Digital Commons Network^™

Exploring Dna Damage Recognition Using Molecular Modeling, Haoquan Li

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

8-oxo-7,8,-dihydroguanine (oxoG) is one of the most prevalent DNA lesions, and has been linked to cancer and age-related diseases due to its ability to promote mutations. The oxoG damage can be removed by the Formamidopyrimidine-DNA glycosylase (Fpg) in prokaryotes and by human 8-oxoguanine glycosylase 1 (hOGG1) in human cells. Fpg and hOGG1 are structurally unrelated, but they have the same function of excising oxoG by extruding the oxoG out from the DNA helix into the enzyme's active site. Previous studies have revealed the damage recognition interactions in the active sites of these enzymes; however, their extremely fast diffusion rates along …

Formation And Inhibition Of Islet Amyloid In Type 2 Diabetes, Ling-Hsien Tu

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

Amyloid fibrils are insoluble protein aggregates found in organs and tissues, and are structurally dominated by β -strands. Amyloid formation has been implicated in a wide range of human diseases. Each disease is characterized by a specific protein or peptide that aggregates in certain conditions. For example, the amyloid β protein (Aβ ) forms amyloid plaques in the brain of patients with Alzheimer's disease and this leads to neuronal degeneration. Parkinson's disease, another common neurodegenerative disorder, is associated with the intracellular aggregation of alpha-synuclein to form Lewy bodies in the brains of patients. This dissertation focuses on a polypeptide hormone, …

Attentional Control And Unpleasant Stimuli: An Event-Related Potential Study In Individuals With Generalized Anxiety Disorder And Major Depressive Disorder, Annmarie Macnamara

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

Theories of attentional control posit that both anxiety and depression should be associated with reduced filtering of task-irrelevant stimuli; reduced attentional control may also underlie an early attentional bias toward unpleasant stimuli that has been observed in individuals with Generalized Anxiety Disorder (GAD). Major Depressive Disorder (MDD), on the other hand, has been less consistently associated such an attentional bias, and individuals with comorbid GAD/MDD often fail to exhibit an attentional bias toward unpleasant stimuli. To determine whether individuals with GAD and those with comorbid GAD/MDD would exhibit reduced attentional control (i.e. | difficulty moderating attention to task-irrelevant stimuli), and …

Bayesian Methods For Feature Extraction And Classification Of Fetal Heart Rate Signals, Shishir Dash

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

A central problem in biomedical signal processing research is that of computer aided classification. We consider the problem of computer-aided diagnosis of intrapartum fetal status based on simultaneously recorded fetal heart rate (FHR) and uterine pressure (UP) signals. Clinically, visual diagnosis of the fetal heart rate signal is of critical importance when evaluating the status of pregnancy and delivery. This is because oxygen inadequacy, a major cause of adverse fetal outcomes, has a direct effect on the fetal heart rate. Purely visual assessment of fetal heart rate segments has, however, proven to have high intra- and inter observer variability, which …

Mid-Infrared Gasb-Based Type-I Quantum Wells Diode Lasers Utilizing Cascade Pumping Scheme, Rui Liang

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

Mid infrared semiconductor diode lasers have broad range of applications, including light detection and ranging, infrared countermeasures, medical treatment and spectroscopy. Compact and efficient devices operating in continuous-wave (CW) regime at room temperature (RT) are preferred for those applications. This work is focusing on the development of GaSb-based type-I quantum wells (QWs) diode lasers in the spectral range of 2.2 - 3.4 µm, with high output power and Diffraction-Limited beam. The novel design of cascade type-I QWs diode lasers was proposed. The interband tunneling through the " leaky" window in band alignment at GaSb/InAs heterointerface was used to realize cascade …

Design Of Ultra-Sensitive Fluorescence Detection System For Applications In Molecular Biology., Ivan Tovkach

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

I present a new universal data acquisition system for application for fluorescence detection in life sciences. The system is based on fiberized spectrometer bench with multichannel single photon sensor. Two different spectrometers were designed and tested. One is based on 32 channels PMT and another based on fiberized array of 48 avalanche photo diodes. The developed detection system was tested for three different applications including: DNA sequencing, detection of color encoded beads and fluorescence activated bead sorting. The system is capable of detecting multicolor fluorescence produced by mixtures of fluorescent dyes as well as by micro and nano-objects. In the …

Quantitative Approaches For Deconvolving The Multiple Contributions Of Primary Structure To Protein Fitness, Loretta Au

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

Proteins from the same family often share many structural and functional motifs. Variations in primary structure, however, allow a single protein family to modulate a broad range of biological processes. Several methods can be used to identify sequence conservation, but complementary mutagenesis experiments are often needed to understand the multiple roles that a given amino acid may have in maintaining overall fitness. Limitations related to financial and temporal costs generally constrain these experiments to smaller proteins or peptides, or to only partial sampling of sequence spaces, and we have devised a computational protocol for large-scale mutagenesis to circumvent these obstacles …

Regulation And Function Of Oncogenic Splicing Factor Srsf1, Shipra Das

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

SRSF1 is a prototypical member of the Ser/Arg-rich family of splicing factors. In addition to its involvement in constitutive and alternative splicing, SRSF1 regulates many other aspects of RNA metabolism, including transcription, mRNA export, stability and decay, translation, and miRNA processing. In addition, SRSF1 contributes to maintaining genomic stability, and is an important regulator of the cell cycle and cell viability. In spite of multiple post-transcriptional and translational mechanisms for SRSF1 auto-regulation, it is frequently upregulated in cancer. Here we focus on studying the regulation of SRSF1 expression and function. We have found SRSF1 to be a direct transcriptional target …

Nmr Investigation Of Organic Phosphorus In Calcite, Zelong Zhang

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

The interaction between calcite and dissolved organic phosphate is important to biomineral and geochemical systems. Organic molecules and phosphates can be adsorbed to the calcite surface and incorporated as impurities in the matrix during crystal growth. Although 31P NMR spectroscopy has been extensively used to study the nature of P in a wide variety of natural samples, a lack of understanding of spectroscopic characteristics of organic P occluded in calcite hinders NMR application in this area. Here, a methodology based on 31P NMR is proposed to help determine the speciation of P at low concentrations in calcite based on spectroscopic …

Role Of Nf-Κb Recognition Sites In Rta Transactivation Of Lytic Gene Expression During Murine Gammaherpesvirus 68 Infection, Alexis Leah Santana

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

Herpesviruses establish life-long infections in the host, characterized by phases of productive lytic replication, latency, and reactivation from latency. Gammaherpesvirus infections are associated with the development of lymphomas and tumors; the incidence of cancer is increased upon loss of host immune control. Murine gammaherpesvirus 68 (MHV68) naturally infects small rodents and has genetic and biologic parallels with the human gammaherpesviruses, Epstein-Barr virus and Kaposi’s sarcoma-associated herpesvirus. This model pathogen system provides a platform to examine the interplay of viral and host determinants that shape the latent or lytic fate of an infected cell. The replication and transcription activator (RTA) drives …

The Identification Of Novel Components In The Rnai Machinery In Fission Yeast S. Pombe, An-Yun Chang

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

RNA interference (RNAi) is a mechanism for post-transcriptional gene silencing by RNA slicing or translational inhibition. Studies in the fission yeast S. pombe have demonstrated that RNAi components are additionally involved in transcriptional silencing by signaling chromatin assembly into the silent heterochromatin state. Originally discovered in worms and in plants, RNAi-mediated silencing is conserved in most eukaryotes with a few exceptions, including the budding yeast S. cerevisiae. Taking advantage of this observation, I initiated a candidate gene screen to search for novel components in the RNAi machinery. I identified a putative splicing factor Rct1 as one of the genes that …

Dynamics Of Human Origin Recognition Complex During The Cell Division Cycle, Nihan Kara

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

DNA replication occurs once every cell cycle in normal cells and it is a tightly controlled process that ensures complete duplication of the genome. Perturbations in DNA replication may cause catastrophic consequences for the cell including compromised cell proliferation, genomic instability, or cancer susceptibility. The origin recognition complex (ORC) plays a key role during the initiation of DNA replication. I have studied the dynamics of ORC in human cells throughout the cell division cycle to better understand its function in replication initiation. In human cells, the largest subunit of ORC, Orc1 is regulated during the cell cycle. During early S …

Targeting Cancer Cell Invasion At The Molecular And Cellular Levels: Unraveling The Role Of Kiaa1199 In Cancer Cell Migration And Development Of A Novel 3d Invasion Assay For Anti-Cancer Drug Discovery, Nikki Ann Evensen

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

Cell migration is an early and essential step required for cancer cell invasion and metastasis, which remains a major hurdle in the war against cancer. Therefore, it is imperative that we find novel strategies and targets aimed at preventing this cellular process. The goal of my thesis was two-fold: 1) to characterize the role of KIAA1199 in cancer cell migration and 2) to develop and optimize a novel 3-dimensional (3D) invasion assay. KIAA1199 is highly upregulated in various forms of cancers but its function was hitherto unknown. By employing both loss-of- and gain-of-function studies the role of KIAA1199 in cancer …

Rapidcap, A Mouse Model For Analysis And Therapy Of Prostate Cancer Reveals Drivers Of Pten-Mutant Metastasis., Hyejin Cho

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

The functional loss of PTEN through mutations, deletions, or protein degradation has been found at a high frequency in many human cancers. Therefore, the Pten gene locus has been targeted to generate clinically relevant mouse models for metastatic prostate cancer. The first two chapters include the development and exploration of RapidCaP, a novel mouse model for prostate cancer metastasis, that is based on surgical gene transfer to overcome the need for extensive animal breeding. Through prostate specific delivery of transgenic virus, model generation times have been reduced from several years to a few weeks. Moreover, non-invasive Xenogen-based imaging can be …

A Novel Role For Ciliary Proteins In Zymogen Granule Secretion Of Pancreatic Acinar Cells, Benjamin Sy Cyge

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

Primary cilia are present on nearly all mammalian cells. For many years, they were thought to be functionless, vestigial organelles. In recent years, primary cilia have been found to be essential for many important biological processes. Included in these are chemo - and mechano-sensation, as well as acting as a signaling hub for hedgehog, Wnt, and notch signaling. Further exemplifying their importance, there is a new classification of genetic disorders, collectively referred to as ciliopathies, which manifest due to aberrant growth and regulation of cilia, and aberrant expression of gene products thought to be critical for these processes. Our lab …

Phospho-Naproxen: A Novel Agent For The Control Of Arthritis And Colon Cancer, Vinal Patel

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

Non-steroidal anti-inflammatory drugs (NSAIDs) are frequently used to treat various inflammatory diseases. In particular, the NSAID naproxen is a major first-line treatment for rheumatoid arthritis, an inflammatory disease affecting 1% of the population worldwide. The potential use of NSAIDs also spans to other debilitating and chronic diseases, including cancer. Epidemiological studies have shown that the use of naproxen significantly correlates with a lower risk of colon cancer, the third most common type of cancer in the United States. Although conventional naproxen can subdue arthritic inflammation and reduce the risk of developing colon cancer, its long-term use is associated with significant …

Exploring The Role Of Serotonin On Hypoglossal Motoneuron Excitability And Plasticity Through Postnatal Development Via Mathematical Models, Kyle Graham Horn

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

Neuronal plasticity is a key facet of neurons throughout the central and peripheral nervous system. Unlike most forms of plasticity, however, dysfunctions in respiratory motoneuron plasticity can be fatal. With respect to hypoxic conditions, hypoglossal motoneurons (HMs), which participate in a variety of upper airway behaviors, are considered critical for maintaining upper airway patency. Failure in these neurons can disfacilitate the tongue, rendering an obstruction in the upper airway. This can exacerbate hypoxic conditions, and may potentially contribute to sudden infant death syndrome (SIDS) and obstructive sleep apnea (OSA). Serotonin (5-HT) affects HM excitability through a wide variety of mechanisms, …

The Role Of Nf1 In Drosophila Appetitive Long Term Memory, Chunsu Xu

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

This thesis explores the consequences of mutated neurofibromin gene, NF1, on memory. NF1 disorder is an inheritable genetic disease in humans that is produced by mutation of the gene that encodes the large protein neurofibromin. Mutations in this gene produce fairly non-specific and widespread cognitive defects in human patients, in addition to a variety of other pathologies, such as benign tumors of the peripheral nervous system. It is unknown how NF1 disorder leads to cognitive deficits. Uncovering the mechanism is hampered by the fact that mutations in the NF1 gene have very unpredictable effects. Even identical (monozygotic) twins who have …

Statistical Comparison Of Measurement Platforms, Yuanhao Zhang

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

This thesis proposes a novel statistical method based on the generalized linear errors-in-variables model to compare two measurement platforms with discrete and continuous outcomes respectively. This method overcomes the limitation of the classical platform comparison method with only linear models that can only accommodate two continuous outcome measures. This novel method was applied to model two gene expression measurement platforms: Microarray (continuous) and RNA-Seq (discrete). The comparison result is further validated by differentially expressed gene analysis and biological pathway analysis. The proposed approach would play a significant role: 1) assessing emerging platforms systematically with existing platforms, 2) serving as a …

The Kinesthetic Basis Of Landscape Art, Susan Ellen Pashman

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

The failure of philosophical concepts of the natural environment and of the works of landscape art structured from it to fully describe the perceptual experience of landscape, like the failure of site plans to adequately represent such works, can be attributed to the ocularcentricity that has long infected the notion of landscape. When " kinesthesia" replaces " vision" as the essential perception in the landscape experience, landscape is both conceived and represented more adequately. I define landscape art as " an expressive art that shapes the experience of moving through immersive volume as a structured sequence of both kinesthetic and …

Alternative Approaches To Rapid Acceleration Of Ion Beams - Harmonic Ratcheting For Fast Rf Acceleration And Laser Driven Acceleration Of Gas Jet Targets, Nathan Cook

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

Energetic ion beams have vast potential in medicine, energy, and basic science, providing significant advantages in applications of radiation therapy, nuclear energy, and high energy physics. Conventional acceleration means are inefficient and costly, imposing stringent requirements on space, power, and speed of the machines designed to address these applications. This thesis considers two contrasting approaches to improving ion beam acceleration: fast acceleration using radio-frequency (RF) technology and laser driven acceleration of ion beams from over-dense plasma. We first consider fast acceleration in a synchrotron using conventional RF cavities. We introduce a ferrite based RF scheme for a rapid cycling synchrotron …

Influence Of Maturation On Hypoxic Ventilatory Responses In P0-P30 Neonatal Rat In Vivo, Inefta M. Reid

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

Hypoxia is a common feature of many pathologies including but not limited to asthma, spinal cord injury, chronic obstructive sleep pulmonary disease, and sudden infant death syndrome (SIDS). Even though neuromodulatory effects mediated by maturation have been widely studied in other disciplines, such efforts have been lacking in the area of respiratory control. This dissertation is motivated by questions such as how does a known change in respiratory neurotransmitters manifest differently in the modulation of known respiratory output, especially in response to moderate, mild, and sever hypoxia. Aimed at understanding the characteristics and underlying mechanisms involved maturation of the hypoxic …

Modeling Brain Structures From Hundreds Of Hypoglossal Motoneurons To Millions Of Cerebellar Cells, Heraldo Memelli

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

Computational neuroscience is a rapidly growing field in the quest to discover how the human brain works. Mathematical modeling and computer simulations increasingly help neuroscientists test hypotheses and explore neuronal mechanisms from the level of single cells to billions of neurons. In this PhD thesis, we have implemented and analyzed computational models of two mammalian brain structures: the hypoglossal nucleus and the cerebellum. As a first project, we have developed a detailed computational model for a network of Hypoglossal Motoneurons (HMs). HMs are located in the brainstem and exhibit synchronous firing activity. They are coupled by gap junctions, direct electrical …

Benchmarks 2015, August 21, The Rockefeller University

BenchMarks 2015

BenchMarks. Friday, August 21, 2015

The community newsletter of The Rockefeller University

BenchMarks is published monthly and is distributed on the campus of The Rockefeller University. It produced by the Office of Communications and Public Affairs

Fall 2015 E-Certi Newsletter, Center For Educational Research And Teaching Innovation

CAFE Faculty Newsletters

Hello S&T Instructors - It’s the start of another academic year with new challenges and opportunities, including a record number of incoming students. In this issue we feature some innovative and award-winning instructors, including Joel Burken, Theresa Swift and Greg Story. Also find information about the upcoming Curators’ Teaching Summit and learn about projects that have been funded where S&T instructors will be examining and assessing best teaching practices.

Canadian Community College Faculty And Teaching And Learning Professional Development, Carol Ann Samhaber

Walden Dissertations and Doctoral Studies

Many colleges have faced the challenge of engaging faculty in teaching and learning professional development. The purpose of this project study was to investigate why full-time school of business faculty at a small community college in Canada do not complete college course design and student assessment training. Faculty members are urged to complete these trainings in order to implement their courses to successfully prepare students to graduate from college and launch professional careers. The research questions in this study focused on faculty perceptions regarding factors that have prevented their completion of this college's course design and student assessment professional development. …

The Risk Of Secondary Lymphedema Due To Procedures In The Affected Arm Post-Mastectomy: A Literature Review, Lindsay Perna

HIM 1990-2015

The risk for upper extremity lymphedema post-mastectomy in women surgically treated for breast cancer is a concern since it is often painful, aesthetically displeasing, and can increase the risk of infection. However, there is a paucity of data examining if diagnostic procedures performed in the ipsilateral arm post-mastectomy increases the risk of lymphedema. The purpose of this research is to examine the relationship between diagnostic procedures performed in the ipsilateral arm post-mastectomy and the occurrence of lymphedema with or without related complications. A systematic review of the literature was conducted from multiple, online databases available from 1992 through 2014, and …

On The Topology Of The Permutation Pattern Poset, Peter R. W. Mcnamara, Einar Steingrímsson

Faculty Journal Articles

The set of all permutations, ordered by pattern containment, forms a poset. This paper presents the first explicit major results on the topology of intervals in this poset. We show that almost all (open) intervals in this poset have a disconnected subinterval and are thus not shellable. Nevertheless, there seem to be large classes of intervals that are shellable and thus have the homotopy type of a wedge of spheres. We prove this to be the case for all intervals of layered permutations that have no disconnected subintervals of rank 3 or more. We also characterize in a simple way …

Effects Of Different Agricultural Management Systems On Arbuscular Mycorrhizal Fungal Diversity, Community Structure, And Ecosystem Services., Charles Bradford Gottshall

Electronic Theses and Dissertations

Disturbances associated with row-crop agricultural management systems include mechanical (tillage and cultivation) and chemical (fertilizer, pesticides, herbicides, fungicides) inputs and are often co-occurring. Many soil microbes are sensitive to these disturbances, including arbuscular mycorrhizal fungi (AMF), important plant mutualists in agricultural systems. AMF associate with many crop plants and provide direct benefits through root pathogen protection, drought resistance, nutrient acquisition and uptake, as well as contribute to ecosystem services by improving overall soil fertility. Examining how different row-crop management system disturbances affect the AMF community is important for understanding and enhancing benefits provided by these important mutualists, and key to …

Youth Graffiti Vandalism : Liminal Perspectives In The Light Of Masculinity, Social Contract Theory And Transformative Process., Alton C. Frabetti

Electronic Theses and Dissertations

American adolescents experience liminality as their rights, obligations and cognitive development place them in a transitional life-period between childhood and adulthood. This liminal period inspires compensatory activities, such as identification with mainstream popular styles, radical adherence to an ideology or religion, or, for those especially struggling, destructive behavior. Graffiti is one such compensatory activity. Its practitioners' risky conduct, as well as their overall claims to exalted artistic activity, are especially appealing to certain males attempting to construct a retrogressive notion of masculinity and self-esteem in response to the further condition of male liminal identity. The practice of graffiti confronts the …