Life Sciences Commons^™

Dianthus Ucarii (Caryophyllaceae): A New Species From The Northwest Of Turkey, Ergi̇n Hamzaoğlu, Murat Koç, İlker Büyük

Turkish Journal of Botany

Dianthus ucarii Hamzaoğlu & Koç (Caryophyllaceae) is described as a new species to science based on material collected in Kırklareli Province in northwestern Turkey. The new taxon belongs to sect. Carthusiani (Boiss.) F.N.Williams and it is closely related to Dianthus pinifolius Sm., an Eastern Mediterranean element. A description, illustration, and identification key for the new species are given. In addition, D. ucarii and D. pinifolius are compared in terms of general morphology and molecular phylogeny.

Contributions To The Macrofungi Of Bingöl, Turkey, Yusuf Uzun, İsmai̇l Acar, Mustafa Emre Akçay, Abdullah Kaya

Turkish Journal of Botany

The present study was carried out on macrofungi samples collected from Bingöl Province between 2006 and 2010. As a result of field and laboratory investigations 112 species belonging to Ascomycota and Basidiomycota were determined. Ten of them are new records for the Turkish mycobiota: Orbilia auricolor (A. Bloxam) Sacc.; Orbilia luteorubella (Nyl.) P. Karst.; Mollisia lividofusca (Fr.) Gillet; Calycina languida (P. Karst.) Baral, R. Galán & G. Platas; Vibrissea filisporia (Bonord.) Korf & A. Sánchez; Iodophanus carneus (Pers.) Korf; Amanita gilbertii Beauseign.; Conocybe brachypodii (Velen.) Hauskn. & Svrcek; Coprinopsis cordispora (T. Gibbs) Gminder; and Paxillus vernalis Watling.

The Isolation And Characterization Of The First Auxin Conjugate Amido-Hydrolase From Physcomitrella Patens, Richard Sylvester Skibitski

Theses, Dissertations and Culminating Projects

Auxin is arguably the most important phytohormone found in the plant kingdom. The hormone is required for a multitude of growth control functions, including gravitropism and phototropism. Auxin homeostatic control is achieved in plants by a process of conjugation in which auxin is inactivated by being bound to another molecule, such as an amino acid or sugar. Auxin can be kept in a large, inactive pool by this method of chemical '‘conjugation” and the amide or ester bonds hydrolyzed as needed to provide “free” active hormone to the plant. The IAR3 gene family is highly conserved in Plantae and function …

Road Salt Impact On A Stream-Dwelling Salamander, Eurycea Bislineata : A Low Threshold For Behavioral And Physiological Effects, Kelly Ann Krolik

Theses, Dissertations and Culminating Projects

Road salt runoff into aquatic habitats is a major ecological issue for amphibian species due to potential toxic effects from chemicals such as hydrocarbons, de-icing agents and salts. Road salt runoff can affect different aspects of amphibian biology, such as osmotic balance, growth, reproduction, behavior, and survival. This study investigated the behavioral and physiological salinity tolerance of adult two-lined salamanders, Eurycea bislineata. Two-lined salamanders are found in small streams and rivulets and may be exposed directly to salt runoff. In laboratory behavior trials, E. bislineata showed strong aversion to increasing salinity concentrations. They spent less time in higher NaCl concentrations …

Predicting Genome Terminus Sequences Of Bacillus Cereus-Group Bacteriophage Using Next Generation Sequencing Data, Cheng-Han Chung, Michael H. Walter, Luobin Yang, Shu-Chuan (Grace) Chen, Vern Winston, Michael A. Thomas

Faculty Work

Background: Most tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends.

Result: We sequenced 48 Bacillus cereus phage isolates and analyzed Next-generation sequencing (NGS) data to resolve the genome configuration of these novel phages. Most assembled contigs featured reads that mapped to both contig ends and formed circularized contigs. Independent assemblies of 31 nearly identical I48-like Bacillus phage isolates allowed us to observe that the assembly programs tended to produce random cleavage on circularized contigs. However, currently available assemblers were not capable of …

Widespread Tau Seeding Activity At Early Braak Stages, Jennifer L. Furman, Jaime Vaquer-Alicea, Charles L. White, Nigel J. Cairns, Peter T. Nelson, Marc I. Diamond

Pathology and Laboratory Medicine Faculty Publications

Transcellular propagation of tau aggregates may underlie the progression of pathology in Alzheimer's disease (AD) and other tauopathies. Braak staging (B1, B2, B3) is based on phospho-tau accumulation within connected brain regions: entorhinal cortex (B1); hippocampus/limbic system (B2); and frontal and parietal lobes (B3). We previously developed a specific and sensitive assay that uses flow cytometry to quantify tissue seeding activity based on fluorescence resonance energy transfer (FRET) in cells that stably express tau reporter proteins. In a tauopathy mouse model, we have detected seeding activity far in advance of histopathological changes. It remains unknown whether individuals with AD also …

Lncrna Ak001796 Is Essential For The Survival Of Aggressive Breast Cancer Cells, Sumayya Adib Al-Chalabi

Legacy Theses & Dissertations (2009 - 2024)

Abstract:

Raman Spectroscopy And Chemometrics For Forensic Bloodstain Analysis : Species Differentiation, Donor Age Estimation, And Dating Of Bloodstains, Kyle C. Doty

Legacy Theses & Dissertations (2009 - 2024)

The field of forensic science is constantly growing, so the advancement of old and unreliable techniques is at the forefront of what will lead to future progress and improvement. Current methods for identification and analysis of bloodstains are underwhelming due to the insignificant amount of information provided in a destructive, unreliable, and unsafe manner. As is the purpose of this research, creating new methodologies that are rapid, nondestructive, robust, statistically reliable, and safe would significantly advance the way bloodstains are currently analyzed, while providing more useful and relevant information for investigations and criminal proceedings. Raman spectroscopy, along with advanced statistical …

Genetic Counselor Workforce Trends In The United States : 2002 To 2016, Charlene J. Schulz

Legacy Theses & Dissertations (2009 - 2024)

The purpose of this study was to identify and measure trends in genetic counselor (GC) workforce supply in the United States from 2002 to 2016. Using data collected biennially from the National Society of Genetic Counselors’ Professional Status Survey (PSS), I calculated overall percent change in GC employment across specific work settings over the past 14 years. I also measured change in the relative percentage of GCs who provide direct patient counseling (i.e. clinical GCs) to determine if the percentage of clinical GCs decreased over time. Analyses were performed to determine if associations existed between GC work settings and 1) …

Development And Characterization Of Novel Anti-Bat Monoclonal Antibodies For Studying Bat Immunity, Cailyn Cowan

Legacy Theses & Dissertations (2009 - 2024)

Abstract

Discovering Small Molecule Inhibitors Targeted To Ligand-Stimulated Rage-Diaph1 Signaling Transduction, Jinhong Pan

Legacy Theses & Dissertations (2009 - 2024)

The receptor of advanced glycation end product (RAGE) is a multiligand receptor of the immunoglobulin superfamily of cell surface molecules, which plays an important role in immune responses. Full-length RAGE includes three extracellular immunoglobulin domains, a transmembrane domain and an intracellular domain. It is a pattern recognition receptor that can bind diverse ligands. NMR spectroscopy and x-ray crystallization studies of the extracellular domains of RAGE indicate that RAGE ligands bind by distinct charge- and hydrophobicity-dependent mechanisms. It is found that calgranulin binding to the C1C2 domain or AGEs binding to the V domain activates extracellular signaling, which triggers interactions of …

Differentiation, Distribution, And Diversity Of The Borrelia Burgdorferi Sensu Lato Virulence Gene, Ospc, And The Overwintering Survivability Of The Tick Vector, Ixodes Scapularis, Melissa Beth Stone

Legacy Theses & Dissertations (2009 - 2024)

The causative agents of Lyme disease, or Lyme Borreliosis, are spirochetes in the Borrelia burgdorferi sensu lato (s.l.) species complex that are transmitted by ticks in the genus Ixodes. Certain B. burgdorferi s.l. genotypes are more likely to cause invasive, disseminated infection in humans, and the gene, ospC, has been identified as a molecular marker that can be used to predict virulence. ospC is the most polymorphic locus in the B. burgdorferi s.l. genome, and different alleles have been assigned to Major ospC Groups based on sequence dissimilarity. Issues with the Major ospC Group definition and nomenclature are pervasive in …

Profiling Resistance To P450-Activated Food Carcinogens Using Toxicogenomic Approaches In Budding Yeast, Nicholas Stjohn

Legacy Theses & Dissertations (2009 - 2024)

The human response to environmental carcinogens, some of which require metabolic activation, is highly variable. Factors such as environment, lifestyle, and genetics all influence the rates of exposure to and ultimate bioactivation of these compounds. Genetic factors include mutations to cell-cycle regulation, cell proliferation, and DNA repair genes; however, epidemiological studies may lack significance due to inadequate patient numbers. We used budding yeast as a model organism to determine genetic susceptibility to food-associated carcinogens, including aflatoxin (AFB1) and heterocyclic aromatic amines (HAAs). Budding yeast does not contain P450s that activate these compounds, so expression vectors were induced that contain human …

Novel Approaches To Mitigating Bacterial Biofilm Formation And Intercellular Communication, Stephen Kasper

Legacy Theses & Dissertations (2009 - 2024)

Long thought of as solitary single-cell organisms, it is now widely accepted that bacteria can act and cooperate as social organisms. Phenomena such as biofilm formation and quorum sensing (QS) are two intimately intertwined cooperative behaviors that significantly contribute to the pathogenesis of many bacteria. Biofilms are surface associated communities of bacteria encased in a secreted extracellular matrix, which provides several advantages over an individualized lifestyle, such as increased protection from antimicrobial agents as well as enhanced opportunity for the exchange of genetic material. Bacterial QS is a system of population-based communication through the production, sensing, and response to chemical …

Altered Lipid Metabolism And Adipocyte Activity Support Her2+ Breast Cancer Progression, Jason Wong

Legacy Theses & Dissertations (2009 - 2024)

Overexpression of HER2 (ERBB2/neu) in breast cancer is an established clinical marker for aggressive disease and increased mortality. HER2+ breast cancers have increased protein levels of Human Epidermal Growth Factor Receptor 2 and overexpression of its coding gene, ERBB2. Many HER2+ tumors feature concomitant co-expression of the Nuclear Receptor subfamily 1, Group D, Member 1 (NR1D1/RevERBα) which regulates adipogenesis and circadian rhythm; the dysregulation of these two processes are known risk factors for breast cancer. HER2+ breast cancer cells have increased lipid synthesis, with evidence suggesting that NR1D1 is responsible for the upregulation of several genes in the de novo …

Structural And Functional Characterization Of An Unusual Camp Responsive Transcription Factor, Cmr, In Tb Complex Mycobacteria, Sridevi Ranganathan

Legacy Theses & Dissertations (2009 - 2024)

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis in humans, is an intracellular pathogen that infects millions of people every year. Mtb can survive inside the host for extended periods of time by sensing and adapting to the host environmental stressors. Transcriptional gene regulation plays a critical role in this adaptation. This dissertation focuses on understanding the structural and functional aspects of one such transcriptional regulatory unit, Cmr (Rv1675c), in Mtb.

Study Of Biologically Important Macromolecules By Nuclear Magnetic Resonance, Christopher Michael Demott

Legacy Theses & Dissertations (2009 - 2024)

Intrinsically disordered proteins or unstructured segments within proteins play an important role in cellular physiology and pathology. A combination of peptide aptamers selected by using the yeast-two-hybrid scheme, and in-cell NMR identified high affinity binders to a transiently structured intrinsically disordered proteins (IDP). This method was validated using the prokaryotic ubiquitin-like protein, Pup, of the Mycobacterium proteasome. We discover two peptide aptamers that bind to opposite sites of a transient helix in Pup, an intrinsically disordered protein, that have vastly different effects on the survival of Mycobacterium bovis BCG.

Multifunctional Nanomaterials Utilizing Hybridization Chain Reaction For Molecular Diagnostics And Bioanalytical Applications, Md Muhit Rana

Legacy Theses & Dissertations (2009 - 2024)

DNA nanotechnology has shown great promise in molecular diagnostic, bioanalytical and biomedical applications. The great challenge of detecting target analytes, biomarkers and small molecules, in molecular diagnostics is low yield sensitivity. To address this challenge, different nanomaterials have been used for a long time and to date there is no such cost-effective bioanalytical technique which can detect these target biomarkers (DNA, RNA, circulating DNA/miRNA) or environmental heavy metal ions (Hg2+ and Ag+) in a cost-effective and efficient manner.

A Laser-Pulse Photolysis Study Of The Mechanism Of Potentiation Of The Glua2qflip Ampa Receptors By Cx546, Yu-Chuan Shen

Legacy Theses & Dissertations (2009 - 2024)

Insufficient activity of the α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate ion channels is involved in neurological disorders and developmental problems, such as schizophrenia, one of the most serious psychiatric diseases. Use of regulatory agents to enhance AMPA receptor activity under the circumstance has been shown therapeutically beneficial. Specifically, small-molecule compounds generally termed as potentiators or positive modulators of AMPA receptors have long been pursued as drug candidates for a potential treatment of these neurological disorders and diseases. The goal of my MS thesis work is to investigate the mechanism of potentiation on AMPA receptor by a classic potentiator known as CX546. The …

Elucidating The Transcriptional Regulation Underlying Neural Induction, Sarah E. Hirsch

Legacy Theses & Dissertations (2009 - 2024)

The brain is one of the most complicated structures in the human body and its development is also elusive. Great strides have been made in expounding some of the complex mechanisms of neural development, which allows for the creation of innovative, less invasive, and more effective treatments for neurodevelopmental and neurodegenerative disorders. The advent of stem cell technology has brought therapy development for these disorders closer to a reality, as stem cells provide a platform to model early stages of human neural development. This is of great importance, as only through studying neurodevelopment will the various transcriptional and molecular components …

Disease In A Dish : Modeling Tau Pathology For Future Antibody Testing, Leneea Toyisha Warner

Legacy Theses & Dissertations (2009 - 2024)

ABSTRACT

Analysis Of Candidate Genes For Seizure Susceptibility In Epileptogenesis, Brittany O'Brien

Legacy Theses & Dissertations (2009 - 2024)

The occurrence of recurrent spontaneous seizures is the hallmark of epilepsy. The key to understanding how a normal brain can develop epilepsy through a process known as epileptogenesis is identifying susceptibility factors. Previously, various strains of inbred mice from the hybrid mouse diversity panel were subjected to multiple seizures via the repeated flurothyl model (RFM) for epileptogenesis. The results demonstrated differences in kindling among the inbred strains; specifically two main trends in the generalized seizure threshold (GST) data were kindling-sensitive and kindling-resistant strains. In addition, genome wide association studies done from these mice demonstrated a quantitative trait locus (QTL) on …

Organ-Specific Contribution Of P450 Enzymes To Bioactivation And Acute Respiratory Tract Toxicity Of Naphthalene, Nataliia Kovalchuk

Legacy Theses & Dissertations (2009 - 2024)

Naphthalene (NA) is an omnipresent air pollutant and respiratory toxicant and a possible human lung carcinogen. NA induces cytotoxicity in airways following bioactivation by CYP (P450) enzymes. The overall goal of this study was to examine the relative contributions of hepatic and pulmonary CYPs to bioactivation, disposition and NA-induced pneumotoxicity in vivo. Substantial differences in the expression and enzymatic activity of P450s occur in various organs in human populations, which could modify susceptibility to NA-induced airway damage. The central hypothesis for this study was that NA has the potential to cause lung toxicity in humans and that the metabolism of …

The Role Of N-Myc Downstream Regulated Gene 1 In Breast Cancer Lipid Metabolism, Christopher James Sevinsky

Legacy Theses & Dissertations (2009 - 2024)

Altered carbohydrate and lipid metabolism are increasingly well characterized hallmarks of aggressive breast cancers. While aerobic glycolysis, or “the Warburg effect”, is a well-established metabolic adaptation exploited by tumor cells, the understanding of unique aspects of cancer lipid metabolism lags behind. This is especially true regarding the coordination of complex lipid synthesis and trafficking pathways, which remains poorly understood. N-Myc Downstream Regulated Gene1 (NDRG1) is overexpressed in many solid tumors, but its function is unclear. The importance of NDRG1 is best exemplified by the effect of null mutations on human physiology: inactivating mutations give rise to the severe autosomal recessive …

Mass Spectrometric Analysis And Machine Learning Enable Microorganism Classification Based On Rna Posttranscriptional Modifications, Colin Christopher Aldrich

Legacy Theses & Dissertations (2009 - 2024)

RNA post-transcriptional modifications (PTMs) are dynamic features that can be up- or down-regulated by the health and metabolic state of a cell. These covalent modifications are installed and removed on RNA nucleosides by enzymes controlled by the activation and deactivation of specific genes. The goal of this research was to demonstrate that RNA PTMs can serve as a unique feature for the classification/identification of microorganisms. We utilized a scheme based on electrospray ionization mass spectrometry (ESI-MS) to obtain global PTM profiles from total RNA extracted from various microorganisms in optimal growth conditions as well as Salmonella typhimurium (S. typhimurium) spiked …

Biomarkers And Metabolic Mechanisms Of Tobacco Smoke-Induced Lung Disease, Matthew Alan Hartog

Legacy Theses & Dissertations (2009 - 2024)

The overall goal of the research conducted in this dissertation is to determine the role of cytochrome (CYP) P450-mediated xenobiotic bioactivation in the development of tobacco smoke-induced lung toxicity. The central hypothesis of this work is that CYP-mediated bioactivation of specific tobacco smoke constituents is an important contributor to the generation of tobacco smoke-induced lung inflammation and injury. The specific aims are 1) to demonstrate that CYP-mediated metabolism contributes to the onset of lung inflammation following tobacco smoke inhalation; 2) to demonstrate that specific tobacco smoke constituents undergo CYP-mediated bioactivation in vivo; 3) to demonstrate that CYP-mediated bioactivation of tobacco …

A Kinetic Study Of Regulation Of Glua1 Homomeric And Heteromeric Ampa Receptors By 2,3-Benzodiazepines, Yin-Shuo (Andrew) Wu

Legacy Theses & Dissertations (2009 - 2024)

AMPA receptors are a subtype of the ionotropic glutamate receptor family. They are ligand-gated or glutamate-activated, transmembrane ion channels that mediate the majority of excitatory synaptic transmission in the central nervous system. AMPA receptors are essential for neuronal development and brain functions, including learning and memory. Over-activation of calcium permeable AMPA receptors has been linked to some neurological diseases such as stroke, Alzheimer’s disease and amyotrophic lateral sclerosis. Inhibitors of glutamate receptors are therefore drug candidates for the potential treatment of these neurological diseases. One of the most promising classes of AMPA receptor antagonists is 2,3-benzodiazepine derivatives, thought to be …

A "Default Option" While Online Grocery Shopping To Enhance Nutrition Within A Food Insecure Population, Jaime Ashley Coffino

Legacy Theses & Dissertations (2009 - 2024)

There is a need for sustainable interventions that improve diet-related health within the food insecure community. We examined if use of a “default” prefilled online grocery shopping cart, compared to nutrition education, would result in the purchase of healthier food items. Fifty participants (M age = 46.4 ± 12.46 years; M body mass index = 28.59 ± 6.48 kg/m2; 74.0% male) were randomized to: (1) read a brochure containing nutrition information (n = 23) or (2) be presented with a “default” prefilled online shopping cart containing groceries that meet nutritional guidelines to which they could freely make changes before completing …

Detecting And Analyzing Trna Modification Systems And Homologs Using In Silico And Colorectal Cancer Models, Khadijah Onanuga

Legacy Theses & Dissertations (2009 - 2024)

tRNA modifications can be considered epitranscriptomic signaling components that regulate translation and play integral roles in stress response pathways. As such, tRNA modification enzymes have roles in cancer etiology and potential utility as biomarkers of pathological states. For my thesis project I have used computational and wet bench approaches to study tRNA modification systems. Chapter two of my thesis deals with tRNA modification detection, as current methods are costly, time consuming, and require RNA fragmentation. I present a single-molecule-based approach for RNA modification detection, which involves in slico studies using a 5-layered graphene nanopore. Our simulations using a 1.5 nm …

Wheezing & Food Allergies In Infants Delivered Via Cesarean Section : The Upstate Kids Study, Temilayo Elizabeth Adeyeye

Legacy Theses & Dissertations (2009 - 2024)

This dissertation sought to assess the effect of cesarean delivery (CD) on the risk of developing wheezing or food allergies in early childhood; and whether breastfeeding mediates the association between CD and the outcomes. We also aimed to highlight the differences in immunoglobulin concentrations by mode of delivery (MOD) in newborn dried blood spots (DBS), and the subsequent development of wheezing and food allergies in infants during the first three years of life. Data from the Upstate KIDS cohort was analyzed. Modified Poisson regression was used to compare the risks for wheezing and food allergies by MOD. We used a …