Digital Commons Network^™

Analysis Of Zip1 And Sgs1 Protein Interaction In Budding Yeast, Sana F. Hussain

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

Meiotic crossovers (COs) are essential for proper chromosomal separation. Interhomologue recombination is promoted by the synaptonemal complex (SC), which connects paired homologous chromosomes together. Zip1, an integral component of the SC, antagonizes Sgs1 helicase function during meiotic recombination to promote COs. Specifically, Zip1 and other ZMM proteins shield strand invasion intermediates from Sgs1 activity, thus preventing Sgs1 from disassembling them. It has been previously discovered that Zip1 interacts with Sgs1 in two-hybrid experiments, and that full length Zip1 binds to Sgs1 in vitro. These interactions suggest that the antagonism may be due to direct interactions between Sgs1 and Zip1. This …

Molecular Movie Magic: Real-Time Picosecond To Microsecond Structural Dynamics Of Photoactive Flavoproteins, Richard James Brust

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

Femtosecond (fs) excitation of photoreceptors results in protein structural changes that occur on the microsecond to millisecond timescale or longer. It is thus of fundamental interest to understand how these fast timescale events dictate large scale protein dynamics that occur on much longer (106 orders of magnitude) timescales. AppA is a blue light using FAD (BLUF) protein which acts as a transcriptional antirepressor in Rhodobacter sphaeroides. The ultrafast photocycle and IR spectra are well characterized and involve a near instantaneous (<100 fs) response of the protein matrix that surrounds the chromophore. While there has been extensive study on the ultrafast time scales there has never been an observation of the kinetics of the light induced structural changes in the protein. Here we investigated the ultrafast (ps) to ms structural dynamics through transient IR. The data show that significant structural changes occur on the sub microsecond timescale following photoactivation. In addition our work has expanded to other BLUF proteins. BlsA is a BLUF protein found in the pathogenic bacterium Acinetobacter baumannii. Vibrational data together with homology modeling identify significant differences in β 5 strand caused by photoactivation, a region of BLUF photoreceptors proposed to be essential for signal modulation, that are unique for BlsA. In addition, the BLUF protein PixD, from Synechocystis, was characterized by transient IR, where photoexcitation results in radical pair formation, an event not observed in AppA. Transient IR also revealed that light state formation is complete within nanoseconds for PixD, suggesting a unique mechanism for single and multidomain BLUF systems. | 254 pages

Drug Discovery Through Combination Of Computational Screening And Design, Chemical Synthesis And Biological Evaluations, William Theodore Berger

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

A long-standing problem with the use of conventional cancer chemotherapy is the inherent lack of tumor specificity. Tumor-targeting drug-delivery systems (TTDS) have since been explored to overcome this deficiency. These drug conjugates can deliver potent cytotoxic drugs specifically to tumors and tumor cells with minimal systemic toxicity. Among various tumor-targeting molecules discussed, Designed Ankyrin Repeat Proteins (DARPins) represent a new approach to tumor targeting. In particular, DARPins targeting CD326 Epithelial Cell Adhesion Molecule (EpCAM) receptors provide an effective cancer target, as EpCAM is critical to the regulation of cellular matrix composition and overall cancer aggressiveness. Botulism is a human illness …

Comparisons Of Intermediate Oxidation State Sulfur Compounds In The Episodically, Lan Thi Tong

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

The anoxic Cariaco Basin located on the Venezuela continental shelf and the seasonally anoxic Forge River located on the south shore of Long Island are two quite different aquatic systems. However, they are both characterized by the pulsed intrusion of oxygen into sulfidic waters, where sulfur intermediates including sulfite (SO32-), thiosulfate (S2O32-), and zero-valent sulfur (So) are usually found. In this study, I investigated the distribution of sulfur intermediates and the relative importance of chemical and biological hydrogen sulfide oxidation to the sulfur intermediates distribution in these two systems. The sulfide oxidation rate, determined using Forge River water with an …

The Genetic Diversity Of Endangered Fishes In The Northwest Atlantic, Shannon Joy O'Leary

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

Genetic diversity is the fundamental building block of biodiversity, harboring the adaptive potential of populations. The magnitude of the two main factors eroding genetic diversity, inbreeding and genetic drift, increases as the effective population size (Ne) decreases. Ne describes the number of reproductively mature adults effectively contributing to the next generation. In populations with overlapping generations, the effective number of breeders (Nb). Loss of genetic diversity has long been a concern for terrestrial and freshwater organisms, but traditionally less so for fisheries management due to the paradigm that marine fish populations are large, panmictic and thus resistant to the erosion …

Biomimetic Calcium Phosphate Coatings Synthesized By Electrochemical Deposition And Air Plasma Spray: Morphology, Composition And Bioactive Performance, Ling Li

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

In this project, with the aim to develop bioactive biomimetic coatings for dental and orthopedic applications, calcium phosphate based coatings deposited by electrochemical deposition and plasma spray were investigated. Different combinations of process parameters were used to achieve coatings with various chemical compositions and morphologies. The obtained coating composition was investigated by energy dispersive X-ray spectroscopy and X-ray diffraction. The microstructure of the coatings were studied through scanning electron microscopy while the cytocompatibility and bioactivity of the strontium-doped calcium phosphate coatings were evaluated using bone cell culture using MC3T3-E1 osteoblast-like cells. A set of designed experiments were performed to study …

Comparisons Of Intermediate Oxidation State Sulfur Compounds In The Episodically, Lan Thi Tong

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

The anoxic Cariaco Basin located on the Venezuela continental shelf and the seasonally anoxic Forge River located on the south shore of Long Island are two quite different aquatic systems. However, they are both characterized by the pulsed intrusion of oxygen into sulfidic waters, where sulfur intermediates including sulfite (SO32-), thiosulfate (S2O32-), and zero-valent sulfur (So) are usually found. In this study, I investigated the distribution of sulfur intermediates and the relative importance of chemical and biological hydrogen sulfide oxidation to the sulfur intermediates distribution in these two systems. The sulfide oxidation rate, determined using Forge River water with an …

The Dynamical Basis Of The Decanalization Of Gene Expression In Kr Uppel Mutant Embryos, Lena Panok

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

Canalization is the ability of an organism's phenotype to remain stable under a perturbation in their genotype or the environment. It has been noted that there is no canalization or canalization is to a much smaller degree in mutants than in wild type. Waddington's idea was to understand canalization through studying gene interactions. We investigate the mechanisms of canalization of gap gene patterns in D.melanogaster through dynamical analysis of the gene circuit. To carry out this investigation we construct a dynamical model of the evolution of the concentration of protein products of the gap genes in time. Our model, which …

Manufacturing Malinche: Socio-Sexual Narratives Of Imperialism, Colonialism, And Nationalism, Sibyl Gallus-Price

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

Malinche's ever changing myth has contributed to the view that one woman is answerable for the legacy of conquest. This view, evoking worship and revile, operates more as a litmus test of the prevailing weltanschauung than as a claim of historical authenticity. In the context of imperialism, colonialism, and post-colonialism, this study seeks to examine the socio-sexual system as it defines the production of an enduring national mythic symbol. Exposing the ideological underpinnings of the narratives that have contributed to the Malinche myth, exemplar works will demonstrate the impact of: the ontological understanding of gendered models of imperialism; the historical …

Synthesis Of Sb-T-12301 Analogues And Tumor-Targeting Taxane-Based Drug Conjugates Using Biotin As Tumor-Targeting Module, Changwei Wang

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

Cancer is one of the most serious diseases of the world, leading to one of eight deaths. Although the medical advancements have contributed greatly to the decline of other diseases, treatments for cancer have remained only modestly effective. Traditional chemotherapeutics such as Taxol and Taxotere generally lack specificity, and repeated administration often leads to multi-drug resistance (MDR). To increase the efficacy and specificity of drugs, both the synthesis and evaluation of lead compounds and the development of drug delivery system are equally important. SB-T-1214 and three novel taxanes, SB-T-12301 and two of its analogues, were synthesized by the standard Ojima-Holton …

The Design, Synthesis And Biological Evaluation Of Novel Taxoid Anticancer Agents And Their Tumor-Targeted Drug Conjugates, Joshua Seitz

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

Cancer is the second leading cause of death in the United States and is responsible for one in eight deaths worldwide. Traditional chemotherapeutics target the processes involved in cell division and consequently produce dangerous and dose-limiting side effects. In an effort to identify the therapeutic windown of these drugs, tumor targeted drug conjugates (TTDCs) are currently under development. The Ojima lab has developed and extensive panel of next-generation taxoids that possess the requisite sub-nanomolar potency for incorporation into effective conjugates. A small library of 17 taxoids was synthesized and their cytotoxicity investigated. Selected taxoids were synthesized on the half-gram to …

On The Optimization Of Grid Systems, Kai Wang

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

Grid systems are widely used to transfer power and information in various forms in many engineering and scientific areas such as grid computing systems, electrical grids, control grid and etc. A good handling of task partition, task allocation and load balancing can significantly increase a grid systems' efficiency. In this dissertation, balancing the loads in electrical grid systems and optimizing grid computing systems are analyzed. Unbalanced loads on feeders increase power system investment and operating costs. Three-phase lateral loads phase swapping is one of the popular methods to balance such systems. We employed a dynamic programming algorithm that makes optimal …

A Stochastic Segmentation Model For Recurrent Copy Number Alterations In Grouped Array-Cgh Data, Ying Cai

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

With the recent advances in high resolution microarrays and next generation sequencing, DNA copy number can now be profiled in a high throughput global manner. This has enabled the systematic study of DNA copy number alterations in tumors, as well as the profiling of inherited population-wide copy number variants. Studies of DNA copy number usually involve many samples that fall into different groups, e.g. tumor subtype or ethnic group. It is often of interest to find recurrent alterations within each group. We develop a stochastic segmentation model for detecting recurrent DNA copy number alterations in grouped array-CGH data. In our …

Characteristics Of Aerosolized Ice Forming Marine Biogenic Particles, Peter Aaron Alpert

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

Ice particles are ubiquitous in the atmosphere existing as the sole constituents of glaciated cirrus clouds or coexisting with supercooled liquid droplets in mixed-phase clouds. Aerosol particles serving as heterogeneous ice nuclei for ice crystal formation impact the global radiative balance by modification of cloud radiative properties, and thus climate. Atmospheric ice formation is not a well understood process and represents great uncertainty for climate prediction. The oceans which cover the majority of the earth's surface host nearly half the total global primary productivity and contribute to the greatest aerosol production by mass. However, the effect of biological activity on …

Genetic Variability Of Spined Soldier Bugs (Hemiptera: Pentatomidae) Sampled From Distinct Field Sites And Laboratory Colonies In The United States, Fatima Mustafa, Muhammad Ullah, Kathleen M. Kneeland, Thomas A. Coudron, W. Wyatt Hoback, S. R. Skoda, Jaime Molina-Ochoa, John E. Foster

Department of Entomology: Faculty Publications

The spined soldier bug, Podisus maculiventris (Say), is an important biological control agent of agricultural and forest pests; and it preys on eggs and larvae of lepidopteran and coleopteran species. Genetic variability among field samples collected from Michigan, Mississippi, Missouri, Florida and established laboratory colonies was examined using Amplified Fragment Length Polymorphism-Polymerase Chain Reaction (AFLP-PCR). Four AFLP primer pairs generated a total of 340 molecular markers for evaluation. Results from Analysis of Molecular Variance showed that the majority of the genetic variation occurred within populations (individuals from each sample site). Nei’s method indicated reduced genetic diversity in laboratory populations compared …

Proteomic Profiling Of Burkholderia Cenocepacia Clonal Isolates With Different Virulence Potential Retrieved From A Cystic Fibrosis Patient During Chronic Lung Infection., Siobhan Mcclean, Máire Callaghan, Jean Tyrrell, Isabelle Sa Correia

Articles

Respiratory infections with Burkholderia cepacia complex (Bcc) bacteria in cystic fibrosis (CF) are associated with a worse prognosis and increased risk of death. In this work, we assessed the virulence potential of three B. cenocepacia clonal isolates obtained from a CF patient between the onset of infection (isolate IST439) and before death with cepacia syndrome 3.5 years later (isolate IST4113 followed by IST4134), based on their ability to invade epithelial cells and compromise epithelial monolayer integrity. The two clonal isolates retrieved during late-stage disease were significantly more virulent than IST439. Proteomic profiling by 2-D DIGE of the last isolate recovered …

A Ranavirus-Related Mortality Event And The First Report Of Ranavirus In New Jersey, Kirsten Monsen-Collar, Lisa Hazard, Paola Dolcemascolo

Department of Biology Faculty Scholarship and Creative Works

No abstract provided.

Domestic Relations, Barry B. Mcgough, Elinor H. Hitt

Mercer Law Review

This Article addresses significant case law that arose during the survey period. There were no statutory changes specific to domestic relations during this period, though substantial changes were made to the evidence code.

Loss Of Vascular Endothelial Growth Factor A (Vegfa) Isoforms In The Testes Of Male Mice Causes Subfertility, Reduces Sperm Numbers, And Alters Expression Of Genes That Regulate Undifferentiated Spermatogonia, Ningxia Lu, Kevin M. De Avila, Debra T. Clopton, William E. Pohlmeier, Vanessa M. Brauer, Renee M. Mcfee, John S. Weber, Napoleone Ferrara, David W. Silversides, Andrea S. Cupp

Department of Animal Science: Faculty Publications

Vascular endothelial growth factor A (VEGFA) isoform treatment has been demonstrated to alter spermatogonial stem cell homeostasis. Therefore, we generated pDmrt1-Cre;Vegfa^−/− (knockout, KO) mice by crossing pDmrt1-Cre mice to floxed Vegfa mice to test whether loss of all VEGFA isoforms in Sertoli and germ cells would impair spermatogenesis. When first mated, KO males took 14 days longer to get control females pregnant (P < .02) and tended to take longer for all subsequent parturition intervals (9 days; P < .07). Heterozygous males sired fewer pups per litter (P < .03) and after the first litter took 10 days longer (P < .05) to impregnate females, suggesting a more progressive loss of fertility. Reproductive organs were collected from 6-month-old male mice. There were fewer sperm per tubule in the corpus epididymides (P < .001) and fewer ZBTB16-stained undifferentiated spermatogonia (P < .003) in the testes of KO males. Testicular mRNA abundance for Bcl2 (P < .02), Bcl2:Bax (P < .02), Neurog3 (P < .007), and Ret was greater (P = .0005), tended to be greater for Sin3a and tended to be reduced for total Foxo1 (P < .07) in KO males. Immunofluorescence for CD31 and VE-Cadherin showed no differences in testis vasculature; however, CD31-positive staining was evident in undifferentiated spermatogonia only in KO testes. Therefore, loss of VEGFA isoforms in Sertoli and germ cells alters genes necessary for long-term maintenance of undifferentiated spermatogonia, ultimately reducing sperm numbers and resulting in subfertility.

Library Instruction Credibility: How Do We Establish It? How Do We Publicize It?, Frances A. May, Yunfei Du

LOEX Conference Proceedings 2011

What I would like to propose is not a presentation but a strategy session. Over the ten years I have spent as an instruction librarian, I have come to realize that what we need is quantitative data showing the benefits that students derive from library instruction. It needs to be gathered and published in non-library forums, such as educational or subject specific journals. Once the benefits are publicized and understood by educators and faculty, we may be able to move beyond the fifty minute, one shot instruction session, and make an information literate society a reality.

To do this, we …

Subway Rail Car Filter Sampling Tool, Brian Hong, Julia Pollard, Philip Ybarra

Mechanical Engineering

The following design report has been prepared by Team Slice for both Cal Poly’s Mechanical Engineering Department and Lawrence Livermore National Laboratory. This report provides an overview of the design ideation process of creating a subway rail car filter sampling tool. This cutting tool will take samples of HVAC filters from subway railcars in New York City, NY. These samples will then be used for processing in biological terror emergency response situations. This device will provide an easy, safe, and user friendly tool to cut filter samples. The current method of cutting is a pair of scissors or shears, which …

Design Of A Sustainable Toilet, Meghan Pranger, Tommy Lauderdale, Joseph Benyon, Kyle Moore

Mechanical Engineering

No abstract provided.

Severe, Fatal Multisystem Manifestations In A Patient With Dolichol Kinase-Congenital Disorder Of Glycosylation., Michelle T Lieu, Bobby G Ng, Jeffrey S Rush, Tim Wood, Monica J Basehore, Madhuri Hegde, Richard C Chang, Jose E Abdenur, Hudson H Freeze, Raymond Y Wang

Molecular and Cellular Biochemistry Faculty Publications

Congenital disorders of glycosylation are a group of metabolic disorders with an expansive and highly variable clinical presentation caused by abnormal glycosylation of proteins and lipids. Dolichol kinase (DOLK) catalyzes the final step in biosynthesis of dolichol phosphate (Dol-P), which is the oligosaccharide carrier required for protein N-glycosylation. Human DOLK deficiency, also known as DOLK-CDG or CDG-Im, results in a syndrome that has been reported to manifest with dilated cardiomyopathy of variable severity. A male neonate born to non-consanguineous parents of Palestinian origin presented with dysmorphic features, genital abnormalities, talipes equinovarus, and severe, refractory generalized seizures. Additional multi-systemic manifestations developed …

Phytophthora Foliage Blight Of Garden Phlox: Phytophthora Nicotianae On Phlox Paniculata, Daniel Drechsler

All Theses

Phytophthora foliage blight of garden phlox (Phlox paniculata ) - caused by Phytophthora nicotianae - is a devastating disease that has been seen consistently in nursery production facilities in South Carolina. However, this disease has not been characterized previously. This project was composed of three separate studies, each of which followed one of the three major components of the disease triangle (i.e., the synchronous occurrence of a susceptible host and a virulent pathogen within a conducive environment) to investigate the pathogenicity of P. nicotianae on P. paniculata . In one study, the efficacies of three inoculation methodologies to cause …

Connecting The Dots: Understanding Migration In The Context Of Other Periods Of The Annual Cycle, Kristina Lee Paxton

Dissertations

Migration is a fundamental characteristic of the life history of many organisms. Large-scale seasonal movements expose migratory species to an array of differing environmental conditions such that the ecology, behavior, and life history strategies of migratory species must balance selection pressures associated with each phase of the annual cycle. Therefore, scientists increasingly realize that to understand the ecology of a migratory species in any one phase of the annual cycle requires an understanding of how other phases may interact with and influence the period of interest. That said, following individuals throughout the year poses a serious challenge.

The focus of …

Minimal Medium For Optimal Growth And Lipid Production Of The Microalgae Scenedesmus Dimorphus, Colin Welter, Jacob Schwenk, Bahar Kanani, John Van Blargan, Joanne M. Belovich

Chemical & Biomedical Engineering Faculty Publications

The culture of Scenedesmus dimorphus at the laboratory scale has often been in standard microalgae media, such as 3N-Basal Bold medium (3N-BB), which contains 15 different chemicals. Given the extremely tight profit margins of large-scale production of biofuel from microalgae, it is important to identify the minimally sufficient quantities of nutrients necessary to maximize lipid productivity. The individual and interactive effects of six groupings of the components of 3N-BB medium on growth rate, lipid content, and total biomass yield of S. dimorphus were determined. Trace metal and vitamin concentrations were reduced to 1/6 the level of 3N-BB medium without adversely …

Nanta Hosh Chahta Immi? (What Are Choctaw Lifeways?): Cultural Preservation In The Casino Era, Sean Everette Gantt

Anthropology ETDs

This dissertation investigates the long-term impacts of tribal economic development programs on the cultural preservation efforts of the Mississippi Band of Choctaw Indians (MBCI). Since the 1970s the Mississippi Choctaw have initiated many different economic enterprises ranging from manufacturing plants to resort development, owning and operating a diversified portfolio of manufacturing, service, retail, and tourism enterprises. This history of engaging with western business models offers a unique perspective for analyzing the long-term effects of these practices on a tribal community. My work with the MBCI engages a long debate over the use of capitalist business models in tribal economic development …

Peer Feedback To Facilitate Project-Based Learning In An Online Environment, Yu-Hui Ching, Yu-Chang Hsu

Educational Technology Faculty Publications and Presentations

There has been limited research examining the pedagogical benefits of peer feedback for facilitating project-based learning in an online environment. Using a mixed method approach, this paper examines graduate students’ participation and perceptions of peer feedback activity that supports project-based learning in an online instructional design course. Our findings indicate that peer feedback can be implemented in an online learning environment to effectively support project-based learning. Students actively participated in the peer feedback activity and responded positively about how the peer feedback activity facilitated their project-based learning experiences. The results of content analysis exploring the peer feedback reveal that learners …

Wolves Facilitate The Recovery Of Browse-Sensitive Understory Herbs In Wisconsin Forests, Krystle Bouchard, Jane E. Wiedenhoeft, Adrian P. Wydeven, Thomas P. Rooney

Biological Sciences Faculty Publications

We asked whether wolf re-colonization would facilitate increased growth and reproduction of three browse-sensitive plant species. We hypothesized plant size and the proportion of reproductive individuals would be lowest in areas with no wolves, intermediate where wolves had been present for 4-6 years, and highest where wolves had been present for 12-13 years. Two plant species exhibited significantly greater reproduction where wolves were present for 12-13 years. Mean leaf size of indicator plants was significantly greater in areas where wolves were present for 12-13 years, as compared with that in areas where wolves were not present or were present for …

An Argument And Plan For Promoting The Teaching And Learning Of Neglected Tropical Diseases, Kevin M. Bonney

Publications and Research

Neglected tropical diseases constitute a significant public health burden, affecting over one billion people globally, yet this group of diseases is underrepresented in the appropriation of both monetary and intellectual capital for developing improved therapies and public health campaigns. The topic of neglected tropical diseases has been similarly marginalized in the biology classrooms of our nation’s high schools and colleges, despite offering an opportunity to teach and learn about a diverse area of microbiology with far-reaching public health, social, and economic implications. Discussed herein is an argument for increasing the representation of neglected tropical diseases in microbiology education as a …