Digital Commons Network^™

Determining Ligand-Binding Induced Conformational Changes In H-Nox Domains, Farzan Mirza Gorgani

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

Nitric Oxide (NO) has diverse and important roles in prokaryote and eukaryote biology. In addition to its role as a powerful toxin used to kill pathogens and tumor cells, NO also functions as a signaling molecule that mediates mechanisms such as vasodilatation, neurotransmission and biofilm formation. Our objective is to elucidate the role of NO in bacterial biofilm formation. Due to their resistance to antibiotics, biofilms are known to plague hospitals and immune compromised patients. As a first step in this objective, we are interested in characterizing the bacterial NO sensor Heme-Nitric oxide/OXygen binding domain (H-NOX). We predict that H-NOX …

Life After Beanbag Genetics: Theoretical And Empirical Studies On Epistasis And Penetrance, Joseph Lachance

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

Population genetics reduces the description of a population to a set of genotype frequencies. Because of this, it has been called"beanbag genetics.". However, greater complexity and biological realism can be incorporated into this framework. Two examples of this include interactions between different genes (epistasis) and individuals with the same genotype that have different phenotypes (incomplete penetrance). During the course of my Ph.D. work, both of these topics were investigated using theoretical population genetics and Drosophila genetics. One unifying theme was that genes do not exist in isolation: they occur within genetic and environmental contexts. In turn, these contexts were found …

Solid State Nmr And Pair Distribution Function Studies Of Silicon Electrodes For Lithium-Ion Batteries, Baris Key

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

The universally used negative electrode material in a LIB is carbon, because of its moderate capacity (372 mAhg-1 for graphite), cyclability and high rate capability. However, new, low cost, safe electrode materials with higher capacities are still urgently required for both portable and transportation applications. Silicon anodes are particularly attractive alternatives to carbon with extremely high gravimetric energy densities (3572 mAhg-1). Compared to graphite, silicon has a massive volumetric capacity of 8322 mAhcm-3 (calculated based on the original volume of silicon) which is approximately ten times that graphite. At room temperature, upon electrochemical lithiation, silicon undergoes a crystalline to amorphous …

The Specificity Of Vesicle Trafficking During Prospore Membrane Formation In Yeast, Hui-Ju Yang

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

This research focuses on the production of new plasma membranes during gametogenesis in yeast. The initiation of these membranes is started by vesicle fusion at spindle pole bodies (SPBs) during Meiosis II. I have asked how these vesicles specifically fuse at SPBs but not at other locations, and demonstrated that binding interactions between soluble NSF attachment protein receptors (SNAREs) confer one layer of specificity to vesicle fusion at SPBs. Furthermore, I showed that SPBs can actively regulate a Rab GTPase, suggesting a role for SPBs in vesicle docking. My work highlights the ancestral dual roles of centrioles in microtubule organization …

Statistical Models For Snp Detection, Shengnan Cai

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

Variations in DNA sequences of humans have a strong association with many diseases. Single Nucleotide Polymorphism (SNP) is the most common type of DNA variations. Our research is to detect SNPs from the data generated by Polymerase Chain Reaction (PCR) and next generation sequencing methods. In the first part of the study, we had a relatively small data set with fewer known SNPs as the training data. We developed a classification model based on the cross validation method. From the first part of the research, we gained knowledge of the properties of the data. In the next phase, we obtained …

Repression Of Meiotic Gene Expression By Regulated Rna Stability And By Antisense Transcription In Schizosaccharomyces Pombe, Huei-Mei Chen

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

Meiosis produces haploid gametes from diploid germ cells. Many genes are used only for meiosis and cause harm if they are expressed in vegetative (non-meiotic) cells. My dissertation research focused on mechanisms that keep meiotic functions completely off in vegetative cells in a model organism, the fission yeast Schizosaccharomyces pombe. Early meiotic genes drive a specialized S-phase and meiotic recombination events. I found that at least 30 early meiotic genes in S. pombe are transcribed even in vegetative cells where they are kept off by degradation of their transcripts through a novel mechanism directed by Mmi1, an RNA binding protein. …

Modulation Of Monocytic Activation Following Spinal Cord Injury Reduces Secondary Injury And Neurodegeneration, Jaime Ann Emmetsberger

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

Spinal cord injury (SCI) sets off a cascade of biochemical and cellular events that destroy neurons, cause demyelination, and trigger an inflammatory immune response. Microglia, the immune-competent cells of the central nervous system, migrate to the site of injury, become activated and are thought to contribute to secondary damage and neurodegeneration following SCI. Conversely, growth factors and cytokines released by activated microglia may promote regeneration. Controversy exists over the neurodegenerative verses the neuroregenerative roles of activated microglia, and which role predominates following SCI. The activation state of microglia determines their neurotoxic and neurotrophic properties that influence the surrounding environment to …

Seasonal Aggregations Of The Florida Manatee (Trichechus Manatus Latirostris) In The Port Everglades And Intracoastal Regions Of Fort Lauderdale, Florida., Jaime M. Goldman

HCNSO Student Theses and Dissertations

The Florida manatee (Trichechus manatus latirostris), a subspecies of the West Indian manatee, is one of the most endangered marine mammals in United States waters. The Florida manatee is the only manatee that ranges into subtropical and temperate regions. During the winter months manatees adopt a “refuging strategy” where they aggregate at warm-water sources immediately following decreases in the ambient water temperature to below 20° C (68° F) in order to avoid cold stress syndrome (CSS). During the winter manatees aggregate in warm water refuges, including natural warm water springs and the effluent discharges of power plants.

The …

Role Of Hypoxia-Inducible Factor-1 Alpha In Neural Stem/Progenitor Cell Function Following Hypoxia, Kate M. Harms Candelario

Biomedical Sciences ETDs

Stroke can be caused by focal ischemia due to cerebral artery occlusion or by global ischemia that occurs when global blood supply to the brain is interrupted. The acute phase of ischemic brain injury is followed by a more prolonged period of revascularization and repair that can last for several months. One hallmark of this repair phase includes an endogenous neural stem/progenitor cell (NSPC) regenerative response that occurs concomitant with angiogenesis. Several studies suggest that the cytogenic response is beneficial for recovery following stroke, however, more studies need to be done to determine whether the beneficial effects are due to …

Biotech Biofuels: How Patents May Save Biofuels And Create Empires, Adam Wolek

Chicago-Kent Law Review

The United States' primary transportation energy sources are fossil fuels, namely, gasoline and diesel. These products have high environmental, security, and financial costs. A strong emphasis has been placed on biofuels, especially ethanol and biodiesel, to lessen reliance on fossil fuels. Historically, high production costs, lack of infrastructure, return on investment anxieties, and concerns about scaling-up production have slowed the development of these alternative technologies. Today, biotechnological solutions are lowering productions costs and making large scale production more economically feasible. Patents can lessen anxieties about investment as they can provide longer-term protection and market exclusivity for patented technologies. As biofuels …

C-Jun Inhibits Mammary Apoptosis In Vivo., Sanjay Katiyar, Mathew C Casimiro, Luis Dettin, Xiaoming Ju, Erwin F Wagner, Hirokazu Tanaka, Richard Pestell

Department of Cancer Biology Faculty Papers

c-jun, which is overexpressed in a number of human cancers encodes a critical component of the AP-1 complex. c-jun has been shown to either induce or inhibit cellular apoptosis. Germ line deletion of both c-jun alleles is embryonically lethal. To determine the role of the endogenous c-jun gene in apoptosis, we performed mammary epithelial cell-targeted somatic deletion using floxed c-jun (c-jun(f/f)) conditional knockout mice. Laser capture microdissection demonstrated endogenous c-jun inhibits expression of apoptosis inducing genes and reactive oxygen species (ROS)-reducing genes (MnSOD, catalase). ROS have been implicated in apoptosis and undergo enzymatic elimination via MnSOD and CuZnSOD with further …

Considerations On Unsupervised Spectral Data Unmixing And Complexity Pursuit, Stefan Robila

Department of Computer Science Faculty Scholarship and Creative Works

Hyperspectral sensors carry the distinctive advantage of recording hundreds of contiguous spectral images for the same scene providing an extraordinary amount of information that leads to precise differentiation of materials present in the scene even when such materials contribute only to few pixels [1]. With the advent of more and more powerful sensing platforms, coupled with reduction in manufacturing costs and diversification of technologies, hyperspectral imaging has become a powerful approach in remote sensing with applications spanning all traditional fields (such as agriculture, mining, military, resource management, etc.) as well as new ones (manufacturing quality control, pollution detection, health and …

Microdiscectomy For Lumbosacral Disc Herniation And Frequency Of Failed Disc Surgery, Muhammad Shahzad Shamim, Maria Adnan Parekh, Muhammad Ehsan Bari, Ather Enam, Faraz Khursheed

Section of Neurosurgery

Background: Microdiscectomy for lumbosacral disc herniations is one of the most commonly performed neurosurgical procedures. The Patient demographics, symptomatology, and recovery are highly variable, and surgical outcomes depend on several factors, including Patient demographics. Failed disc surgery refers to failure of improvement in Patient's symptoms following microdiscectomy, and has been observed to occur in up to 12% of Patients. To date, no study form Pakistan has looked into Patient demographics and failed disc surgery rates within the local context.
Objective:The aim of this study was to review the demographics of the Patient population presenting for surgical treatment of lumbosacral …

Framing The Social, Political, And Environmental Risks And Benefits Of Geoengineering: Balancing The Hard-To-Imagine Against The Hard-To-Measure, Gareth Davies

Tulsa Law Review

No abstract provided.

Flank Gland-Secreted Putative Chemosignals Pertaining To Photoperiod, Endocrine States, And Sociosexual Behavior In Golden Hamsters, Ying-Juan Liu, Da-Wei Wang, Lixing Sun, Jin-Hua Zhang, Jian-Xu Zhang

All Faculty Scholarship for the College of the Sciences

Behavioral studies have shown that flank glands are involved in chemical communication in golden hamsters Mesocricetus auratus but little chemical analysis has been conducted on volatiles arising from these glands. Using gas chromatography- mass spectrometry, we detected compounds from the flank glands of males, only eight of which were also produced in females. Based on these chemical data we performed a number of further experiments. By manipulating light we found that males exposed to short-photoperiods developed smaller flank glands than those exposed to long-photoperiods. Six flank gland volatiles reduced in relative abundance, which possibly coded for reproductive status of males …

Core Genome Components And Lineage Specific Expansions In Malaria Parasites Plasmodium, Hong Cai, Jianying Gu, Yufeng Wang

Publications and Research

Background The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, which can lead us to a better understanding of how the parasites develop the genetic variability that is associated with their response to environmental challenges and other adaptive phenotypes. Results We present the results of a comprehensive analysis of the genomes of six Plasmodium species, including two species that infect humans, one that infects monkeys, and three …

The Gel Documentation System: A Cornerstone To The Implementation Of The Introduction To Biotechnology And Introduction To Bioinformatics Cross-Disciplinary Course Series (Final Report), Marcy Kelly, Gregory Lampard, Constance Knapp

Cornerstone 3 Reports : Interdisciplinary Informatics

Our original goal was to offer Pace undergraduate students opportunities to be introduced to both Biotechnology and Computer Science as it relates to Bioinformatics. We proposed a two course series, offered to both computer science and biology students that will increase both biological and computer science literacy of our students. The two courses are Introduction to Biotechnology (BIO 372) and Introduction to Bioinformatics.

Biofuel Ethanol Production By Saccharomyces Bayanus, The Champagne Yeast, Kristen Miller

All Theses

The importance of biofuel ethanol is growing as the demand for clean, renewable fuels produced from non-food sources increases. The United States relies mainly on corn and the yeast Saccharomyces cerevisiae for the production of ethanol. A shift to cellulosic feedstocks, as the main source of biomass for ethanol production, would alleviate the pressure on farmers to produce corn for both the food industry and the ethanol industry. Example cellulosic feedstocks include switchgrass, sorghum, and canary grass. The cellulosic feedstocks are typically grown on land that cannot support economic food production, and thus lay unused.
For cellulosic feedstocks to be …

Neomycin-Enhanced Carbodiimide Cross-Linking For Glycosaminoglycan Stability In Bioprosthetic Heart Valves, Joshua Leong

All Theses

Valvular heart diseases lead to over 290,000 heart valve replacements worldwide each year, and approximately half of these involve replacement with a bioprosthetic heart valve (BHV) [1]. BHVs exhibit excellent hemocompatibility, but suffer from inadequate long-term durability with most adult implanted valves failing within 12 to 15 years after implantation [2]. Although this may be adequate for some individuals, BHV implantation may be contraindicated in younger individuals to avoid reoperation. Even in elder recipients, valve dysfunction can still cause death or reoperation that could be avoided with increased BHV durability. Therefore, investigation into methods of increasing BHV durability can not …

Pilot-Scale Constructed Wetland Treatment System For Ammonia Removal From Oil-Field Produced Water, Yun Song

All Theses

This investigation examined the feasibility of using free-water surface constructed wetland systems (CWTSs) to decrease the ammonia concentration in oil-field produced water. The objective of this research was to design constructed wetland experiments to determine specific conditions that decrease aqueous ammonia concentrations in simulated oilfield produced water. The design of these experiments was based on biogeochemical pathways of nitrification and denitrification. The experiments included three scales: bench-scale, single-cell, and pilot-scale. Bench-scale reactors contained wetland plants (Typha latifolia) and hydrosoil in 5-gallon buckets. Single wetland cells were constructed by adding hydrosoil and plants (T. latifolia and Schoenoplectus californicus) to 70-gallon containers. …

Sex Differences In Deltafosb Induction In Reward-Related Brain Regions Of The Rat Brain, Cam Liu

McNair Scholars Research Journal

No abstract provided.

Sex Differences In Orexin Expression After Chronic Cocaine Conditioning, Brocke Addison

McNair Scholars Research Journal

No abstract provided.

Full Issue, The Mcnair Team

McNair Scholars Research Journal

No abstract provided.

Geoengineering And International Law: The Search For Common Legal Ground, Ralph Bodle

Tulsa Law Review

No abstract provided.

Synthesis, Stabilization, And Characterization Of Metal Nanoparticles, Gregory White Ii

All Dissertations

Wet chemical synthesis techniques offer the ability to control various nanoparticle characteristics including size, shape, dispersibility in both aqueous and organic solvents, and tailored surface chemistries appropriate for different applications. Large quantities of stabilizing ligands or surfactants are often required during synthesis to achieve these nanoparticle characteristics. Unfortunately, excess reaction byproducts, surfactants, and ligands remaining in solution after nanoparticle synthesis can impede application, and therefore post-synthesis purification must be employed. A liquid-liquid solvent/anti-solvent pair (typically ethanol/toluene or ethanol/hexane for gold nanoparticles, GNPs) can be used to both purify and size-selectively fractionate hydrophobically modified nanoparticles. Alternatively, carbon dioxide may be used …

From Seed To Fruit: A Posthuman Journey From Stage To Page, Nicole E. Wood

Theses

This thesis uses Cybernetic Fruit: A Posthuman Fairytale (a show directed by Shauna MacDonald and Nico Wood) to explore notions of posthumanism. The thesis of this project is that every being possesses beingness (one could say, a soul), be it raccoon, raspberry, or rock; that nothing is perfect or ever can be, for perfection and imperfection (like order and disorder) are human constructions spun from human vantage points and seen with a human-level of resolution; that collaboration fosters propagation of a posthuman discourse and compassionate behavior; and finally, that staging philosophical inquiry, in the flesh and for the community, is …

Index To Volume 78

Nebraska Bird Review

Adams,

Cody 125

David 125

Akers, Danny 131

Alexander, Irene 26

Allen, Paul 125

Allison, Scott 26

Amadon, D. 69

American Ornithologists' Union 34, 82

Amos, A. F. 33

Andelt, Frank 125

Anderson-Ray, Janet 40

Andresen, Kari 125

Anhinga 70, 162

Ani, Groove-billed 75, 164

Arp, Duane 125

Assenmacher, Gerhard 150

Audubon, John J. 104, 121

Avocet, American 38, 48, 50, 65, 70, 93, 137

Reporting Results Of Data Analysis, Preparing Scientific Manuscripts, And Website Development Efforts, Christopher N. Jacques

The Prairie Naturalist

Preparation of scientific manuscripts and use and presentation of statistics have been topics of several commentaries from previous journal Editors-in-Chief, and have been submitted as invited papers, so I would like to share my perspective as the current Editor-in-Chief (Editor) of The Prairie Naturalist (Journal). Because there is not complete consensus among the experts about when hypothesis testing versus information theoretic methods, or Bayesian versus frequentist methods are suitable, previous Editors have avoided presenting their perspectives (Thompson 2010). I also will avoid presenting my perspective as Editor. I will, however, present my perspective on several of these approaches and then …

Cropland Nesting By Long-Billed Curlews In Southern Alberta, James H. Devries, Steven O. Rimer, Elizabeth M. Walsh

The Prairie Naturalist

Long-billed curlews (Numenius americanus) are described primarily as a grassland nesting species. However, no studies to date have quantified nest habitat selection among available habitats. During a study of waterfowl nest habitat selection and success in landscapes ranging from cropland to grassland-dominated, we found 9 curlew nests of which 8 were located in active cropland within cropland-dominated landscapes. Cropland nests occurred in fall-seeded winter wheat and spring-seeded barley and nests were clumped in distribution. Four cropland nests and 1 nest in native grass pasture hatched young. Further research is needed to characterize nesting habitat selection and reproductive success …

Review Of Weeds Of The Midwestern United States & Central Canada, Edited By Charles T. Bryson And Michael S. Defelice, James Stubbendieck

The Prairie Naturalist

This volume is the culmination of work by more than 40 weed scientists and botanists. Its stated purpose is to help identifY the great diversity of weedy and invasive plants that interface with agriculture, industry, and natural ecosystems in central North America. The geographic range covered by this book extends from southeastern Saskatchewan to eastern Kansas, northern Kentucky, northwestern Pennsylvania, and southwestern Quebec. This is a welcome edition because a current book on unwanted plants has not been available for the eastern two-thirds of this region. The book is arranged taxonomically by family and alphabetically by species within each family. …