Biochemistry, Biophysics, and Structural Biology Commons^™

A Watershed Analysis Of Long Pond South: Implications For Water Quality And Land-Use Management [Presentation], Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: Long Pond, South (2007, 1995)

No abstract provided.

A Watershed Analysis Of Long Pond South: Implications For Water Quality And Land Use Management, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: Long Pond, South (2007, 1995)

The water quality of the South Basin of Long Pond, located in the Belgrade Lakes region of Maine, was investigated by the Colby Environmental Assessment Team (CEAT) from May to September of 2007. The physical, chemical, and biological characteristics of water quality were analyzed to evaluate the current health of the lake. The Long Pond South watershed was examined to investigate the effect of land-use patterns, including residential and commercial development, on the lake water quality. Data were also collected from road and shoreline surveys to produce maps highlighting areas that could potentially contribute to the degradation of water quality. …

Selective Cholesterol Dynamics Between Lipoproteins And Caveolae/Lipid Rafts, Stephen M. Storey, Adalberto M. Gallegos, Barbara P. Atshaves, Avery L. Mcintosh, Gregory G. Martin, Rebecca D. Parr, Kerstin K. Landrock, Ann B. Kier, Judith M. Ball, Friedhelm Schroeder

Faculty Publications

Although low-density lipoprotein (LDL) receptor-mediated cholesterol uptake through clathrin-coated pits is now well understood, the molecular details and organizing principles for selective cholesterol uptake/efflux (reverse cholesterol transport, RCT) from peripheral cells remain to be resolved. It is not yet completely clear whether RCT between serum lipoproteins and the plasma membrane occurs primarily through lipid rafts/caveolae or from non-raft domains. To begin to address these issues, lipid raft/caveolae-, caveolae-, and non-raft-enriched fractions were resolved from purified plasma membranes isolated from L-cell fibroblasts and MDCK cells by detergent-free affinity chromatography and compared with detergent-resistant membranes isolated from the same cells. Fluorescent sterol …

The Generation And Scavenging Of Radicals Via Cerium And Nanoceria, Eric Glenn Heckert

Electronic Theses and Dissertations

Cerium is the most abundant of the rare earth metals, found on average at a level of 66 parts per million in the earth's crust. The unique redox properties of cerium and cerium oxide nanoparticles have led to its use in a wide variety of industrial and commercial uses such as oxygen sensors, fertilizers and as a catalyst to remove toxic gases in automobile exhaust. The use of cerium has also garnered interest in the nanotechnology field. Nanoceria has been generated in its oxide form as nanoparticles and nanorods. Recently, nanoceria has been shown to protect against oxidative stress in …

Mechanisms Promoting Phosphorylation Of The Nf2 Tumor Suppressor And Its Effects On Schwann Cell Development, Courtney Lynn Thaxton

Electronic Theses and Dissertations

Neurofibromatosis type 2 is an autosomal dominant disease characterized by the formation of schwannomas and other peripheral neuropathies. The nf2 gene encodes the protein Schwannomin, or merlin. Schwannomin (Sch) is a membrane-cytoskeletal linking protein that suppresses cell proliferation at high cell density and modulates cell shape. Sch's tumor suppressive activity is regulated by its localization, conformation, and phosphorylation at serine 518 (S518). Sch's localization is dependent on binding the scaffold protein, paxillin. Phosphorylation of Sch at S518 regulates its conformation and tumor suppressor function. In a negative feedback loop, unphosphorylated Sch restricts cell proliferation downstream of Rac and p21-activated kinase …

Targeting Thioredoxin Reductase 1 Reduction In Cancer Cells Inhibits Self-Sufficient Growth And Dna Replication, Min-Hyuk Yoo, Xue-Ming Xu, Bradley A. Carlson, Andrew D. Patterson, Vadim N. Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

Thioredoxin reductase 1 (TR1) is a major redox regulator in mammalian cells. As an important antioxidant selenoprotein, TR1 is thought to participate in cancer prevention, but is also known to be over-expressed in many cancer cells. Numerous cancer drugs inhibit TR1, and this protein has been proposed as a target for cancer therapy. We previously reported that reduction of TR1 levels in cancer cells reversed many malignant characteristics suggesting that deficiency in TR1 function is antitumorigenic. The molecular basis for TR1’s role in cancer development, however, is not understood. Herein, we found that, among selenoproteins, TR1 is uniquely overexpressed in …

Shear Stress Induced Mtor Signaling In Cultured A7r5 Aortic Smooth Muscle Cell Line, Sriram Prasad Mupparaju

Theses, Dissertations and Capstones

Vascular intervention procedures such as balloon angioplasty and stent implantation lead to denudation of endothelium exposing the underlying smooth muscle layer to effects of blood shear stress. The effect of shear stress on smooth muscle cell signaling has not been studied in depth. In this study, we examined time dependent changes in activation of Akt, mTOR and p70S6k related signaling in response to orbital shear stress on cultured A7r5 cells. A7r5 cells cultured to subconfluence on 150mm culture dishes were subjected to orbital shear of 9.8dynes/cm 2 for zero, 5 min, 15 min, 30 min, 1h, 4h and 24h. The …

Physical Characteristics Of An Individual: The Identification Of Biomarkers For Biological Age Determination, Michelle Alvarez

Electronic Theses and Dissertations

It is now a matter of routine for the forensic scientist to obtain the genetic profile of an individual from DNA recovered from a biological stain deposited at a crime scene. Potential contributors of the stain must either be known to investigators (i.e. a developed suspect) or the questioned profile must be searched against a database of DNA profiles such as those maintained in the CODIS National DNA database. However, in those instances where there is no developed suspect and no match is obtained after interrogation of appropriate DNA databases, the DNA profile per se presently provides no meaningful information …

Glutamate Excitotoxicity In Epilepsy And Ischemia, Mangala Meenakshi Soundarapandian

Electronic Theses and Dissertations

'Excitotoxicity' represents the excitatory amino acid mediated degeneration of neurons. Glutamate is the major excitatory neurotransmitter in the brain. Glutamate excitotoxicity has been implicated in a number of neurodegenerative disorders like Stroke, Epilepsy, Alzheimer's disease and traumatic brain injury. This neurotoxicity is summed up by the 'glutamate hypothesis' which describes the cause of neuronal cell death as an excessive release of glutamate causing over excitation of the glutamate receptors and subsequent increase in influx of calcium leading to cell death. An effort to counteract this neurotoxicity has lead to the development of glutamate receptor antagonists that can effectively serve as …

Effect Of N-Halosucinimides On 5-, 7- And 5,7-8-Quinolinol Sulfonic Acids / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

8-Quinolinol 5-, 7- and 5,7-sulfonic acids were treated with N-halosuccinimides (NXS) where the halogen atom was chlorine, bromine or iodine under different conditions of solvent, temperature and time. Under neutral or basic conditions the sulfonic acid group was retained while in dilute acid the S03H group was largely displaced by halogen. Excess NXS caused additional electrophilic substitution. Mild hydrolysis of 5-iodo-8-quinolinol- 7-sulfonic acid and 7-iodo-8-quinolinol-5-sulfonic acid with 15% sulfuric acid in acetic acid formed the 5- and 7-iodo-8-quinolinol respectively in high yield

Lim Kinase 1 Modulates Expression Of Matrix Metalloproteinases And Associates With Gamma-Tubulin: Dual Role In Invasion And Mito, Tenekua Tapia

Electronic Theses and Dissertations

LIM kinase 1 (LIMK1) is a unique dual specificity serine/threonine kinase containing two N-terminal LIM domains in tandem, a PDZ domain and a C-terminal catalytic domain. LIMK1 is involved in modulation of actin cytoskeleton through inactivating phosphorylation of the ADF (actin depolymerization factor) family protein cofilin. Recent studies have shown that LIMK1 is upregulated in breast and prostate cancer cells and tissues, promotes metastasis in animals and induces acquisition of an invasive phenotype when ectopically expressed in benign prostate epithelial (BPH) cells. Furthermore, overexpression of LIMK1 was associated with altered sub cellular localization of the membrane type 1 matrix metalloprotease …

Helical Packing Regulates Structural Transitions In Bax, Nuska Tschammer

Electronic Theses and Dissertations

Apoptosis is essential for development and the maintenance of cellular homeostasis and is frequently dysregulated in disease states. Proteins of the BCL-2 family are key modulators of this process and are thus ideal therapeutic targets. In response to diverse apoptotic stimuli, the pro-apoptotic member of BCL-2 family, BAX, redistributes from the cytosol to the mitochondria or endoplasmic reticulum and primes cells for death. The structural changes that enable this lethal protein to transition from a cytosolic form to a membrane-bound form remain poorly understood. Elucidating this process is a necessary step in the development of BAX as a novel therapeutic …

Retrocyclin Rc-101 Overcomes Cationic Mutations On The Heptad Repeat 2 Of Hiv-1 Gp41, Christopher Fuhrman

Electronic Theses and Dissertations

Retrocyclin RC-101, a θ-defensin with lectin-like properties, potently inhibits infection by many HIV-1 subtypes by binding to the heptad repeat (HR)-2 region of gp41 and preventing six-helix bundle formation. In the present study, we used in silico computational exploration to identify residues of HR2 that interacted with RC-101 and then analyzed the HIV-1 Sequence Database at LANL for residue variations in the HR1 and HR2 segments that could plausibly impart in vivo resistance. Docking RC-101 to gp41 peptides in silico confirmed its strong preference for HR2 over HR1, and implicated residues crucial for its ability to bind HR2. We mutagenized …

Biosynthesis Of Selenocysteine On Its Trna In Eukaryotes, Xue-Ming Xu, Bradley A. Carlson, Heiko Mix, Yan Zhang, Kazima Saira, Richard S. Glass, Marla J. Berry, Vadim Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

Selenocysteine (Sec) is cotranslationally inserted into protein in response to UGA codons and is the 21st amino acid in the genetic code. However, the means by which Sec is synthesized in eukaryotes is not known. Herein, comparative genomics and experimental analyses revealed that the mammalian Sec synthase (SecS) is the previously identified pyridoxal phosphate-containing protein known as the soluble liver antigen. SecS required selenophosphate and Ophosphoseryl- tRNA ^[Ser]Sec as substrates to generate selenocysteyl-tRNA ^[Ser]Sec. Moreover, it was found that Sec was synthesized on the tRNA scaffold from selenide, ATP, and serine using tRNA ^[Ser]Sec, seryl-tRNA synthetase, Ophosphoseryl- tRNA …

Enhancing Fertiliser Use Efficiency For Transplanted Vegetables, Dennis Phillips, Aileen Reid, Gavin D'Adhemar

Horticulture research reports

Horticulture Australia (HAL) Project No. VG04018.

Project VG 04018 ‘Enhancing fertiliser use efficiency for transplanted vegetables’ showed that spraying highly concentrated solutions containing nitrogen over newly transplanted vegetable seedlings for between 14 and 21 days after planting can increase marketable yields by as much as 300% compared to other methods of fertiliser application. Crops that this method has been successfully tested on in this study by the W.A. Department of Agriculture and Food include iceberg and Cos lettuce, broccoli, cauliflower, Chinese cabbage (wombok), celery and cabbage.

The research was conducted on virgin sandy soils of the Swan Coastal Plain near …

The Effects Of Trivalent Arsenicals And Thioredoxin Reductase Inhibitors On Selenium Metabolism In Lung Cell Culture Models, Sarah Ryann Talbot

Electronic Theses and Dissertations

Arsenic exposure, through various routes, is associated with the development of cancer of the skin, lung, liver, kidney, and bladder. Treatment of cells in culture with trivalent arsenicals has been shown to increase reactive oxygen species (ROS). In particular, monomethylarsonous acid (MMAIII), a trivalent metabolite of arsenite, is highly cytotoxic and possibly carcinogenic. Three trivalent arsenicals; arsenite, arsenic trioxide (ATO), and MMAIII, are also known inhibitors of the selenoprotein thioredoxin reductase (TrxR). Selenium, an essential micronutrient in mammals, is needed in the form of selenocysteine for activity of this enzyme and other selenoproteins. TrxR is part of a key component …

Strokes Of Existence: The Connection Of All Things, Mari Gorman

Graduate Student Publications and Research

Acted or real—and all life is real whether one is acting or not—the common denominator and consistent, ubiquitous reality of life and all behavior is that it manifests in the form of relationships on all scales. But what is a relationship? Until now, the answer to this question has not been sufficiently known. As a result of many years of empirical research that began with the aim of discovering what is going on in a gifted actor when s/he is playing a character that can be observed and experienced as a living, intuitive being, and based on the knowledge that …

Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha

Faculty Publications, Chemistry

Insertion of hydrophobic groups in a silica matrix, by addition of propyl- or trifluoropropyltrimethoxysilane, leads to a surprising increase in the helical content of apomyoglobin following encapsulation by the sol–gel technique

Characterization Of Power Induced Heating And Damage In Fiber Optic Probes For Near-Field Scanning Optical Microscopy, Nicholas E. Dickenson, E. S. Erickson, O. L. Mooren, R. C. Dunn

Chemistry and Biochemistry Faculty Publications

Tip-induced sample heating in near-field scanning optical microscopy (NSOM) is studied for fiber optic probes fabricated using the chemical etching technique. To characterize sample heating from etched NSOM probes, the spectra of a thermochromic polymer sample are measured as a function of probe output power, as was previously reported for pulled NSOM probes. The results reveal that sample heating increases rapidly to ~55–60°C as output powers reach ~50 nW. At higher output powers, the sample heating remains approximately constant up to the maximum power studied of ~450 nW. The sample heating profiles measured for etched NSOM probes are consistent with …

A New N-Terminal Recognition Domain In Caveolin-1 Interacts With Sterol Carrier Protein-2 (Scp-2), Rebecca D. Parr, Gregory G. Martin, Heather A. Hostetler, Megan E. Schroeder, Kiran D. Mir, Ann B. Kier, Judith M. Ball, Friedhelm Schroeder

Faculty Publications

Although plasma membrane domains, such as caveolae, provide an organizing principle for signaling pathways and cholesterol homeostasis in the cell, relatively little is known regarding specific mechanisms, whereby intracellular lipid-binding proteins are targeted to caveolae. Therefore, the interaction between caveolin-1 and sterol carrier protein-2 (SCP-2), a protein that binds and transfers both cholesterol and signaling lipids (e.g., phosphatidylinositides and sphingolipids), was examined by yeast two-hybrid, in vitro binding and fluorescence resonance energy transfer (FRET) analyses. Results of the in vivo and in vitro assays identified for the first time the N-terminal amino acids (aa) 1−32 amphipathic α helix of SCP-2 …

A Model Of Dna Knotting And Linking, Erica Flapan, Dorothy Buck

Pomona Faculty Publications and Research

We present a model of how DNA knots and links are formed as a result of a single recombination event, or multiple rounds of (processive) recombination events, starting with an unknotted, unlinked, or a (2,m)-torus knot or link substrate. Given these substrates, according to our model all DNA products of a single recombination event or processive recombination fall into a single family of knots and links.

Emissions From Forest Fires Near Mexico City, Robert J. Yokelson, S. P. Urbanski, E. L. Atlas, D. W. Toohey, E. C. Alvarado, J. D. Crounse, P. O. Wennberg, M. E. Fisher, C. E. Wold, T. L. Campos, K. Adachi, P. R. Buseck, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

The emissions of NOx (defined as NO (nitric oxide) + NO2 (nitrogen dioxide)) and hydrogen cyanide (HCN), per unit amount of fuel burned, from fires in the pine forests that dominate the mountains surrounding Mexico City (MC) are about 2 times higher than normally observed for forest burning. The ammonia (NH3) emissions are about average for forest burning. The upper limit for the mass ratio of NOx to volatile organic compounds (VOC) for these MC-area mountain fires was similar to 0.38, which is similar to the NOx/VOC ratio in the MC urban area emissions inventory of 0.34, but much larger …

The Tropical Forest And Fire Emissions Experiment: Overview And Airborne Fire Emission Factor Measurements, Robert J. Yokelson, T. Karl, Paulo Artaxo, Donald R. Blake, Ted J. Christian, David W. T. Griffith, Alex Guenther, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

The Tropical Forest and Fire Emissions Experiment (TROFFEE) used laboratory measurements followed by airborne and ground based field campaigns during the 2004 Amazon dry season to quantify the emissions from pristine tropical forest and several plantations as well as the emissions, fuel consumption, and fire ecology of tropical deforestation fires. The airborne campaign used an Embraer 110B aircraft outfitted with whole air sampling in canisters, mass-calibrated nephelometry, ozone by UV absorbance, Fourier transform infrared spectroscopy (FTIR), and proton-transfer mass spectrometry (PTR-MS) to measure PM(10), O(3), CO(2), CO, NO, NO(2), HONO, HCN, NH(3), OCS, DMS, CH(4), and up to 48 non-methane …

Wide Diversity In Structure And Expression Profiles Among Members Of The Caenorhabditis Elegans Globin Protein Family, David Hoogewijs, Eva Geuens, Sylvia Dewilde, Andy Vierstraete, Luc Moens, Serge Vinogradov, Jacques R. Vanfleteren

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

The emergence of high throughput genome sequencing facilities and powerful high performance bioinformatic tools has highlighted hitherto unexpected wide occurrence of globins in the three kingdoms of life. In silico analysis of the genome of C. elegans identified 33 putative globin genes. It remains a mystery why this tiny animal might need so many globins. As an inroad to understanding this complexity we initiated a structural and functional analysis of the globin family in C. elegans.

Results

All 33 C. elegans putative globin genes are transcribed. The translated sequences have the essential signatures of single domain bona fide …

Resistance Of The Target Islet Tissue To Autoimmune Destruction Contributes To Genetic Susceptibility In Type 1 Diabetes., Natasha J. Hill, Aleksandr Stotland, Michelle Solomon, Patrick Secrest, Elizabeth Getzoff, Nora Sarvetnick

Journal Articles: Regenerative Medicine

Type 1 diabetes occurs when self-reactive T lymphocytes destroy the insulin-producing islet beta cells of the pancreas. The defects causing this disease have often been assumed to occur exclusively in the immune system. We present evidence that genetic variation at the Idd9 diabetes susceptibility locus determines the resilience of the targets of autoimmunity, the islets, to destruction. Susceptible islets exhibit hyper-responsiveness to inflammatory cytokines resulting in enhanced cell death and increased expression of the death receptor Fas. Fas upregulation in beta cells is mediated by TNFR2, and colocalization of TNFR2 with the adaptor TRAF2 in NOD beta cells is altered. …

“Carbachol Regulation Of Erk And The Transcription Factor Elk-1 In Mcf-7 Breast Cancer Cells, John M. Schmitt, Andrea Wagner

Faculty Publications - Department of Biological & Molecular Science

Abstract Cancer has numerous molecular, biochemical and physiological hallmarks including uncontrolled cell growth and proliferation. Previous studies on MCF-7 breast cancer cells have shown that both intracellular calcium levels and the extracellular signal-regulated protein kinase (ERK) is activated downstream of the G-protein coupled receptor (GPCR) agonist, carbachol. Calcium/calmodulin regulate the calcium/calmodulin-dependent kinase (CaM Ks) family of proteins that have been proposed to regulate ERK and transcription. Our goal was to determine the mechanism of carbachol activation on ERK and the transcription factor Elk-1 in MCF-7 cells. Our results suggest that 10 μM carbachol treatment of MCF-7 cells triggers ERK1/2 phosphorylation …

Beta-Lactamase: An Ideal Reporter System For Monitoring Gene Expression In Live Eukaryotic Cells, Sohail A. Qureshi

Department of Biological & Biomedical Sciences

To gain insightful information about the mechanisms through which genes are activated and repressed requires gene reporter systems that are sensitive, robust, and cost-effective. Although numerous reporter gene technologies are commercially available, none are as sophisticated and user-friendly as beta-lactamase (BLA) when it comes to studying gene expression in live cells. This article presents an overview of the BLA technology and describes how it can be exploited for studying rare events such as homologous recombination in somatic cells and be used to deliver any DNA sequence of choice anywhere within the genome.

Pathways Of Anaerobic Carbon Cycling Across An Ombrotrophic–Minerotrophic Peatland Gradient, Jason K. Keller, Scott D. Bridgham

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatland soils represent globally significant stores of carbon, and understanding carbon cycling pathways in these ecosystems has important implications for global climate change. We measured aceticlastic and autotrophic methanogenesis, sulfate reduction, denitrification, and iron reduction in a bog, an intermediate fen, and a rich fen in the Upper Peninsula of Michigan for one growing season. In 3-d anaerobic incubations of slurried peat, denitrification and iron reduction were minor components of anaerobic carbon mineralization. Experiments using 14C-labeled methanogenic substrates showed that methanogenesis in these peatlands was primarily through the aceticlastic pathway, except early in the growing season in more ombrotrophic peatlands, …

Isolation, Characterization, And Degradation Of Bakuchiol From Psoralidium Tenuiflorum, Pei-Jan Hsu

Theses, Dissertations and Culminating Projects

Bioactivity guided fractionation of the EtOAc extract from Psoralidium tenuiflorum afforded the known compound bakuchiol as a racemic mixture. This compound was purified by liquid-liquid partitions and chromatographic techniques followed by characterization with ]H NMR, 13C NMR, and GCMS which agreed with previous literature. Previously, bakuchiol was reported from Psoralea corylirolia and Posoralea glandulosa in nature which are from the same family as P. tenuiflorum. This compound exhibited Staphylococcus epidermidis cytotoxicity.

Two Dimensional NMR (HHCOSY and HETCOR) of bakuchiol indicated a disagreement with the previously described NMR structural assignment; a reassignment is described herein.

Long-term storage followed by attempted reisolation …

The Effect Of 1,25-Dihydroxy Vitamin D3 On At1 Cell Receptor Expression In Human Iliac Artery Endothelial Cells (Hiaec), Jenny Thomas

Theses and Dissertations

The renin-angiotensin system (RAS) plays an important part in homeostasis through angiotensin IPs role as a vasoconstrictor. Defects in the renin angiotensin system can lead to hypertension, heart attack, and stroke (Weir, 1999). Studies have shown an inverse relationship between Vitamin D3 and blood pressure (Li et al., 2002). While studies have been performed on vitamin D's effect on renin expression, little is known about vitamin D's effect on the angiotensin II high-affinity type 1 (ATi) receptor. The hypothesis for this study was that human iliac artery endothelial cells (HIAEC) supplemented with 1,25-dihydroxy vitamin D3 will express less AT] receptor …