Life Sciences Commons^™

Weed Risk Assessment For Aquatic Plants: Modification Of A New Zealand System For The United States, Doria R. Gordon, Crysta A. Gantz, Christopher L. Jerde, W Lindsay Chadderton, Reuben P. Keller, Paul D. Champion

School of Environmental Sustainability: Faculty Publications and Other Works

We tested the accuracy of an invasive aquatic plant risk assessment system in the United States that we modified from a system originally developed by New Zealand’s Biosecurity Program. The US system is comprised of 38 questions that address biological, historical, and environmental tolerance traits. Values associated with each response are summed to produce a total score for each species that indicates its risk of invasion. To calibrate and test this risk assessment, we identified 39 aquatic plant species that are major invaders in the continental US, 31 species that have naturalized but have no documented impacts (minor invaders), and …

Spartin Protein Associates With Phospholipids Via Its Plant-Related Senescence Domain And Functions As A Lipid Transfer Protein, Maureen Ashlee Shaw

Theses (1 year embargo)

Troyer syndrome is a hereditary spastic paraplegia caused by a mutation that leads to a complete loss of expression of spartin protein. The plant-related senescence domain in spartin is highly conserved and present in over 150 proteins, but its function is unknown. Our results indicate that spartin associates with phospholipids via its senescence domain.

Phospholipids are important components of intracellular membranes and play roles in many cellular processes. Knock-down of spartin results in impaired cell division. The phospholipid phosphatidylinositol 3-phosphate (PI3P) is present at midbodies, where it recruits proteins for cytokinesis. Our findings demonstrate that spartin colocalizes with PI3P at …

Vascular Kv7 (Kcnq) Potassium Channels As Therapeutic Targets In Cerebral Vasospasm, Bharath Kumar Mani

Dissertations (6 month embargo)

Cerebral vasospasm, a grave sequel to subarachnoid hemorrhage (SAH), is characterized by prolonged severe constriction of arteries in the base of the brain, including the basilar artery. Spasmogens (serotonin, endothelin and vasopressin), elevated in response to SAH, induce persistent depolarization of the myocytes in the artery wall, leading to continuous influx of calcium (Ca2+) through voltage-sensitive Ca2+ channels (VSCC) resulting in hyperconstriction (spasm). The spasm of the arteries restricts blood flow to the brain, inducing ischemic neurological deficits and consequential high morbidity and mortality. The cellular pathogenesis of cerebral vasospasm is poorly understood and the therapeutic options are limited.

Kv7 …

The Role Of Cyp33 In Mll Mediated Gene Repression, Steven D. Poppen

Dissertations

Mixed Lineage Leukemia (MLL) is a multidomain protein whose gene is translocated in a subset of AML leukemias. Translocation of the MLL gene is present in approximately five percent of adult acute leukemias and ten percent of pediatric leukemias (Daser, A 2004, Look, A 1997, Huret, J 2001) Patients presenting in the clinic at the time of diagnosis with an MLL fusion have been shown to respond poorly to treatment and have a worse prognosis than matched wild type MLL patients (Rubnitz, J 1994, Rubnitz, J 1999). Novel therapies therefore are needed in order to more effectively treat patients with …

Cell Biology Of Foxp3+ Regulatory T Cells, Mariko Takami

Dissertations

T cells play a central role in the immune response to fight against pathogens and orchestrate other immune cells. An overreactive immune response can lead to autoimmune diseases, therefore the immune system must possess negative regulation mechanisms. In the periphery, naturally arising regulatory T cells (nTregs) negatively regulate immune responses and play an important role in maintaining immune homeostasis. When antigens are present, conventional CD4+ T cells recognize their cognate antigen and proliferate. After pathogen clearance, expanded effector T cells eventually decline in number due to activation induced cell death (AICD) to terminate immune response. However, it is not understood …

Compositional Determinants Of The Pharmacological Actions Of Heparins, Angel Lee Gray-Shah

Dissertations

This dissertation primarily focuses on how differences in molecular weight (MW) and structural composition affect the pharmacological activity of heparin and its derivatives. Heparins are a mixture of glycosaminoglycans chains which are used to prevent thrombosis in a number of clinical indications. Heparins promote the inhibition of blood coagulation via their plasmatic cofactors antithrombin (AT) and heparin cofactor II (HCII).

In these studies, various heparins with molecular weights ranging from 2.6 to 16.5 kDa were investigated. Not only the molecular weight but also the oligosaccharide composition greatly varied in these agents. One of the major objectives of this research was …

The Binding Properties And Functional Consequences Of Ryr2-Cam Interaction, Yi Yang

Dissertations

The aim of my dissertation is to understand the regulation of RyR2. The whole dissertation is composed of two parts. The first part focused on RyR2-CaM interaction. The second focused on synthetic RyR2 domain peptide (DPc10), which worked as a powerful molecular tool for RyR2 functional and structural studies.

CaM has been long identified as an important cardiac RyR regulator. Broad studies suggest CaM is a critical RyR2 stabilizer and CaM-RyR2 interaction is a critical molecular substrate for arrhythmias and HF pathogenesis, but the in situ binding properties for CaM-RyR2 are still unknown. Here we, Using FRET detection and permeabilized …

Assessing The Use Of Non-Lethal Tail Clips For Measuring Stable Isotopes Of Plethodontid Salamanders, Joseph Milanovich, John C. Maerz

Biology: Faculty Publications and Other Works

Stable isotopes are increasingly used in ecology to study the diets, trophic position, and migratory patterns of wildlife including herpetofauna. When using stable isotopes, it is important to consider which tissues can or should be sampled, and how selecting tissues may affect the inferences drawn from stable isotope data. Amphibians offer fewer tissues than other larger organisms that can be harvested in sufficient quantity without killing the animal; however, many salamanders have tails that readily autotomize and regenerate. We used three species of plethodontid salamander (Plethodon cinereus, P. metcalfi, and Desmognathus quadramaculatus) to determine whether distal tail tissue had carbon …

Computational And Experimental Analyses Of Retrotransposon-Associated Minisatellite Dnas In The Soybean Genome, Lauren S. Mogil, Kamil Slowikowski, Howard M. Laten

Biology: Faculty Publications and Other Works

BACKGROUND:

Retrotransposons are mobile DNA elements that spread through genomes via the action of element-encoded reverse transcriptases. They are ubiquitous constituents of most eukaryotic genomes, especially those of higher plants. The pericentromeric regions of soybean (Glycine max) chromosomes contain >3,200 intact copies of the Gmr9/GmOgre retrotransposon. Between the 3' end of the coding region and the long terminal repeat, this retrotransposon family contains a polymorphic minisatellite region composed of five distinct, interleaved minisatellite families. To better understand the possible role and origin of retrotransposon-associated minisatellites, a computational project to map and physically characterize all members of these families in the …

Positive Emotions And Immune Respose To Influenza In Medically Stable Older Adults, Maryann J. Gierloff

Dissertations

Influenza results in substantial human suffering and health care costs. Evidence from psychoneuroimmunology suggests that emotions influence the immune system and may alter susceptibility to infectious diseases, like influenza. The purpose of this investigation was to evaluate the influence of psychological factors, health behaviors, circulating levels of proinflammatory cytokines and the development of influenza-like illness in older adults. Medically stable participants, 55 years of age and over, were enrolled from the general community and an elderly community. Psychological factors (emotions and perceived stress), health behaviors (sleep and physical activity) and plasma cytokine levels (IL-6 and IL-1B) were evaluated with respect …

Serine 910 Phosphorylation Of Focal Adhesion Kinase Is Critical For Costamere Assembly, Miensheng Chu

Dissertations

Tyrosine-phosphorylated FAK is required for the hypertrophic response of cardiomyocytes to growth factors and mechanical load, but the role of FAK serine phosphorylation in this process is unknown. Endothelin-1 (ET-1; 1-100nM, 2-30min) and other hypertrophic factors induced a time- and dose-dependent increase in FAK-S910 phosphorylation in neonatal rat ventricular myocytes (NRVM). FAK-S910 phosphorylation required ET_AR-dependent activation of PKCδ and Src via parallel Raf-1→MEK1/2→ERK1/2 and MEK5→ERK5 signaling pathways. Using co-immunoprecipitation, TIRF-microscopy and FRAP, ET-1 stimulation of NRVM expressing a nonphosphorylatable, S910A-FAK mutant decreased the interaction of paxillin and vinculin within costameres. This interaction was important in stabilizing α-actinin within …

Receptor-Mediated Hypertrophic Signaling Via Protein Kinase D And Histone Deacetylase 5 In Adult Myocytes, Chia-Wei Jenny Chang

Dissertations

Hemodynamic stress and neurohumoral signaling are common causes of cardiac hypertrophy. These extrinsic stress stimuli typically act on GPCR and induce a cascade of signal transduction to re-program terminally differentiated myocytes to grow in length or width. The compensatory hypertrophic response can enhance cardiac output briefly due to increased work load. However, prolonged stress results in maladaptive changes in the heart and gradually deteriorates ventricular function to supply blood throughout the body. Sustained hypertrophic signaling can also progress toward heart failure.

My dissertation research focuses on the hypertrophic signaling in adult cardiac myocytes in response to neurohumoral stimuli, ET-1 and …

Molecular Mechanisms Regulating Chemokine Receptor Cxcr4 Signaling And Trafficking, Rohit Malik

Dissertations

CXCR4 is a G protein-coupled receptor (GPCR) that binds to the chemokine, stromal cell-derived factor-1 (SDF-1alpha; a.k.a. CXCL12). The SDF-1alpha/CXCR4 signaling axis plays an essential role during embryogenesis in the development of the heart, brain and vasculature and in the adult mediating immune cell trafficking and stem cell homing to the bone marrow. Dysregulation of SDF-1alpha/CXCR4 signaling is linked to several pathological conditions, including cardiovascular disease, immunological disorders as well as cancer growth and metastasis. However, the mechanisms that govern CXCR4 signaling remain poorly understood. In this dissertation project, we attempt to further our understanding of the molecular mechanisms that …

Effects Of Binge Alcohol Exposure On Canonical Wnt Signaling During Fracture Repair, Kristen Leigh Lauing

Dissertations

Excessive alcohol consumption is associated with increased fracture risk, delayed bone healing and fracture non-union. Binge alcohol consumption has occurred in 25-40% of all orthopaedic trauma cases. The canonical Wnt pathway, through tight regulation of stabilized beta-catenin, plays an essential and pivotal role in the formation of new bone and cartilage to initiate bone repair. We sought to determine the molecular mechanisms behind alcohol-related fracture complications by testing the hypothesis that binge alcohol exposure deregulates canonical Wnt signaling in the fracture callus, leading to impaired healing.

To test this, C57BL/6 or beta-catenin/TCF-reporter male mice were exposed to intraperitoneal alcohol or …

The Effect Of Glucose On Transcription At Cpxr- And Ompr-Regulated Promoters, Andrew Charles Cosgrove

Master's Theses

While reversible acetylation of proteins has been well studied in eukaryotes and is now recognized in bacteria, global protein acetylation in bacteria is a recently appreciated phenomenon. Protein acetylation is known to affect almost every aspect of cellular physiology in eukaryotes and there is proteomic evidence that this may also hold true in bacteria. In eukaryotes, lysines are acetylated by acetyltransferases that use acetyl-CoA as the acetyl group source, and de-acetylated by deacetylases. In bacteria, this reversible process uses enzymes homologous to those used by eukaryotes.

Our lab has recently found that acetylation of RNA polymerase (RNAP) can activate transcription …

Binge Ethanol Leads To Decreased Macrophage Accumulation In Infected Cutaneous Wounds, Sara Hlavin

Master's Theses

Trauma patients who consumed alcohol prior to sustaining injuries have higher rates of morbidity and mortality than those with comparable injuries who did not drink. Additionally, those who drank had impaired wound healing and increased susceptibility to infection. Despite these clinical observations, few studies have explored the effect of ethanol on the innate immune cell function in a healing wound or how this may alter resolution of cutaneous infection. A murine model of ethanol and cutaneous wound infection was used to examine bacterial growth and recruitment of innate immune cells. Mice were given either ethanol (2.2 g/kg) or saline 30 …

Characterization Of The Clostridium Difficile Biofilm, Michelle Laning

Master's Theses

Clostridium difficile is a Gram-positive, spore forming bacterium and an opportunistic gastrointestinal pathogen. Clostridium difficile infection (CDI) is a common nosocomial infection. Upon antibiotic treatment, patients can be colonized with C. difficile from ingestion of spores. After colonization, cells produce toxins creating symptoms from diarrhea to pseudomembranous colitis, and many patients develop recurrent infections. Interactions between host epithelium and the bacteria is a critical step in infection, yet the interaction is not well understood. It is not known how C. difficile evades host immune responses. These are important mechanisms to answer in advancing CDI treatment. A biofilm could contribute to …

Urinary Antimicrobial Peptides And The Urinary Microbiota In A Uti-Susceptible Population Of Female Pelvic Floor Surgery Patients, Vanessa Nienhouse

Master's Theses

Urinary tract infections (UTI)s are a national priority. Women who undergo surgery for pelvic floor disorders such as pelvic organ prolapse (POP) or urinary incontinence (UI) are at increased risk for UTI, as 10-30% will contract a post-instrumentation UTI (postI-UTI) within six weeks after surgery. Currently, the factors that contribute to the high rate of postI-UTI are unknown, and there is currently no clinical assessment to identify at-risk patients. However, antimicrobial peptides (AMPs) and characteristics of the urinary microbiota have the potential to serve as biomarkers, identifying patients at UTI risk and facilitating clinical prevention studies.

While it was previously …

Organization And Composition Of The Α21-Ii Region Of Human Chromosome 21, William Ziccardi

Master's Theses

The purpose of this project was to develop a better map of the alpha 21-II region of human chromosome 21 in regards to size and primary sequence of the five alphoid clusters that comprise the region and to explore the evolutionary relationships that exist within and between these clusters. Several HC21 BACs were identified as containing strong sequence identities to alpha 21-II clones and were mapped to various alpha 21-II clusters. It was revealed that both monomeric and HOR alphoid clusters can be found in the alpha 21-II region. Phylogenetic analysis revealed separate evolutionary histories for the monomeric and HOR …

Determination Of An Interaction Between Nipped B-Like Protein And Mll, Adam Robert Marek

Master's Theses

The Mixed Lineage Leukemia (MLL) protein serves as a positive transcriptional regulator during hematopoietic and embryonic development. The MLL gene can undergo chromosomal translocations producing leukemia-causing fusions that retain the MLL amino-terminus, including the repression domain. A recent yeast two-hybrid screening used the MLL repression domain as bait and yielded nine positive clones of Nipped B-like (NIPBL).

NIPBL is a crucial member of the cohesin complex, which functions in the segregation of sister chromatids during cell division. However, recent evidence suggests the cohesin complex can also function as a transcriptional regulator.

In this study, we wanted to confirm this interaction …

Evolution Of Interactomes, Monica Micek

Master's Theses

Protein-protein interactions are part of all biological processes and are responsible for directing the development and maintenance of all systems in a species. Identifying such interactions provides insight into molecular processes in addition to their importance in understanding disease. Identifying protein-protein interactions experimentally is expensive, both in terms of cost and effort, and can generate erroneous results. Thus computational methods are key in reducing the scope of experimental assays, providing predictions for subsequent verification. Herein I present a new computational tool for the prediction of protein-protein interactions which, looking at sequence data alone, can identify putative interacting proteins as a …

Organization Of The Centromeric Satellite I Cluster And D21z1 Short Arm Junction Region Of Human Chromosome 21, Riddhi V. Patel

Master's Theses

To study chromosomal segregation errors causing Down syndrome one needs a chromosome 21 (HC21) specific centromeric marker, which presently does not exist. Alphoid DNA is the only repetitive sequence at all human centromeres. The current map of HC21 has a gap in the p-arm alphoid (D21Z1) junction region and the centromeric satellite I (satI) sequence. This satellite I cluster was shown not to be a specific centromeric marker since it is also on HC13. There are actually multiple satI families on both HC13 and HC21. This project also filled the gap in the HC21map and characterized the D21Z1 p- arm …

Characterization Of The Coca Chemokine Receptor Four Agonist Activity Of Ubiquitin, Daniel M. Staren

Master's Theses

Ubiquitin has previously been identified as another natural agonist of CXC chemokine receptor 4 (CXCR4). In addition, recent evidence suggests that ubiquitin may activate CXCR4 through a binding site on the receptor, which is distinct from the binding site for the cognate ligand stromal cell-derived factor (SDF)-1α. The cellular consequences of ubiquitin induced CXCR4 activation, however, are still poorly defined and a side-by-side comparison of CXCR4 mediated functions after activation with SDF-1α and ubiquitin is lacking. Such information will be instrumental to better understand the physiological function of CXCR4 and to further define its role as a therapeutic target in …

Understanding The Regulation Of Metabolic Enzyme Acetylation In E. Coli, Arti Walker-Peddakotla

Master's Theses

Global protein acetylation is a newly discovered phenomenon in bacteria. Of the more than 250 acetylations reported in E. coli, many are of metabolic enzymes. Thus, acetylation could represent a novel posttranslational mechanism of metabolic control. Yet, almost nothing is known about the regulation of these acetylations or of their metabolic outcomes. Here, we report that the cAMP receptor protein (CRP) regulates protein acetylation in E. coli and provide evidence that protein acetylation modulates the flux of carbon through central metabolism. When we grew cells in mixed amino acids supplemented with glucose and cAMP, global protein acetylation increased in a …

Kv7 K+ Channels In Airway Smooth Muscle Cells As Target For Asthma Therapy, Priyanka Prakash Kakad

Master's Theses

Airway hyperresponsiveness (AHR) is an important etiological feature of asthma, the molecular mechanisms of which are poorly understood, thus preventing development of specific and effective therapies. We investigate the role played by Kv7 voltage-activated potassium channels in the pathophysiology of AHR and evaluate the significance of their regulation in treatment of asthma. Our studies provide the first evidence for expression of multiple Kv7 channels in guinea pig and human airways and demonstrate that the expression of Kv7 channels is reduced in allergen-sensitized guinea pig airways. Our ex vivo functional studies reveal that clinically available Kv7 channel activators attenuate the bronchoconstrictor …

Promoting Thymopoiesis With Age: Potential Role Of The Transcription Factor Foxn1, Erin Christine Zook

Dissertations

It is known that the elderly are more susceptible to illnesses and infections and respond poorly to immunization. A contributing factor to a decrease in the immune response in the elderly is the decline in the production of naïve T cell by the thymus. In the thymus, the notch receptor expressed on early T cell progenitors (ETP) binds to its ligand expressed on thymic epithelial cells (TEC), signaling ETP to develop through a series of developmental stages before maturing into naive T cells. Because ETP are non-self renewing, the thymus relies on the bone marrow (BM) for a continuous supply …

An Investigation Of The Phospholamban-Serca Regulatory Interaction With Fluorescence Resonance Energy Transfer, Philip Adam Bidwell

Dissertations

With Fluorescence Resonance Energy Transfer (FRET), we are able to detect changes in the structure and affinity of the PLB-SERCA regulatory complex in live cells. Using this approach, we have detected a high level of PLB-SERCA interaction even at Ca2+ concentrations known to fully relieve PLB inhibition of SERCA, suggesting that dissociation is not required for relief of inhibition. We also detect no real-time change in PLB-SERCA binding over the course of a single Ca2+ transient in paced myocytes. The effect of Ca2+ on the PLB-SERCA interaction is best described as a reduced affinity with no change in the structure …

Miip: The Monomer Identification And Isolation Program, Christopher Bun, William Ziccardi, Jeffrey Doering, Catherine Putonti

Bioinformatics Faculty Publications

Repetitive elements within genomic DNA are both functionally and evolutionarily informative. Discovering these sequences ab initio is computationally challenging, compounded by the fact that selection on these repeats is often relaxed; thus sequence identity between repetitive elements can vary significantly. Here we present a new application, the Monomer Identification and Isolation Program (MiIP), which provides functionality to both search for a particular repeat as well as discover repetitive elements within a larger genomic sequence. To compare MiIP’s performance with other repeat detection tools, analysis was conducted for synthetic sequences as well as several α21-II clones and HC21 BAC sequences. The …

Cbdb: The Codon Bias Database, Adam Hilterbrand, Joseph Saelens, Catherine Putonti

Bioinformatics Faculty Publications

Background

In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift. Furthermore, correlations between codon usage within host genomes and their viral pathogens have been observed for a myriad of host-virus systems. As such, numerous studies have investigated codon usage and codon bias in an effort to better understand how species evolve. Numerous metrics have been developed to identify biases in codon usage. In addition, a few data repositories of codon bias data are available, …

Rotating Magnets Produce A Prompt Analgesia Effect In Rats, Zhong Chen, Hui Ye, Haiyun Xu, Shukang An, Anmin Jin, Chusong Zhou, Shaoan Yang

Biology: Faculty Publications and Other Works

The beneficial effects of chronic/repeated magnetic stimulation on humans have been examined in previous studies. Although pain relief effects have been reported several weeks after magnetic treatment, no report is available regarding the prompt effect of magnetic stimulations. In this study, a novel apparatus was developed to generate time-varying magnetic fields with rotating magnets. Adult, conscious rats were exposed to the rotating magnets in a posture in which their spines were parallel to the induced electric current. The magnetic field suppressed the paw withdrawal reflex in the anesthetized rats, and the suppression effect disappeared 5 minutes after magnets stopped rotating. …