Biochemistry, Biophysics, and Structural Biology Commons^™

Extracullular Atp Regulates Il-1beta Release From Microglial Cells Via Purinergic Receptor After In Vitro Trauma, Chengya Liang

Electronic Theses and Dissertations

Traumatic brain injury (TBI) induces a state of microglialactivation, which includes upregulation of macrophage functions and release inflammatory mediators such as certain inflammatory cytokines. Current literature suggests that interleukin-1Beta is an important cytokine mediator, which is dramatically increased after brain injury. Previous studies indicate that ATP is released by traumatically injured astrocytes and serves as a cell-to-cell mediator through purinergic receptors after in vitro injury. However, the mechanism of interleukin-1Beta release after traumatic brain injury remains poorly defined and is difficult to study using in vivo models. Using an in vitro model for traumatic brain injury (cell strain or stretch), …

An Investigation Into The Effects Of Structural Isomers Of Salicylic Acid On Propionibacterium Acnes, Ireland Burch

Capstone Research Projects

Acne is caused when the sebaceous glands in the skin are unable to secrete an oily substance, called sebum, onto the surface of the skin. This is because the opening of the follicle is clogged from a mixture of skin cells and sebum. The opening of the follicle becomes plugged when the cells from the lining of the follicle are shed too quickly and clump together. Because Propionibacterium acnes (P. acnes) bacteria feed off sebum, they are then able to grow in the plugged follicle. Acne is caused by the inflammation that results from the chemicals and enzymes produced from …

Isolation Ofphosphoglucose Isomerase From Peas, Tyler Dubs

Capstone Research Projects

No abstract provided.

Synergistic Mixtures Of Fungitoxic Monochloro And Dichloro-8-Quinolinols Against Five Fungi / Herman Gershon, Muriel Gershon, & Donald D. Clarke Harding Laboratory, The New York Botanical Garden, Bronx, Ny 10458-5126, Usa; Department Of Chemistry, Fordham University, Bronx, Ny 10458-9993, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

Fourteen mono- and dichloro-8-quinolinols were tested against five fungi (Aspergillus niger, A. oryzae, Myrothecium verrucaria, Trichoderma viride, and Mucor circinelloides) and compared with the fungitoxicity of 8- quinolinol in Yeast Nitrogen Base containing l% D-glucose and 0.088% L-asparagine. All of the compounds were more fungitoxic than 8-quinolinol except for the surprising activity of 8-quinolinol against A. oryzae. Mixtures of the MICs of monochloro- and dichloro-8-quinolinols in which the halogens were in different positions of the quinoline ring showed synergism. Comparable mixtures in which one position of each compound was occupied by the same halogen showed additive activity. In a different …

Intravenous 2-Deoxy-D-Glucose Injection Rapidly Elevates Levels Of The Phosphorylated Forms Of P44/42 Mitogen-Activated Protein Kinases (Extracellularly Regulated Kinases 1/2) In Rat Hypothalamic Parvicellular Paraventricular Neurons, Arshad Khan, Alan Watts

Selected Works Temporary Series

No abstract provided.

Distributions Of Z-Dna And Nuclear Factor I In Human Chromosome 22: A Model For Coupled Transcriptional Regulation, P. Christoph Champ, Sandor Maurice, Jeff Vargason, Tracy Camp, P. Shing Ho

Faculty Publications - Department of Biological & Molecular Science

An analysis of the human chromosome 22 genomic sequence shows that both Z-DNA forming regions (ZDRs) and promoter sites for nuclear factor-I (NFI) are correlated with the locations of known and predicted genes across the chromosome and accumulate around the transcriptional start sites of the known genes. Thus, the occurrence of Z-DNA across human genomic sequences mirrors that of a known eukaryotic transcription factor. In addition, 43 of the 383 fully annotated chromosomal genes have ZDRs within 2 nucleosomes upstream of strong NFIs. This suggests a distinct class of human genes that may potentially be transcriptionally regulated by a mechanism …

Development Of A Gene Transfer System In Clostridium Scindens Vpi 12708, Rashmi Ramasubbaiah

Masters Theses & Specialist Projects

Clostridium scindens VPI 12708 (previously known as Eubacterium sp. VPI 12708) is a bile-acid dehydroxylating bacterium originally isolated from the feces of a colon cancer patient. Many genes required for bile acid 7-a dehydroxylation are found on a large bile acid inducible operon (bai) that has been extensively studied. However the bai promoter, which directs expression of the bai operon, has yet to be characterized due, in part, to a lack of a functional genetic transfer system for this strain. A spontaneous rifampinresistant Clostridium scindens VPI 12708 mutant was used as a recipient to determine the efficacy of conjugation as …

Quantitative Non-Isotopic Nitrocellulose Filter Binding Assays: Bacterial Mnsod-Dna Interactions, Joshua D. Czerwinski, David P. Mascotti

Chemistry

No abstract provided.

Investigating Fluctuating Asymmetry Of The Larval Damselfly, Calopteryx Maculata (Odonata: Calopterigidae), Edward Kelliher

Undergraduate Review

Fluctuating asymmetry (FA), or subtle random deviations from perfect bilateral symmetry, has recently become a useful tool in allowing researchers to understand more about an organism's health, fitness, developmental stability and environmental stressors. Ultimately, FA studies can be used as an indirect measurement of the quality of an aquatic system over time. We measured and examined the femur segments of the larval damselfly, Calopteryx maculata from sites on the Town, Hockomock, and Salisbury Plain Rivers, of Plymouth County, Massachusetts to determine FA levels. After accounting for measurement error, preliminary results show that variations in symmetry are not correlated to individual …

Identification Of Phosphorylase Kinase Alpha Subunit Binding Partners In Skeletal Muscle, Soleil Archila

Masters Theses & Specialist Projects

IDENTIFICATION OF PHOSPHORYLASE KINASE ALPHA SUBUNIT BINDING PARTNERS IN SKELETAL MUSCLE Soleil Archila August 2004 67 Pages Directed by: Nancy A. Rice, Sigrid Jacobshagen, and Claire A. Rinehart Department of Biology Western Kentucky University Phosphorylase kinase (PhK) integrates neural, hormonal, and metabolic signals in skeletal muscle to tightly regulate glycogen breakdown and energy production. Structurally, PhK is among the largest and most complex kinases known with a stoichiometry of (αβγδ)4 and a mass of 1.3x106 Da. The catalytic γ subunit is allosterically controlled through alterations in quaternary structure initiated by the regulatory α, β and δ subunits. In this study …

Evaluation Of Multiple Models To Distinguish Closely Related Forms Of Disease Using Dna Microarray Data: An Application To Multiple Myeloma, Johanna S. Hardin, Michael Waddell, C. David Page, Fenghuang Zhan, Bart Barlogie, John Shaughnessy, John J. Crowley

Pomona Faculty Publications and Research

Motivation: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are caused by inherited or acquired genetic mutations that manifest themselves in altered gene expression patterns in the clonally related cancer cells. Microarray technology allows for qualitative and quantitative measurements of the expression levels of thousands of genes simultaneously, and it has now been used both to classify cancers that are morphologically indistinguishable and to predict response to therapy. It is …

Actr/Aib1 Functions As An E2f1 Coactivator To Promote Breast Cancer Cell Proliferation And Antiestrogen Resistance, Maggie C. Louie, June X. Zou, Alina Rabinovich, Hong-Wu Chen

Collected Faculty Scholarship

Overexpression or amplification of ACTR (also named AIB1, RAC3, p/CIP, TRAM-1, and SRC-3), a member of the p160 family of coactivators for nuclear hormone receptors, has been frequently detected in multiple types of human tumors, including breast cancer. However, its role in cancer cell proliferation and the underlying mechanism are unclear. Here, we show that overexpression of ACTR not only enhances estrogen-stimulated cell proliferation but also, more strikingly, completely negates the cell cycle arrest effect by tamoxifen and pure antiestrogens. Unexpectedly, we found that ACTR directly interacts, through its N-terminal domain, with E2F1 and is recruited to E2F target gene …

Intravenous 2-Deoxy-D-Glucose Injection Rapidly Elevates Levels Of The Phosphorylated Forms Of P44/42 Mitogen-Activated Protein Kinases (Extracellularly Regulated Kinases 1/2) In Rat Hypothalamic Parvicellular Paraventricular Neurons, Khan, Alan Watts

Departmental Papers (Biology)

No abstract provided.

Hospital Universitario, “La Paz”, Madrid, Spain, Michael G. Zeece, Gautam Sarath, John P. Markwell, N. Palmer, J. Steckelberg, J. Schultz

Gautam Sarath Publications

RATIONALE: Proteomic technology has been shown to have distinct advantages for allergen characterization and identification. Therefore, we have used 2-D electrophoresis and protein microarrays to characterize the profile of allergens and assess their level in lentils.

METHODS: Lentil varieties were extracted and centrifuged to obtain 2S, 7S and 11S fractions. The profile of IgE-binding proteins in these fractions was assessed using lentil-allergic sera, by immunoblotting of 2-D electrophoretic separations. The level of IgE-binding was also assessed using protein microarrays. Arrays of covalently attached proteins were first incubated with lentil-allergic sera, followed by incubation with fluorescently- labeled anti-IgE detection antibody. Laser-induced …

Integrated Allosteric Regulation In The S. Cerevisiae Carbamylphosphate Synthetase – Aspartate Transcarbamylase Multifunctional Protein, Valã©Rie Serre, Bernadette Penverne, Jean-Luc Souciet, Serge Potier, Hedeel Guy, David Evans, Patrick Vicart, Guy Hervã©

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

The S. cerevisiae carbamylphosphate synthetase – aspartate transcarbamylase multifunctional protein catalyses the first two reactions of the pyrimidine pathway. In this organism, these two reactions are feedback inhibited by the end product UTP. In the present work, the mechanisms of these integrated inhibitions were studied.

Results

The results obtained show that the inhibition is competitive in the case of carbamylphosphate synthetase and non-competitive in the case of aspartate transcarbamylase. They also identify the substrate whose binding is altered by this nucleotide and the step of the carbamylphosphate synthetase reaction which is inhibited. Furthermore, the structure of the domains …

Survival Of Mycobacterium Avium Subspecies Paratuberculosis In The Pol, John Rumsey

Electronic Theses and Dissertations

Mycobacterium avium subspecies paratuberculosis (map) is an intracellular pathogen that is known to parasitize macrophages and monocytes. Map infiltrates gastrointestinal tract host tissue where it is the known etiological agent of johne's disease in ruminants and implicated in the etiology of crohn's disease in humans. Map's ability to survive within macrophages enables it to disseminate throughout the rest of the host, possibly infecting other circulating blood leukocytes. In this study, the survival and fate of map strain atcc 43015 (human isolate) following phagocytosis was determined using in vitro murine macrophage cell line j774a.1 and polymorphonuclear cells (pmnc's) from five crohn's …

Can Martian Life Exist Under Dry Conditions?, Michael Kendrick

Inquiry: The University of Arkansas Undergraduate Research Journal

Recently, we have begun to hear more and more about news coming from Mars. With the recent confirmation of evidence of liquid water in Mars' past, evidence indicating liquid water in Mars' present, and as many missions planned for this decade and the next than have successfully reached the planet in the last 40 years, life on Mars is beginning to become a more relevant issue in our study of the planet. Although there have been no indications of multicellular life on Mars, there may be a possibility of microbial life in the subsurface. Since it appears that all of …

Characterization Of Protein Prenyltransferases And Protein Prenylation In Plasmodium Falciparum, Thiago Gaspar Dasilva

Electronic Theses and Dissertations

Malaria kills at least one million people each year, mostly children - a death every 30 seconds. Almost one half of the world population is at risk from malaria. Antimalarial drugs are the only means for the treatment of about 500 million annual global malaria cases. Because of prevalent drug-resistance it is extremely urgent to identify new drug targets. Many proteins involved in eukaryotic signal transduction and cell cycle progression undergo post-translational lipid modification by a prenyl group. Protein prenyltransferases, which catalyze the post-translational prenyl modification, have been established as a target for anticancer therapy. Research done in our laboratory …

Phosphorylation Of Vesicular Stomatitis Virus Phosphoprotein P Is Indispensable For Virus Growth†, Subash C. Das, Asit K. Pattnaik

School of Veterinary and Biomedical Sciences: Faculty Publications

The phosphoprotein (P) of vesicular stomatitis virus (VSV) is an essential subunit of the viral RNAdependent RNA polymerase (RdRp) complex. It is phosphorylated at two different domains. Using defective interfering (DI) RNA or minigenomic RNA templates, we previously demonstrated that phosphorylation within the amino-terminal domain I is essential for transcription, whereas phosphorylation within the carboxyterminal domain II is necessary for replication. For the present study, we examined the role of the phosphorylation of residues in these domains in the life cycle of VSV. Various mutant P coding sequences were inserted into a full-length cDNA clone of VSV, and the virus …

Interactions Between Small Heat Shock Protein Subunits And Substrate In Small Heat Shock Protein-Substrate Complexes, Kenneth L. Friedrich, Kim C. Giese, Nicole R. Baun, Elizabeth Vierling

Department of Biochemistry: Faculty Publications

Small heat shock proteins (sHSPs) are dynamic oligomeric

proteins that bind unfolding proteins and protect

them from irreversible aggregation. This binding results

in the formation of sHSP-substrate complexes from

which substrate can later be refolded. Interactions between

sHSP and substrate in sHSP-substrate complexes

and the mechanism by which substrate is transferred to

ATP-dependent chaperones for refolding are poorly defined.

We have established C-terminal affinity-tagged

sHSPs from a eukaryote (pea HSP18.1) and a prokaryote

(Synechocystis HSP16.6) as tools to investigate these issues.

We demonstrate that sHSP subunit exchange for

HSP18.1 and HSP16.6 is temperature-dependent and

rapid at the optimal growth …

Methionine Sulfoxide Reductase Regulation Of Yeast Lifespan Reveals Reactive Oxygen Species-Dependent And -Independent Components Of Aging, Ahmet Koc, Audrey P. Gasch, Julian C. Rutherford, Hwa-Young Kim, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Aging is thought to be caused by the accumulation of damage, primarily from oxidative modifications of cellular components by reactive oxygen species (ROS). Here we used yeast methionine sulfoxide reductases MsrA and MsrB to address this hypothesis. In the presence of oxygen, these antioxidants could increase yeast lifespan and did so independent of the lifespan extension offered by caloric restriction. However, under ROS-deficient, strictly anaerobic conditions, yeast lifespan was shorter, not affected by MsrA or MsrB, and further reduced by caloric restriction. In addition, we identified changes in the global gene expression associated with aging in yeast, and they did …

The Identity Of Proteins Associated With A Small Heat Shock Protein During Heat Stress In Vivo Indicates That These Chaperones Protect A Wide Range Of Cellular Functions, Eman Basha, Garrett J. Lee, Linda A. Breci, Andrew C. Hausrath, Nicole R. Baun, Kim C. Giese, Elizabeth Vierling

Department of Biochemistry: Faculty Publications

The small heat shock proteins (sHSPs) are a ubiquitous

class of ATP-independent chaperones believed to

prevent irreversible protein aggregation and to facilitate

subsequent protein renaturation in cooperation

with ATP-dependent chaperones. Although sHSP chaperone

activity has been studied extensively in vitro, understanding

the mechanism of sHSP function requires

identification of proteins that are sHSP substrates in

vivo. We have used both immunoprecipitation and affinity

chromatography to recover 42 proteins that specifically

interact with Synechocystis Hsp16.6 in vivo during

heat treatment. These proteins can all be released from

Hsp16.6 by the ATP-dependent activity of DnaK and cochaperones

and are heat-labile. …

Theoretical Neuroscience: Modeling The Activation Mechanism Of Potassium Channels In Neurons, Kevin Twedt

Presidential Scholars Theses (1990 – 2006)

We have modeled the electrostatic interaction between the S4 segment of the potassium channel molecule and the surrounding water molecules on both the intracellular and extracellular sides of the neural axon cell membrane. Two methods were used to approximate this interaction: (i) a macroscopic evaluation in which the water was treated as a dielectric medium with dielectric constant 80; (ii) a microscopic evaluation considering the effects of each individual water molecule fixed in position within the water pockets surrounding the S4 segment. The potential energy of the S4 due to the water pockets was plotted against the rotation of the …

Influence Of Short-Term Variations In Food On Survival Of Crassotrea Gigas Larvae: A Modeling Study, Eric N. Powell, Eleanor A, Bochenek, John M. Klinck, Eileen E. Hofmann

OES Faculty Publications

A biochemically-based model was developed to simulate the growth, development, and metamorphosis of larvae of the Pacific oyster, Crassostrea gigas. The model defines larvae in terms of their protein, lipid, carbohydrate, and ash content and includes variation in growth efficiency and egg quality to better simulate cohort population dynamics. Changes in tissue composition occur as the larva grows and in response to the biochemical composition of the food. The premise behind this modeling study was that certain periods of larval life are more critical than others with respect to the availability of food and that food quality is as …

The Effects Of Cucurbitacin E And Genistein In Mcf-7 Breast Cancer Cells, Angela Carlson

The Journal of Undergraduate Research

No abstract provided.

Activation Kinetics Of Skinned Cardiac Muscle By Laser Photolysis Of Nitrophenyl-Egta, Hunter Martin, Marcus G. Bell, Graham C. Ellis-Davis, Robert J. Barsotti

PCOM Scholarly Works

The kinetics of Ca2+-induced contractions of chemically skinned guinea pig trabeculae was studied using laser photolysis of NP-EGTA. The amount of free Ca2+ released was altered by varying the output from a frequency-doubled ruby laser focused on the trabeculae, while maintaining constant total [NP-EGTA] and [Ca2+]. The time courses of the rise in stiffness and tension were biexponential at 23°C, Ph 7.1, and 200 Mm ionic strength. At full activation (pCa < 5.0), the rates of the rapid phase of the stiffness and tension rise were 56 ± 7 s-1 (n = 7) and 48 ± 6 s-1 (n = 11) while the amplitudes were 21 ± 2 and 23 ± 3%, respectively. These rates had similar dependencies on final [Ca2+] achieved by photolysis: 43 and 50 s-1 per Pca unit, respectively, over a range of [Ca2+] producing from 15% to 90% of maximal isometric tension. At all [Ca2+], the rise in stiffness initially was faster than that of tension. The maximal rates for the slower components of the rise in stiffness and tension were 4.1 ± 0.8 and 6.2 ± 1.0 s-1. The rate of this slower phase exhibited significantly less Ca2+ sensitivity, 1 and 4 s-1 per Pca unit for stiffness and tension, respectively. These data, along with previous studies indicating that the force-generating step in the cross-bridge cycle of cardiac muscle is marginally sensitive to [Ca2+], suggest a mechanism of regulation in which Ca2+ controls the attachment step in the cross-bridge cycle via a rapid equilibrium with the thin filament activation state. Myosin kinetics sets the time course for the rise in stiffness and force generation with the biexponential nature of the mechanical responses to steps in [Ca2+] arising from a shift to slower cross-bridge kinetics as the number of strongly bound cross-bridges increases.

Effects Of Sham Air And Cigarette Smoke On A549 Lung Cells: Implications For Iron-Mediated Oxidative Damage, Jonathan J. Mayo, Pete Kohlhepp, Dianzheng Zhang, Joy J. Winzerling

PCOM Scholarly Works

Inhalation of airborne pollution particles that contain iron can result in a variety of detrimental changes to lung cells and tissues. The lung iron burden can be substantially increased by exposure to cigarette smoke, and cigarette smoke contains iron particulates, as well as several environmental toxins, that could influence intracellular iron status. We are interested in the effects of environmental contaminants on intracellular iron metabolism. We initiated our studies using lung A549 type II epithelial cells as a model, and we evaluated the effects of iron dose and smoke treatment on several parameters of intracellular iron metabolism. We show that …

Molecular Cloning And Characterization Of Two Mouse Peroxisome Proliferator-Activated Receptor Alpha (Ppara) Regulated Peroxisomal Acyl-Coa Thioesterases., Maria Westin, Mary Hunt, Stefan Alexson

Articles

Peroxisomes are organelles that function in the b-oxidation of very-long and long-chain acyl-CoAs, bile acid-CoA intermediates, prostaglandins, leukotrienes, thromboxanes, dicarboxylic fatty acids, pristanic acid and xenobiotic carboxylic acids. The very long- and long-chain acyl-CoAs are mainly chain-shortened and then transported to mitochondria for further metabolism. We have now identified and characterized two peroxisomal acyl- CoA thioesterases, named PTE-Ia and PTE-Ic, which hydrolyze acyl-CoAs to the free fatty acid and coenzyme A. PTE-Ia and PTE-Ic show 82% sequence identity at amino acid level and a putative peroxisomal type 1 targeting signal of –AKL was identified at the carboxy-terminal end of both …

Stimulation Of Capacitative Calcium Entry In Hl-60 Cells By Nanosecond Pulsed Electric Fields, Jody A. White, Peter F. Blackmore, Karl H. Schoenbach, Stephen J. Beebe

Bioelectrics Publications

Nanosecond pulsed electric fields (nsPEFs) are hypothesized to affect intracellular structures in living cells providing a new means to modulate cell signal transduction mechanisms. The effects of nsPEFs on the release of internal calcium and activation of calcium influx in HL-60 cells were investigated by using real time fluorescent microscopy with Fluo-3 and fluorometry with Fura-2. nsPEFs induced an increase in intracellular calcium levels that was seen in all cells. With pulses of 60 ns duration and electric fields between 4 and 15 kV/cm, intracellular calcium increased 200-700 nM, respectively, above basal levels (similar to100 nM), while the uptake of …

Computational Protein Biomarker Prediction: A Case Study For Prostate Cancer, Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.

Mathematics & Statistics Faculty Publications

Background: Recent technological advances in mass spectrometry pose challenges in computational mathematics and statistics to process the mass spectral data into predictive models with clinical and biological significance. We discuss several classification-based approaches to finding protein biomarker candidates using protein profiles obtained via mass spectrometry, and we assess their statistical significance. Our overall goal is to implicate peaks that have a high likelihood of being biologically linked to a given disease state, and thus to narrow the search for biomarker candidates.

Results: Thorough cross-validation studies and randomization tests are performed on a prostate cancer dataset with over 300 patients, obtained …