Digital Commons Network^™

Nitric Oxide Regulation Of C-Di-Gmp Metabolism And Biofilm Formation In Shewanella Woodyi, Niu Liu

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

Biofilms, multi-cellular sessile communities of bacteria, are known to account for bacterial persistence and antibiotic resistance. Nitric oxide (NO) has been shown to induce biofilm dispersal at sub-lethal concentrations in many species. For example, in the cystic-fibrosis associated bacterium, Pseudomonas aeruginosa, NO is reported to regulate biofilm dispersal through cyclic di-GMP signaling. In this thesis work, I demonstrate that Swoo_2750 from Shewanella woodyi encodes a Heme-Nitric oxide/OXygen binding domain (H-NOX), a protein that binds NO with approximately picomolar sensitivity. I demonstrate further that SwH-NOX is co-cistronic and directly interacts with Swoo_2751, a bi-functional diguanylate cyclase (DGC), which exhibits both c-di-GMP …

Preservation Of Proteinaceous Materials In Marine Environments, Tiantian Tang

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

Proteinaceous materials are major components of marine organic matter, and can account for up to 80% of the organic nitrogen in marine organisms. Although proteinaceous materials are generally considered to be labile, some of them are protected from heterotrophic attack and remineralization. In this study, we discussed the possible mechanisms how proteinaceous materials are preserved and transported in marine environments. First, the accumulation of refractory prokaryotic cell membranes has been suggested as one of the possible sources of the proteinaceous materials observed in the deep ocean. The refractory nature of these membranes presumably results from the highly diverse and complicated …

The Effects Of Marine Particle Composition On Phytoplankton Coagulation Efficiency And The Use Of Th-234 As A Proxy For Particulate Organic Carbon Flux, Jennifer Szlosek Chow

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

This dissertation investigates two parameters important for estimating and predicting organic matter export from the surface ocean: controls on the POC/234Th of marine particles and the coagulation efficiency of algal cells. Specifically, the sources of variability in POC/234Th and coagulation efficiency of Emiliania huxleyi are studied. The research explores two methods commonly employed &ndash the 234Th -proxy method for estimating POC flux, and Couette flow device experiments for experimentally deriving coagulation efficiency values. Applications of 234Th /238U disequilibrium as a flux proxy for particulate organic carbon (POC) in the oceans commonly rely on characterizing the POC/234Th in filterable particles and …

Study Of Phosphatidylinositol 3-Kinase In The Regulation Of Autophagy, Zhixun Dou

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

Autophagy is an evolutionarily conserved membrane trafficking process that maintains cell and tissue homeostasis. Autophagy plays essential roles in response to starvation and stress, and is involved in organelle homeostasis. Dysregulation of autophagy is implicated in diseases such as neurodegeneration and cancer. The induction of autophagy depends on phosphatidylinositol 3-phosphate (PI(3)P), the product of the Class III Phosphatidylinositol 3-Kinase (PI3K), Vps34. In metazoans, autophagy is thought to be inhibited by Class I PI3Ks, which are activated by cell surface trophic factor receptors and produce PI(3,4,5)P3 that activates the Akt-TOR kinase cascade and negatively regulates autophagy. Class IA PI3Ks are heterodimeric …

Cystoscopic Optical Coherence Tomography And Ultrahigh Resolution Optical Doppler Tomography For Quantitative Structural And Functional Imaging, Hugang Ren

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

This dissertation presents the design, development as well as preclinical and clinical validations of a cystoscopic optical coherence tomography (OCT) system and an ultrahigh resolution optical Doppler tomography (ODT) system for quantitative structural and functional imaging. The core of this dissertation can be divided into three sections. In the first section of the dissertation, which includes Chapter 3-Chapter 4, we validated the design and development of cystoscopic OCT (COCT) for bladder cancer diagnosis in vivo. To break the penetration depth barrier of the light, endoscopic imaging via fiber-optic technique has been developed. In this dissertation, we focused on bladder cancer …

Influence Of Deformable Substrates On Macroscopic And Microscopic Phenomenon Of Tissue, Divya Bhatnagar

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

One of the most important aspects by which cells adapt to their environment is their interaction with their extracellular matrix. The goal of this thesis is to design deformable substrates with controllable mechanical and biochemical properties and to understand cell-substrate interaction at both microscopic and macroscopic scales. First part of the thesis aims to develop biodegradable hydrogels as delivery vehicles for cellular and small molecular therapeutics and also for potential tissue engineering constructs. The second part deals with development of an assessment tool for analyzing changes in tissue mechanics. In the first part of this thesis, we studied the interaction …

Enhancement Or Attenuation Of Disease By Deletion Of Genes From Citrus Tristeza Virus, Satyanarayana Tatineni, William O. Dawson

Department of Plant Pathology: Faculty Publications

Stem pitting is a common virus-induced disease of perennial woody plants induced by a range of different viruses. The phenotype results from sporadic areas of the stem in which normal xylem and phloem development is prevented during growth of stems. These alterations interfere with carbohydrate transport, resulting in reduced plant growth and yield. Citrus tristeza virus (CTV), a phloem-limited closterovirus, induces economically important stem-pitting diseases of citrus. CTV has three nonconserved genes (p33, p18, and p13) that are not related to genes of other viruses and that are not required for systemic infection of some species of citrus, which allowed …

Temperature Responses Of Carbon Monoxide And Hydrogen Uptake By Vegetated And Unvegetated Volcanic Cinders, Caitlin E. King, Gary M. King

Faculty Publications

Ecosystem succession on a large deposit of volcanic cinders emplaced on Kilauea Volcano in 1959 has resulted in a mosaic of closed-canopy forested patches and contiguous unvegetated patches. Unvegetated and unshaded surface cinders (Bare) experience substantial diurnal temperature oscillations ranging from moderate (16°C) to extreme (55°C) conditions. The surface material of adjacent vegetated patches (Canopy) experiences much smaller fluctuations (14-25°C) due to shading. To determine whether surface material from these sites showed adaptations by carbon monoxide (CO) and hydrogen (H2) consumption to changes in ambient temperature regimes accompanying succession, we measured responses of CO and H2 uptake to short-term variations …

Conversion Of Human 5-Lipoxygenase To A 15-Lipoxygenase By A Point Mutation To Mimic Phosphorylation At Serine-663, Nathaniel C. Gilbert, Zhe Rui, David B. Neau, Maria T. Waight, Sue G. Bartlett, William E. Boeglin, Alan R. Brash, Marcia E. Newcomer

Faculty Publications

The enzyme 5-lipoxygenase (5-LOX) initiates biosynthesis of the proinflammatory leukotriene lipid mediators and, together with 15-LOX, is also required for synthesis of the anti-inflammatory lipoxins. The catalytic activity of 5-LOX is regulated through multiple mechanisms, including Ca 2+-targeted membrane binding and phosphorylation at specific serine residues. To investigate the consequences of phosphorylation at S663, we mutated the residue to the phosphorylation mimic Asp, providing a homogenous preparation suitable for catalytic and structural studies. The S663D enzyme exhibits robust 15-LOX activity, as determined by spectrophotometric and HPLC analyses, with only traces of 5-LOX activity remaining; synthesis of the anti-inflammatory lipoxin A4 …

A Novel Haptic Simulator For Evaluating And Training Salient Force-Based Skills For Laparoscopic Surgery, Ravikiran Singapogu

All Dissertations

Laparoscopic surgery has evolved from an 'alternative' surgical technique to currently being considered as a mainstream surgical technique. However, learning this complex technique holds unique challenges to novice surgeons due to their 'distance' from the surgical site. One of the main challenges in acquiring laparoscopic skills is the acquisition of force-based or haptic skills. The neglect of popular training methods (e.g., the Fundamentals of Laparoscopic Surgery, i.e. FLS, curriculum) in addressing this aspect of skills training has led many medical skills professionals to research new, efficient methods for haptic skills training.
The overarching goal of this research was to demonstrate …

Direct Effects Of Glucose And Fructose On Proliferation And Activation Of Jurkat T-Lymphocytes, C.J. Urso

Theses, Dissertations and Culminating Projects

High-fructose com syrup has been used with increasing commonality in recent decades. During this interval there is strong evidence of increased occurrence of autoimmune disease. We hypothesized that increased glucose and fructose concentration activates T-cells. Using Jurkat T-cells as a model, we found that increased glucose and fructose concentration decreased Jurkat T-cell proliferation and death rates at pH 7.4 while at pH 7.2 the above effects did not reach significance. Cells in high glucose and fructose concentration formed clusters that were unbreakable by standard trituration techniques suggesting the expression of high-affinity adhesion molecules characteristic of T-cell activation; this effect was …

Blue Notes, August 1, 2012 (Issue 2012-04), Illinois State University, Department Of Chemistry

Blue Notes

Newsletter of the Illinois State University Department of Chemistry

Microrna-34a Modulates Mdm4 Expression Via A Target Site In The Open Reading Frame, Pooja Mandke, Nicholas Wyatt, Jillian Fraser, Benjamin Bates, Steven J. Berberich, Michael P. Markey

Biochemistry and Molecular Biology Faculty Publications

Background

MDM4, also called MDMX or HDMX in humans, is an important negative regulator of the p53 tumor suppressor. MDM4 is overexpressed in about 17% of all cancers and more frequently in some types, such as colon cancer or retinoblastoma. MDM4 is known to be post-translationally regulated by MDM2-mediated ubiquitination to decrease its protein levels in response to genotoxic stress, resulting in accumulation and activation of p53. At the transcriptional level, MDM4 gene regulation has been less clearly understood. We have reported that DNA damage triggers loss of MDM4 mRNA and a concurrent increase in p53 activity. These experiments attempt …

The Acute And Chronic Effect Of Low Temperature On Survival, Heart Rate And Neural Function In Crayfish (Procambarus Clarkii) And Prawn (Macrobrachium Rosenbergii) Species, Yoo Sun Chung, Richard M. Cooper, Justin Graff, Robin L. Cooper

Biology Faculty Publications

The effect of acute and chronic cold exposure on heart rate (HR) and neuronal function in crayfish Procambarus clarkii and prawns Macrobrachium rosenbergii was addressed. This is particularly important since prawn farms of this species are used for aquaculture in varied climates world wide. The success of P. clarkii as an invasive species throughout the world may in part be due to their ability to acclimate to cold and warm habitats. A set of experiments was devised to address the physiological abilities of these species in managing rapid changes to cold environments as well as their ability to respond to …

Did Mineral Surface Chemistry And Toxicity Contribute To Evolution Of Microbial Extracellular Polymeric Substances?, Jie Xu, Jay M. Campbell, Nianli Zhang, William J. Hickey, Nita Sahai

College of Polymer Science and Polymer Engineering

Modern ecological niches are teeming with an astonishing diversity of microbial life in biofilms closely associated with mineral surfaces, which highlights the remarkable success of microorganisms in conquering the challenges and capitalizing on the benefits presented by the mineral-water interface. Biofilm formation capability likely evolved on early Earth because biofilms provide crucial cell survival functions. The potential toxicity of mineral surfaces toward cells and the complexities of the mineral-water-cell interface in determining the toxicity mechanisms, however, have not been fully appreciated. Here, we report a previously unrecognized role for extracellular polymeric substances (EPS), which form biofilms in shielding cells against …

The Consumption Of Dha During Embryogenesis As An Indicative Of The Need To Supply Dha During Early Larval Development: A Review, Joana Figueiredo, Junda Lin, Justin Anto, Luis Narciso

Marine & Environmental Sciences Faculty Articles

The establishment of an adequate larval diet for crustacean and fish often involves a series of time-consuming and expensive trial and errors. Despite being nutritionally poor, rotifers and Artemia are the most commonly used preys in larviculture. Whether (and to what extent) the prey needs to be enriched with essential fatty acids differs from species to species. We hypothesized that the DHA content of a newly spawned eggs and its consumption through embryogenesis can be a good indicator of the need to enrich the prey with DHA. In order to assess this hypothesis, we performed a search in the scientific …

Camera Creatures: Rhetorics Of Light And Emerging Media, Anthony Collamati

All Dissertations

Camera Creatures addresses the new media landscape in which cameras, in most situations, outnumber pens. The dissertation argues that despite the accessibility and power of imagemaking devices, there persists in the humanities and social sciences a hesitation to engage the possibilities for composing with optical media. A number of factors contributing to this trend are addressed, including the preference for image analysis over imagemaking practices, persistent assumptions of the camera's mechanical objectivity, and a tendency to teach visual invention as collage. As a counter-measure, a proposal is made for investment in the mediation of light, or 'photonic rhetorics.' To explore …

Multiple Independent Origins Of Mitochondrial Control Region Duplications In The Order Psittaciformes, Erin E. Schirtzinger, Erika S. Tavares, Lauren A. Gonzales, Jessica R. Eberhard, Cristina Y. Miyaki, Juan J. Sanchez, Alexis Hernandez, Heinrich Müeller, Gary R. Graves, Robert C. Fleischer, Timothy F. Wright

Faculty Publications

Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and …

Fabrication Of Printed Substrate For Surface Enhanced Raman Spectroscopy, Ali Eshkeiti

Masters Theses

A novel surface enhanced Raman spectroscopy (SERS) substrate was successfully fabricated on a silicon wafer using inkjet printing and on polyethylene terephthalate (PET) using gravure printing. Silver (Ag) nanoparticle (NP) based ink, was used for roughening of the surface of silicon and PET. A thickness of 400 nm was measured for the printed Ag NP printed film on silicon and the thickness of the single and double layered films on PET were measured as 340 nm and 680 nm, respectively by using vertical scanning interferometry. The Ag NP printed SERS substrate was tested for application with heavy metal compounds like …

Antisense Transcription Is Pervasive But Rarely Conserved In Enteric Bacteria, Rahul Raghavan, D. B. Sloan, H. Ochman

Biology Faculty Publications and Presentations

Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To …

In Vivo Quantification Reveals Extensive Natural Variation In Mitochondrial Form And Function In Caenorhabditis Briggsae, Kiley Ann Hicks, Dana K. Howe, Aubrey Leung, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among- isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential …

Movement Patterns In Resident And Translocated Three-Toed Box Turtles (Terrapene Carolina Triunguis), Christopher S. Samuelson

Biology Theses

Wildlife relocations, repatriations, and translocations (RRTs) are strategies that are often used for by conservation managers as a method of reestablishing viable animal populations. The effectiveness of RRT studies has been called into question by some researchers, but more data are needed on the strategy to fully understand its utility. I compared the movement patterns, home range sizes, and body condition between a group of resident and translocated adult three-toed box turtles (Terrapene carolina triunguis). Each turtle from both groups was radio-tracked at least 2-3 times per month except during the winter months. Minimum convex polygons home range sizes estimated …

Likely Effectiveness Of Netting Or Other Capture Programs As A Shark Hazard Mitigation Strategy In Western Australia, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

Genetic Characteristics Of An Ancient Nomadic Group In Northern China, Haijing Wang, Lu Chen, Binwen Ge, Ye Zhang, Hong Zhu, Hui Zhou

Human Biology Open Access Pre-Prints

Nomadic populations have played a significant role in the history of not only China but also in many nations worldwide. Because they had no written language, an important aspect in the study of these people is the discovery of their tombs. It has been generally accepted that Xiongnu was the first empire created by nomadic tribe in the 3rd century B.C. However, little population genetic information is available concerning the Donghu, another flourishing nomadic tribe at the same period because of the restriction of materials until Jinggouzi site was excavated. In order to test the genetic characteristics of ancient people …

Molecular Modeling And Experimental Studies On Ligand Recognition In The Lpa5 G Protein-Coupled Receptor, Jesica Rene Williams

Electronic Theses and Dissertations Archive

Lysophosphatidic acid (LPA) is a phospholipid growth factor mediating numerous biological effects such as platelet aggregation, mast cell activation, cell differentiation, cell migration, and cell survival by acting on specific LPA G protein-coupled receptors. Currently there are nine LPA receptors identified in the literature, LPA1-9. LPA1-3 are members of the endothelial differentiation gene (EDG) family and share approximately 50% sequence identity at the primary sequence level. LPA4-9 are structurally distinct from the EDG receptors with LPA5 sharing approximately 30% sequence identity with LPA4 at the primary sequence level. Due to the emerging role of LPA5 in human platelet activation, cancer, …

Inhibition Of Burkholderia Multivorans Adhesion To Lung Epithelial Cells By Bivalent Lactosides, Ciara Wight, Rosaria Leyden, Paul V. Murphy, Máire Callaghan, Trinidad Velasco-Torrijos, Siobhan Mcclean

Articles

Burkholderia cepacia complex (Bcc) is an opportunistic pathogen in cystic fibrosis patients which is inherently resistant to antimicrobial agents. The mechanisms of attachment and pathogenesis of Bcc, a group of 17 species, are poorly understood. The most commonly identified Bcc species in newly colonised patients, Burkholderia multivorans, continues to be acquired from the environment. Development of therapies which can prevent or reduce the risk of colonization on exposure to Bcc in the environment would be a better alternative to antimicrobial agents. Previously, it has been shown that Bcc strains bound to many glycolipid receptors on lung epithelia. Using a …

Ultrastable Synergistic Tetravalent Rna Nanoparticles For Targeting To Cancers, Farzin Haque, Dan Shu, Yi Shu, Luda S. Shlyakhtenko, Piotr G. Rychahou, B. Mark Evers, Peixuan Guo

Pharmaceutical Sciences Faculty Publications

One of the advantages of nanotechnology is the feasibility to construct therapeutic particles carrying multiple therapeutics with defined structure and stoichiometry. The field of RNA nanotechnology is emerging. However, controlled assembly of stable RNA nanoparticles with multiple functionalities which retain their original role is challenging due to refolding after fusion. Herein, we report the construction of thermodynamically stable X-shaped RNA nanoparticles to carry four therapeutic RNA motifs by self-assembly of reengineered small RNA fragments. We proved that each arm of the four helices in the X-motif can harbor one siRNA, ribozyme, or aptamer without affecting the folding of the central …

Paternal Lineage Analysis Supports An Armenian Rather Than A Central Asian Genetic Origin Of The Hamshenis, Ashot Margaryan, Ashot Harutyunyan, Zaruhi Khachatryan, Armine Khudoyan, Levon Yepiskoposyan

Human Biology Open Access Pre-Prints

The Hamshenis are an isolated geographic group of Armenians with a strong ethnic identity who, until the early decades of the twentieth century, inhabited the Pontus area on the southern coast of the Black Sea. Scholars hold alternative views on their origin, proposing eastern Armenia, western Armenia and Central Asia, respectively, as their most likely homeland. To ascertain whether genetic data from the non-recombining portion of the Y chromosome is supportive any of these suggestions, we screened 82 Armenian males of the Hamsheni descent for 12 biallelic and 6 microsatellite Y-chromosomal markers. These data were compared with the corresponding datasets …

Locating And Protecting Facilities Subject To Random Disruptions And Attacks, Hugh Medal

Graduate Theses and Dissertations

Recent events such as the 2011 Tohoku earthquake and tsunami in Japan have revealed the vulnerability of networks such as supply chains to disruptive events. In particular, it has become apparent that the failure of a few elements of an infrastructure system can cause a system-wide disruption. Thus, it is important to learn more about which elements of infrastructure systems are most critical and how to protect an infrastructure system from the effects of a disruption. This dissertation seeks to enhance the understanding of how to design and protect networked infrastructure systems from disruptions by developing new mathematical models and …

Who Wears Me? Bioimpedance As A Passive Biometric, Cory Cornelius, Jacob Sorber, Ronald Peterson, Joe Skinner, Ryan Halter, David Kotz

Dartmouth Scholarship

Mobile and wearable systems for monitoring health are becoming common. If such an mHealth system knows the identity of its wearer, the system can properly label and store data collected by the system. Existing recognition schemes for such mobile applications and pervasive devices are not particularly usable – they require ıt active engagement with the person (e.g., the input of passwords), or they are too easy to fool (e.g., they depend on the presence of a device that is easily stolen or lost). \par We present a wearable sensor to passively recognize people. Our sensor uses the unique electrical properties …