine if a fair playing …

The Potential Roles Of Long Noncoding Rnas (Lncrna) In Glioblastoma Development, Shuang Liu, Ramkrishna Mitra, Ming-Ming Zhao, Wenhong Fan, Christine M. Eischen, Feng Yin, Zhongming Zhao

Department of Cancer Biology Faculty Papers

Long noncoding RNA (lncRNA) may contribute to the initiation and progression of tumor. In this study, we first systematically compared lncRNA and mRNA expression between glioblastoma and paired normal brain tissues using microarray data. We found 27 lncRNA and 82 mRNA significantly upregulated in glioblastoma, as well as 198 lncRNA and 285 mRNA significantly downregulated in glioblastoma. We identified 138 coexpressed lncRNA–mRNA pairs from these differentially expressed lncRNA and genes. Subsequent pathway analysis of the lncRNA-paired genes indicated that EphrinB–EPHB, p75-mediated signaling, TNFα/NF-κB, and ErbB2/ErbB3 signaling pathways might be altered in glioblastoma. Specifically, lncRNA RAMP2-AS1 had significant decrease of expression …

An Initiative To Improve Primary Prevention Of Heart Disease In Adults With Type Ii Diabetes Based On The Acc/Aha (2013) And Ada (2016) Guidelines, Litzie Garza

Doctor of Nursing Practice

Heart disease is the leading cause of death in the United States and in Texas. Hyperlipidemia is a precursor to cardiovascular disease and is a highly manageable and treatable acute and chronic disease in the outpatient primary care setting. This project is designed to increase clinicians’ adherence to the American College of Cardiology/American Heart Association (2013) and American Diabetes Association (2016) clinical practice guidelines for the prevention of heart disease in 40 to 75 year old adults with type II diabetes through interactive education, an electronic alert, and quality improvement sessions on the treatment and management of cholesterol in a …

Reintroducing Environmental Change Drivers In Biodiversity-Ecosystem Functioning Research., Frederik De Laender, Jason R. Rohr, Roman Ashauer, Donald J Baird, Uta Berger, Nico Eisenhauer, Volker Grimm, Udo Hommen, Lorraine Maltby, Carlos J Meliàn

Integrative Biology Faculty and Staff Publications

For the past 20 years, research on biodiversity and ecosystem functioning (B-EF) has only implicitly considered the underlying role of environmental change. We illustrate that explicitly reintroducing environmental change drivers in B-EF research is needed to predict the functioning of ecosystems facing changes in biodiversity. Next we show how this reintroduction improves experimental control over community composition and structure, which helps to provide mechanistic insight on how multiple aspects of biodiversity relate to function and how biodiversity and function relate in food webs. We also highlight challenges for the proposed reintroduction and suggest analyses and experiments to better understand how …

Fabricating Suspended Carbon Structures Using Su-8 Photolithography, Emanuele Giogli

All Theses

The phenomenon of T-topping has been deemed as an imperfection of the SU-8 photolithography process, due to light diffraction, overexposure of the SU-8, and other process parameters. The first objective of this work is to demonstrate that T-topping can be used as a microfabrication resource to produce suspended structures between photo-patterned high aspect ratio SU-8 posts, as precursors for carbon wires (width>1µm) and bridges (width>1µm). Such carbon structures could be used in a number of applications, such as the fabrication of nanowire based biosensors for the medical and food industry. The second objective is to develop a model …

Career Decision Self‐Efficacy Of Transgender People: Pre‐ And Posttransition, Lore M. Dickey, Daniel Walinsky, Crystal Rofkahr, Kara Richardson‐Cline, Cindy L. Juntunen

Education, Health & Behavior Studies Faculty Publications

Although the mental health needs of transgender and gender‐nonconforming (TGNC) people have recently been addressed more directly than in the past (Bockting, Miner, Swinburne Romine, Hamilton, & Coleman, 2013; dickey, Reisner, & Juntunen, 2015; Meier, Pardo, Labuski, & Babcock, 2013), there remains a dearth of information related to vocational development of this population. Some of the considerations in career counseling and vocational development among TGNC people include differences in developmental concerns related to gender transition, gender presentation, passing (e.g., being perceived by others in one's affirmed gender), and binary and fluid gender identities (Beemyn & Rankin, 2011; Harrison, Grant, & …

Narrative Review Of Vitamin D And Its Specific Impact On Balance Capacity In Older Adults, Ray Marks

Publications and Research

Introduction and Aims: Falls injuries among older adults, a widespread well-established contributor to high disability levels, excess morbidity and mortality rates, have many causes. This review examines the association between vitamin D levels and postural stability or balance control—a fairly consistent predictor of falls among older adults.

Materials and Method: All relevant English language peer reviewed research publications detailing the relationship between vitamin D levels and balance control among the elderly were sought. Key words included “Vitamin D and Balance or Postural Control.” Databases used were Academic Search Complete, PubMed, Scopus, and Web of Science.

Results: Analysis showed no consistent …