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Mechanisms Of Dna Synthesis And Fidelity By Y-Family Translesion And C-Family Replicative Polymerases, Purba Mukherjee
Mechanisms Of Dna Synthesis And Fidelity By Y-Family Translesion And C-Family Replicative Polymerases, Purba Mukherjee
Legacy Theses & Dissertations (2009 - 2024)
Since the discovery of the DNA polymerase by Arthur Kornberg nearly 60 years ago, there have been great advances in understanding the involvement of polymerases in replication and repair. Years of genetic, biochemical and structural studies have lead to the classification of DNA-dependent DNA polymerases into six families: A, B, C, D, X and Y. In this work, I have focussed on two different families, C and Y. Hence this work is divided into two parts. Part one discusses the studies on Y-family polymerases. All Y-family polymerases are involved in replicating past DNA lesions. The ability to tolerate unnatural nucleotides …
Mediation Of Recurrent Hypoglycemia's Physiological And Behavioral Effects In The Hippocampus By Glucocorticoids, Danielle Osborne
Mediation Of Recurrent Hypoglycemia's Physiological And Behavioral Effects In The Hippocampus By Glucocorticoids, Danielle Osborne
Legacy Theses & Dissertations (2009 - 2024)
Recurrent hypoglycemia (RH) occurs with the over administration of insulin resulting in severe hypoglycemia on a repetitive basis. This occurs most commonly among Type I Diabetics who rely on exogenous insulin replacement for management of their disease; however it is becoming increasingly common among Type II Diabetics. Although cognitive deficits are reported during hypoglycemia, the period following restoration of euglycemia has been denoted by improved hippocampally-mediated short-term and working memory in humans and rodents, respectively. RH is also associated with an altered glucocorticoid secretion profile in response to hypoglycemia. In vitro and in vivo approaches were utilized with the goal …
Regulation Of Ty1 Retrovirus-Like Transposon Rna Localization And Translation, Ryan Joseph Palumbo
Regulation Of Ty1 Retrovirus-Like Transposon Rna Localization And Translation, Ryan Joseph Palumbo
Legacy Theses & Dissertations (2009 - 2024)
Replication of the Ty1 retrovirus-like transposon of the yeast Saccharomyces cerevisiae is stringently regulated to reduce the frequency of deleterious retrotransposition events. However, under stress conditions, Ty1 retrotransposition can lead to adaptive genomic alterations. To characterize host regulation of Ty1 retrotransposition, I analyzed ribosome profiling data and showed that Ty1 RNA is efficiently translated. Moreover, the ribosome biogenesis factors BUD21, DBP7, HCR1, LOC1, MRT4, and PUF6 are required for optimal expression of the Ty1 protein Gag.
Mouse Salivary Gland Development Requires Optimal Substrate Compliance, Sarah Beth Peters
Mouse Salivary Gland Development Requires Optimal Substrate Compliance, Sarah Beth Peters
Legacy Theses & Dissertations (2009 - 2024)
The embryonic mouse submandibular salivary gland (mSMG) is a classic model to study mechanochemical signals involved in morphogenesis and differentiation amongst multiple, interacting cell populations. Scaffold compliance is alters cellular phenotype, but little is known about the effects of compliance on organogenesis. The overall aim of this project was to demonstrate that the processes of salivary gland epithelial branching morphogenesis and differentiation require a compliant, in vivo-like environment and are disrupted outside of this range.
Paternal Occupational Pesticide Exposure And Neural Tube Defects In The National Birth Defects Prevention Study, Stacy Marie Pettigrew
Paternal Occupational Pesticide Exposure And Neural Tube Defects In The National Birth Defects Prevention Study, Stacy Marie Pettigrew
Legacy Theses & Dissertations (2009 - 2024)
ABSTRACT
Sound Environment Programming The Post-1945 Moment : Charles Olson, Sun Ra, John Cage, And The Way Back In, Michael Peters
Sound Environment Programming The Post-1945 Moment : Charles Olson, Sun Ra, John Cage, And The Way Back In, Michael Peters
Legacy Theses & Dissertations (2009 - 2024)
On the eve of 1945, when the Manhattan Project's machinations to split the atom were almost in place, another physicist published a little book--What Is Life? Applying physics to biology, Erwin Schrödinger described how genetic "code-script" could create aperiodic (non-repeating) new life from periodic materials, revealing the "secret" of life. This dilemma of life or death defines the post-1945 moment. Fraught with Hamlet-like uncertainty, I argue this moment is the apex of a long-fomenting, eco-historical crisis where Western thinking had severed "Man" from "Nature." Sound Environment Programming is a term I invented to detail how Charles Olson, Sun Ra, and …
Computational Modeling-Driven Study Of Signaling Pathway Affecting Cleft Formation During Submandibular Salivary Gland Development, Shayoni Ray
Legacy Theses & Dissertations (2009 - 2024)
Branching morphogenesis is a conserved mechanism of mammalian organ development (salivary glands, lungs, mammary glands, pancreas, kidney, etc.), and has been a classic topic of study for generations of developmental biologists. During the process of tissue formation, several cellular and molecular and protein signaling events occur at successive stages enabling proper formation of tissue shape and structure. In order to provide a comprehensive understanding of the process of branching morphogenesis, we need a systems level approach to integrate multifactorial information. My overall global hypothesis is that multiple mathematical modeling approaches can be utilized to extract crucial cellular and tissue level …
Monitoring Ligand-Induced Nucleic Acid Conformational Changes Using Ion Mobility Spectrometry-Mass Spectrometry, Bill Kenneth Redick
Monitoring Ligand-Induced Nucleic Acid Conformational Changes Using Ion Mobility Spectrometry-Mass Spectrometry, Bill Kenneth Redick
Legacy Theses & Dissertations (2009 - 2024)
Three-dimensional structures of biopolymers frequently dictate the biological role those molecules play. As such, investigation into structure of nucleic acids can provide important information pertaining to how those nucleic acids work. Many nucleic acid species, especially single-stranded RNA, fold into unique structures that allow them to function properly. Metals, and other cationic species, are often bound to the nucleic acid to make folding into the proper structure more favorable by neutralizing the negative charge on the nucleic acid imparted by the phosphate group. This investigation explores tertiary structure of nucleic acids that have been folded in the presence of ligands …
Raman Spectroscopy Of Blood Serum And Cerebrospinal Fluid And Multivariate Data Analysis For Alzheimer's Disease Diagnostics, Elena Ryzhikova
Raman Spectroscopy Of Blood Serum And Cerebrospinal Fluid And Multivariate Data Analysis For Alzheimer's Disease Diagnostics, Elena Ryzhikova
Legacy Theses & Dissertations (2009 - 2024)
The efficient and accurate diagnosis at the early stages of dementia is a key moment for effective treatment and productive research to find a new ways to combat the disease. It is especially true for Alzheimer's disease (AD) for which there is no effective cure, but several treatments are known to allow slowing down the degenerative processes. Alzheimer's disease (AD) displays only non-specific clinical symptoms of mental decline for decades after the initiation and is very challenging to differentiate even at the later stages when it becomes very aggressive. Despite the great need, current diagnostic tests are unable to diagnose …
Modeling The Early, Aging-Related Changes In Human Recombinant Gammas-Crystallin In Vitro, Christiana Oluwaseun Salami
Modeling The Early, Aging-Related Changes In Human Recombinant Gammas-Crystallin In Vitro, Christiana Oluwaseun Salami
Legacy Theses & Dissertations (2009 - 2024)
Cataract is the leading cause of blindness in the world. Cataractous lenses scatter a significant part of the light entering the eye. Cataract can be of several types: Age-related cataract, secondary cataract, traumatic cataract, congenital cataract, and radiation cataract. Age-related cataract is the most common type of cataract. Several factors contribute to age-onset cataract; among them are the Post-Translational Modifications (PTMs) to the major lens proteins or crystallins, which constitute about 80-90% of the protein content of the lens. Predominant PTMs of the crystallins are oxidation, deamidation, phosphorylation, glycation, and disulfide crosslinking, which tend to increase as the lens ages.
Exposure Assessment And Risk Management Of Engineered Nanoparticles : Investigation In Semiconductor Wafer Processing, Michele Shepard
Exposure Assessment And Risk Management Of Engineered Nanoparticles : Investigation In Semiconductor Wafer Processing, Michele Shepard
Legacy Theses & Dissertations (2009 - 2024)
Engineered nanomaterials (ENMs) are currently used in hundreds of commercial products and industrial processes, with more applications being investigated. Nanomaterials have unique properties that differ from bulk materials. While these properties may enable technological advancements, the potential risks of ENMs to people and the environment are not yet fully understood. Certain low solubility nanoparticles are more toxic than their bulk material, such that existing occupational exposure limits may not be sufficiently protective for workers. Risk assessments are currently challenging due to gaps in data on the numerous emerging materials and applications as well as method uncertainties and limitations.
Sleep Duration And Diabetes In An Adult Population Of Rural Upstate New York, Tarak Shrestha
Sleep Duration And Diabetes In An Adult Population Of Rural Upstate New York, Tarak Shrestha
Legacy Theses & Dissertations (2009 - 2024)
Introduction: Within the past five decades, there has been a rapid increase in the number of diabetic cases in the US. The number of diabetic cases increased from 1.5 million in 1959 to 25.8 million in 2011. Around the same time period, the average sleep duration per night decreased from 8 hours to 6.9 hours.
Perfluorinated Compounds, Thyroid Function, And Neuropsychological Status In Older Residents Of Upper Hudson River Communities, Srishti Shrestha
Perfluorinated Compounds, Thyroid Function, And Neuropsychological Status In Older Residents Of Upper Hudson River Communities, Srishti Shrestha
Legacy Theses & Dissertations (2009 - 2024)
Perfluorinated compounds (PFCs) are widespread in the environment. Minimal data exist regarding the neurotoxicity and thyroid disruptive property of PFCs in aging populations and the possible mediating effects of thyroid hormones (THs). In this study, we assessed associations among PFCs, thyroid function, and neuropsychological status, and determined if the neurotoxic effects of PFCs are mediated by changes in THs in an aging population. We measured perfluorooctanoic acid (PFOA), perfluorooctane sulfonate (PFOS), thyroid stimulating hormone (TSH), total thyroxine (T4), free T4 (fT4), and total triiodothyronine (T3) in serum and performed neuropsychological tests in men and women aged 55-74 years and living …
Regulation Of Immune Response Genes By Vitamin D In Mammary Epithelial Cells With An Emphasis On Cd14, Katrina Marie Simmons
Regulation Of Immune Response Genes By Vitamin D In Mammary Epithelial Cells With An Emphasis On Cd14, Katrina Marie Simmons
Legacy Theses & Dissertations (2009 - 2024)
Vitamin D is primarily known for its role in bone health, however recently vitamin D has been identified as a potent immunomodulator. Most research studying the effects of vitamin D on immune properties have focused on immune cells. Few have evaluated how vitamin D affects the immune functions of barrier epithelial cells, such as human mammary epithelial (HME) cells, that are exposed to pathogens both locally and systemically. The goals of the studies described in this thesis were to comprehensively and mechanistically evaluate the immune effects of vitamin D metabolites, 1α,25-dihydroxyvitamin D (1,25D) and 25-hydroxyvitamin D (25D), on HME cells. …
Time Will Tell : Temporal Reasoning In Clinical Narratives And Beyond, Weiyi Sun
Time Will Tell : Temporal Reasoning In Clinical Narratives And Beyond, Weiyi Sun
Legacy Theses & Dissertations (2009 - 2024)
Temporal reasoning in natural language refers to the extraction and understanding of time-related information conveyed in free text. A clinical narrative temporal reasoning component can enable a spectrum of medical natural language processing (NLP) applications that directly improve patient care documentation efficiency, accessibility and accountability. This dissertation contributes in three subtasks under temporal reasoning: temporal annotation, temporal expression extraction and temporal relation inferences. The temporal annotation work described in the dissertation produced one of the first publicly available clinical narratives. We published one of the first sets of temporal
Probing Secondary And Tertiary Rna Folding Using Force And Temperature, William Stephenson
Probing Secondary And Tertiary Rna Folding Using Force And Temperature, William Stephenson
Legacy Theses & Dissertations (2009 - 2024)
RNA folding is the process whereby a single stranded RNA molecule assumes its three-dimensional functional conformation. Along with the protein folding problem, the RNA folding problem remains as one of the great unsolved problems in biophysics. Generally RNA folding occurs in a hierarchical manner whereby the sequence of an RNA (primary structure) determines which regions will form helical segments (secondary structure) before further rearrangement and base pairing of secondary structure motifs (tertiary structure). Due to the intimate connection between structure and function within molecular biology, increased familiarity with the thermodynamic and kinetic factors that govern RNA folding will permit the …
Crosstalk Between Vitamin D₃- And Testosterone-Mediated Signaling In Prostate Cancer Cells, Wei-Lin Winnie Wang
Crosstalk Between Vitamin D₃- And Testosterone-Mediated Signaling In Prostate Cancer Cells, Wei-Lin Winnie Wang
Legacy Theses & Dissertations (2009 - 2024)
Contrary to the common belief that prostate cancer is a hormone dependent disease, the incidence of prostate cancer and associated mortality actually increases significantly after serum androgen levels decline. This led us to hypothesize that androgen depletion in elder men is an underlying cause for the development and progression of prostate cancer. In addition, serum vitamin D3 levels also decline in older men. Epidemiological and experimental data support an anti-neoplastic activity of vitamin D3 in colorectal and breast cancers through regulation of cell proliferation, apoptosis, cell differentiation and metastasis. The effects of vitamin D3 on prostate cancer …
Instructional Scientific Humor In The Secondary Classroom, Francine Wizner
Instructional Scientific Humor In The Secondary Classroom, Francine Wizner
Legacy Theses & Dissertations (2009 - 2024)
This study is an examination of the manner in which educators employ scientific content humor and how that humor is perceived by their students. Content humor is a useful strategy in drawing the attention of students and improving their receptivity toward scientific information. It is also a useful tool in combating the growing distractions of the electronic classroom. Previous studies have found that humor has a positive effect on knowledge, memory, and understanding. However, few studies have been conducted below the undergraduate level and mainly quantitative measures of student recall have been used to measure learning. This study employed multiple …
The Lipogenic Phenotype Of Her2/Neu-Positive Breast Cancer Cells, Jan Martin Baumann
The Lipogenic Phenotype Of Her2/Neu-Positive Breast Cancer Cells, Jan Martin Baumann
Legacy Theses & Dissertations (2009 - 2024)
Recent work has shown that HER2/neu-positive breast cancer cells rely on a unique Warburg-like metabolism for survival and aggressive behavior. These cells are dependent on fatty acid (FA) synthesis, show markedly increased levels of stored fats and disruption of the synthetic process results in apoptosis. Supplementation of the growth media with physiological concentrations of saturated FAs induces cell death, whereas HER2-normal cells are not affected. This is particularly interesting in the context of new epidemiological data showing that a diet rich in saturated FAs is positively correlated with the development of HER2-negative disease, but not HER2/neu-positive disease.
Symbiotic Associations Between Vibrio Cholerae And Copepods And Their Potential Public Health Impact, Gretchen Boria Pérez
Symbiotic Associations Between Vibrio Cholerae And Copepods And Their Potential Public Health Impact, Gretchen Boria Pérez
Legacy Theses & Dissertations (2009 - 2024)
Vibrio cholerae O1 concentrate in copepods by attaching to their chitinous exoskeleton and gut, making these planktonic crustaceans participants in the spread of cholera in marine and estuarine environments. The role of the symbiosis in the spread of gastrointestinal disease caused by non-O1 serotypes has not been well-studied in fresh water systems. The goal of these studies was to determine whether symbiotic association of V. cholerae with copepods affects virulence of hemolysin/cytolysin toxin, suspected in V. cholerae non-O1 related morbidity. The reverse-transcription-polymerase chain reaction was used to evaluate the relative transcriptional response of hlyA, encoding hemolysin, by a non-O1 strain …
Genetic Diversity And Population Structure Of Brook Trout (Salvelinus Fontinalis) In A Remote Adirondack Watershed, Spencer A. Bruce
Genetic Diversity And Population Structure Of Brook Trout (Salvelinus Fontinalis) In A Remote Adirondack Watershed, Spencer A. Bruce
Legacy Theses & Dissertations (2009 - 2024)
In conservation genetics, the importance of understanding how historical and contemporary processes have contributed to geographic patterns of genetic structure is key to preserving diversity. In New York State there are currently eleven remaining known populations of native brook trout (Salvelnius fontinalis) that inhabit the watersheds for which they are named. These populations are known as "heritage strains", and are currently managed under regulations set by the New York State Department of Environmental Conservation.
Military Contamination And Persistent Organochlorine Pesticide Exposure Among Alaska Natives, Samuel Byrne
Military Contamination And Persistent Organochlorine Pesticide Exposure Among Alaska Natives, Samuel Byrne
Legacy Theses & Dissertations (2009 - 2024)
St. Lawrence Island Alaska is located in the Bering Sea, only 36 miles from Siberia. The island is home to approximately 1600 Siberian Yupik residents, who rely heavily on subsistence hunting and gathering. There are two formerly used defense (FUD) sites on the island, one of which has been the subject of an approximate $110 million cleanup effort. Environmental monitoring suggests localized soil and watershed contamination with PCBs, organochlorine pesticides and heavy metals. Previous research suggests the site may be a source of PCB exposure for local residents. The primary aim of the study was to determine whether subsistence activities …
A Structural And Functional Comparison Of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein (Ncp7) And Other Retroviral Nucleocapsid Proteins, Christopher Richard Cavender
A Structural And Functional Comparison Of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein (Ncp7) And Other Retroviral Nucleocapsid Proteins, Christopher Richard Cavender
Legacy Theses & Dissertations (2009 - 2024)
Human immunodeficiency virus type 1 (HIV-1) is a retrovirus belonging to the lentivirus genus of the orthoretrovirinae family. HIV-1 is widely known for causing acquired immunodeficiency syndrome (AIDS) in humans and being responsible for 1.8 million deaths due to AIDS associated illnesses in 201016.
Community Forests : A Study Of New Hampshire's Town-Owned Forests, Anna Christie-Carnicella
Community Forests : A Study Of New Hampshire's Town-Owned Forests, Anna Christie-Carnicella
Legacy Theses & Dissertations (2009 - 2024)
New England states have a long history of forest management, beginning in the seventeenth century, with community forests evolving over time from communal forests during colonial times to town-owned forests managed by conservation commissions in the present time. New Hampshire towns provided a case study of the current state of town-owned forest protection and management, with a focus on timber management. I administered a survey to 50 randomly sampled towns and received data from 29 about permanent protection and management activities on town-owned forestland (≥ 50 acres). I used this data, demographic, and landscape data, to evaluate permanent protection and …
Molecular Actions Of The Novel Histone Deacetylase Inhibitor Cg-1521 In Models Of Inflammatory Breast Cancer, Namita Chatterjee
Molecular Actions Of The Novel Histone Deacetylase Inhibitor Cg-1521 In Models Of Inflammatory Breast Cancer, Namita Chatterjee
Legacy Theses & Dissertations (2009 - 2024)
Inflammatory breast cancer (IBC) is a rare and particularly lethal form of breast cancer. Despite aggressive therapeutic approaches, the 5-year survival rate is only 34%. As this disease is severely understudied, we have investigated the therapeutic potential of the novel hydroxamic acid-derived histone deacetylase inhibitor (HDACi), CG-1521 in comparison to a structurally similar compound, Trichostatin A (TSA) in two IBC cell lines: SUM149PT and SUM190PT. In these cells, CG-1521 and TSA induce dose- and time-dependent induction of cell cycle arrest and apoptosis regardless of the presence of 17β-estradiol (E2). Interestingly, the cell lines have considerably different sensitivities to these treatments …
Genomic And Physical Analysis Of Rnr1-Containing Autophagosomes During Environmental Stress, Tamir Danon
Genomic And Physical Analysis Of Rnr1-Containing Autophagosomes During Environmental Stress, Tamir Danon
Legacy Theses & Dissertations (2009 - 2024)
Physical & Genetic Analysis of Rnr1 autophagosomes during the DNA damage response
Novel Partner Notification Approaches In New York State, And Antibiotic Resistance In The Management Of Chlamydia Trachomatis Infections, Christopher Frank Davis
Novel Partner Notification Approaches In New York State, And Antibiotic Resistance In The Management Of Chlamydia Trachomatis Infections, Christopher Frank Davis
Legacy Theses & Dissertations (2009 - 2024)
Chlamydia trachomatis (chlamydia) is the most frequently reported notifiable disease in the United States. This dissertation provides an evaluation of chlamydia treatment and control through three different lenses: 1) patient views on a novel strategy to facilitate treatment, 2) student perceptions about materials to promote treatment of sexual partners, and 3) evidence regarding recurrent infection etiology.
Refining Aquatic Macroinvertebrate Community Metrics For The Assessment Of Headwater Streams In New York State, Brian T. Duffy
Refining Aquatic Macroinvertebrate Community Metrics For The Assessment Of Headwater Streams In New York State, Brian T. Duffy
Legacy Theses & Dissertations (2009 - 2024)
The River Continuum Concept describes the structural and functional shift that occurs from sensitive headwater streams to the lowest reaches of large, non-wadeable rivers. New York State (NYS) maintains a long-established biological monitoring program using macroinvertebrate community assemblages for water quality assessment. However, headwater streams are rarely assessed, and no reference models are available, except those calibrated for lower-continuum wadeable streams and rivers. Current patterns of rural landuse change emphasize the need for more accurate assessment of previously neglected headwaters, in order to set natural reference standards for more accurate assessments of water quality. Ecoregion, drainage area (DA), elevation (elev.), …
Study Of Protective Role Of Cytochrome P450s In Inflammatory Bowel Disease Using Cprlow Mouse Model, Xiaoyu Fan
Study Of Protective Role Of Cytochrome P450s In Inflammatory Bowel Disease Using Cprlow Mouse Model, Xiaoyu Fan
Legacy Theses & Dissertations (2009 - 2024)
Glucocorticoids (GCs) are potent regulatory factors for inflammation. The synthesis of GCs involves several cytochrome P450 enzymes, such as mitochondrial CYP11A1, CYP11B1, and microsomal CYP21. Previous studies have indicated that the GCs, including those released from adrenal glands, and those synthesized in extra-adrenal tissues, such as intestine, exert inhibitory effects on inflammatory bowel disease (IBD). In a previous study using an intestinal epithelium (IE)-specific P450 reductase (CPR) knockout (IE-Cpr-null) mouse model, the results suggested that the intestinal P450s had a protective role in DSS-induced acute colitis. In this study, using a hypomorphic CPR mouse model (Cprlow), which presents a global …
Effects Of Extreme Hydrologic Events On Trout Populations And Fish Communities In A Catskill Mountain River, Scott Daniel George
Effects Of Extreme Hydrologic Events On Trout Populations And Fish Communities In A Catskill Mountain River, Scott Daniel George
Legacy Theses & Dissertations (2009 - 2024)
Extreme hydrologic events are becoming more common with changing climatic conditions. Although the impacts of winter and spring floods on lotic ecosystems have been well studied, the effects of summer floods on fish assemblages in mountain streams are less well known. This study took advantage of an extreme precipitation event during the course of an ongoing monitoring program, which allowed the opportunity to quantify the effects of a severe late summer flood on fish communities in a montane watershed. We also evaluated the effect of the flood on the density and age structure of two ecologically important populations of sport …