Biochemistry, Biophysics, and Structural Biology Commons^™

Capillary Liquid Chromatography Using Micro Size Particles, Yanqiao Xiang

Theses and Dissertations

High speed and/or high efficiency separations can be realized using small particles (~ 1 µm) in liquid chromatography (LC). However, due to the large pressure drop caused by small particles, conventional LC pumping systems cannot satisfy the pressure requirements needed to drive the mobile phase through the column. Use of ultrahigh pressure, elevated temperature, or both can overcome these pressure limitations and allow the use of very small particles for high speed and/or high efficiency separations.

In this dissertation, the use of ultrahigh pressures with and without elevated temperatures in capillary LC is described. Very fast separations of various samples …

Flash Artifact Suppression In Two-Dimensional Ultrasound Imaging, Richard Yung Chiao, Gregory Ray Bashford, Mark Peter Feilen, Cynthia Andrews Owen

Biomedical Imaging and Biosignal Analysis Laboratory

Flash artifacts in ultrasound flow images are suppressed to achieve enhanced flow discrimination. Flash artifacts typically occur as region of elevated signal strength (brightness or equivalent color) within an image. A flash suppression algorithm included the steps of estimating the flash within an image and then suppressing the estimated flash. The mechanism for flash suppression is spatial filtering. An extension of this basic method used information from adjacent frames to estimate the flash and/or to smooth the resulting image sequence. Temporal information from adjacent frames is used as an adjunct to improve performance.

A High -Order Finite Difference Method For Solving Bioheat Transfer Equations In Three-Dimensional Triple -Layered Skin Structure, Haofeng Yu

Doctoral Dissertations

Investigations on instantaneous skin burns are useful for an accurate assessment of burn-evaluation and for establishing thermal protections for various purposes. Meanwhile, hyperthermia with radiation is important in the treatment of cancer, and it is essential for developers and users of hyperthermia systems to predict, and interpret correctly the biomass thermal and vascular response to heating. In this dissertation, we employ the well-known Pennes' bioheat transfer equation to predict the degree of skin burn and the temperature distribution in hyperthermia cancer treatment.

A fourth-order compact finite difference scheme is developed to solve Pennes' bioheat transfer equation in a three-dimensional single …

Activation Of The Phosphatidylinositol 3-Kinase/Akt Pathway Contributes To Survival Of Primary Epithelial Cells Infected With The Periodontal Pathogen Porphyromonas Gingivalis, Özlem Yilmaz, Thomas Jungas, Philippe Verbeke, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

Porphyromonas gingivalis, an important periodontal pathogen, infects primary gingival epithelial cells (GECs). Despite the large number of bacteria that replicate inside the GECs, the host cell remains viable. We demonstrate that P. gingivalis triggers rapid and reversible surface phosphatidylserine exposure through a mechanism requiring caspase activation. However, after 1 day of infection, the bacteria no longer induce phosphatidylserine externalization and instead protect infected cells against apoptosis. Infection exerts its effect at the level of mitochondria, as P. gingivalis also blocks depolarization of the mitochondrial transmembrane potential and cytochrome c release. Interestingly, protein kinase B/Akt is phosphorylated during infection, which can …

Hyaluronan Facilitates Invasion Of Colon Carcinoma Cells In Vitro Via Interaction With Cd44, Hyeong-Rok Kim, Marie A. Wheeler, Christopher M. Wilson, Joji Iida, David Eng, Melanie A. Simpson, James B. Mccarthy, Kelli M. Bullard

Department of Biochemistry: Faculty Publications

Hyaluronan (HA) and its biosynthetic enzymes, HA synthases (HAS1, 2, and 3) are thought to participate in cancer progression. We have shown previously that HA production and HAS3 expression are increased in metastatic colon carcinoma cells (SW620) when compared with cells isolated from a primary tumor (SW480). Because invasion of the extracellular matrix is a fundamental event in tumor growth and metastasis, we hypothesized that SW620 cells would show greater invasive capability than SW480 cells, that invasion is HA dependent, and that HA mediates invasion via interaction with a cell-surface receptor. Invasion into artificial basement membrane (Matrigel) was assessed in …

Energy-Landscape-Model Analysis For Irreversibility And Its Pulse-Width Dependence In Cells Subjected To A High-Intensity Ultrashort Electric Pulse, R. P. Joshi, Q. Hu, Karl H. Schoenbach, Stephen J. Beebe

Bioelectrics Publications

We provide a simple, but physical analysis for cell irreversibility and apoptosis in response to an ultrashort (nanosecond), high-intensity electric pulse. Our approach is based on an energy landscape model for determining the temporal evolution of the configurational probability function p(q). The primary focus is on obtaining qualitative predictions of a pulse width dependence to apoptotic cell irreversibility that has been observed experimentally. The analysis couples a distributed electrical model for current flow with the Smoluchowski equation to provide self-consistent, time-dependent transmembrane voltages. The model captures the essence of the experimentally observed pulse-width dependence, and provides a possible physical picture …

Involvement Of Thromboxane A2 And Tyrosine Kinase In The Synergistic Interaction Of Platelet Activating Factor And Calcium Ionophore A23187 In Human Platelet Aggregation, Huma Rasheed, Sheikh Arshad Saeed

Department of Biological & Biomedical Sciences

The present study was carried out to examine the mechanisms of the synergistic interaction of PAF and A23187 mediated platelet aggregation. We found that platelet aggregation mediated by subthreshold concentrations of PAF (5 nM) and A23187 (1 mM) was inhibited by PAF receptor blocker (WEB 2086, IC50 = 0.65 mM) and calcium channel blockers, diltiazem (IC50 = 13 mM) and verapamil (IC50 = 18 mM). Pretreatment of platelets with PAF and A23187 induced rise in intracellular calcium and this effect was also blocked by verapamil. While examining the role of the down stream signaling pathways, we found that platelet aggregation …

Melanoma Chondroitin Sulfate Proteoglycan Enhances Fak And Erk Activation By Distinct Mechanisms, Jianbo Yang, Matthew A. Price, Cheryl L. Neudauer, Christopher Wilson, Soldano Ferrone, Hong Xia, Joji Iida, Melanie A. Simpson, James B. Mccarthy

Department of Biochemistry: Faculty Publications

Melanoma chondroitin sulfate proteoglycan (MCSP) is an early cell surface melanoma progression marker implicated in stimulating tumor cell proliferation, migration, and invasion. Focal adhesion kinase (FAK) plays a pivotal role in integrating growth factor and adhesion-related signaling pathways, facilitating cell spreading and migration. Extracellular signal–regulated kinase (ERK) 1 and 2, implicated in tumor growth and survival, has also been linked to clinical melanoma progression. We have cloned the MCSP core protein and expressed it in the MCSP-negative melanoma cell line WM1552C. Expression of MCSP enhances integrin-mediated cell spreading, FAK phosphorylation, and activation of ERK1/2. MCSP transfectants exhibit extensive MCSP-rich microspikes …

Emissions From Miombo Woodland And Dambo Grassland Savanna Fires, Parikhit Sinha, Peter V. Hobbs, Robert J. Yokelson, Donald R. Blake, Song Gao, Thomas W. Kirschsetter

Chemistry and Biochemistry Faculty Publications

[1] Airborne measurements of trace gases and particles over and downwind of two prescribed savanna fires in Zambia are described. The measurements include profiles through the smoke plumes of condensation nucleus concentrations and normalized excess mixing ratios of particles and gases, emission factors for 42 trace gases and seven particulate species, and vertical profiles of ambient conditions. The fires were ignited in plots of miombo woodland savanna, the most prevalent savanna type in southern Africa, and dambo grassland savanna, an important enclave of miombo woodland ecosystems. Emission factors for the two fires are combined with measurements of fuel loading, combustion …

Thickness Dependence Of Magneto-Transport In Cu-Co Granular Thin Films, Jian Qing Wang, Ngocnga Dao, Ham H. Kim, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

This work explores the thickness dependence of magneto-transport properties in granular thin films with different thickness. These results are compared with silver-based film series studied earlier. It was observed that the thickness dependence of the GMReffect was sensitive to the surface chemistry of the films. The extraordinary Hall effect (EHE) in these films was measured and found to be different from the Ag-based system. In the Cu-based system, the EHE is a weak function of film thickness over the range studied. When the variation of the spontaneous magnetization is taken into account the effective EHE has a universal thickness dependence

Characterization Of Human Udp-Glucose Dehydrogenase: Cys-276 Is Required For The Second Of Two Successive Oxidations, Brandi J. Sommer, Joseph J. Barycki, Melanie A. Simpson

Department of Biochemistry: Faculty Publications

UDP-glucose dehydrogenase (UGDH) catalyzes two oxidations of UDP-glucose to yield UDP-glucuronic acid. Pathological overproduction of extracellular matrix components may be linked to the availability of UDP-glucuronic acid; therefore UGDH is an intriguing therapeutic target. Specific inhibition of human UGDH requires detailed knowledge of its catalytic mechanism, which has not been characterized. In this report, we have cloned, expressed, and affinity-purified the human enzyme and determined its steady state kinetic parameters. The human enzyme is active as a hexamer with values for K_m and V_max that agree well with those reported for a bovine homolog. We used crystal coordinates …

Velocity And Temperature Characterization Of The First Vacuum Stage Expansion In An Inductively Coupled Plasma - Mass Spectrometer, William Neil Radicic

Theses and Dissertations

The inductively coupled plasma - mass spectrometer (ICP-MS) is the analytical instrument of choice for trace element detection and quantification. Despite the popularity of ICP-MS, significant degradation in sensitivity and precision occurs as the result of matrix and instrument-induced effects. The sources of these effects are not well understood, characterized, or correlated to particular plasma operating condition settings or matrix compositions and involve both neutral and charged species. The purpose of this study is to characterize the behavior of metastable Ar (I) atom and Ca (II) ion through the measurement of Doppler velocities and fluorescence line width "temperatures."

For the …

Pv1 Is A Key Structural Component For The Formation Of The Stomatal And Fenestral Diaphragms, Radu V. Stan, Eugene Tkachenko, Ingrid R. Niesman

Dartmouth Scholarship

PV1 is an endothelial-specific integral membrane glycoprotein associated with the stomatal diaphragms of caveolae, transendothelial channels, and vesiculo-vacuolar organelles and the diaphragms of endothelial fenestrae. Multiple PV1 homodimers are found within each stomatal and fenestral diaphragm. We investigated the function of PV1 within these diaphragms and their regulation and found that treatment of endothelial cells in culture with phorbol myristate acetate (PMA) led to upregulation of PV1. This correlated with de novo formation of stomatal diaphragms of caveolae and transendothelial channels as well as fenestrae upon PMA treatment. The newly formed diaphragms could be labeled with anti-PV1 antibodies. The upregulation …

Evaluating The Contributions Of Desolvation And Base-Stacking During Translesion Dna Synthesis, Xuemei Zhang, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

DNA polymerases catalyze the insertion of a nucleoside triphosphate into the growing polymer chain using the template strand as a guide. Numerous factors such as hydrogen bonding interactions, base-stacking contributions, and desolvation play important roles in controlling the efficiency and fidelity of this process. We previously demonstrated that 5-nitro-indolyl-2′-deoxyriboside triphosphate, a non-natural nucleobase with enhanced base-stacking properties, was more efficiently inserted opposite a non-templating DNA lesion compared to natural templating nucleobases (E. Z. Reineks and A. J. Berdis, Biochemistry, 2004, 43, 393–404). The catalytic enhancement was proposed to reflect increased base-stacking interactions of the non-natural nucleobase with the polymerase and …

N9 Alkylation And Glycosylation Of Purines; A Practical Synthesis Of 2-Chloro-2'-Deoxyadenosine, Minghong Zhong

Theses and Dissertations

(a) The Robins reagent [2-acetamido-6-O-(diphenylcarbamoyl)purine] was utilized for glycosylation under Lewis acid conditions. Regioselectivity of glycosylation depends on the glycosyl donor and its 2-O- or 2-N-protecting group. Regioselective N9 glycosylation of 2-acetamido-6-O-(diphenylcarbamoyl)purine with problematic glucosamine has been accomplished by protecting the amino function as a phthalimido group with consequent stabilization of the oxocarbenium cation, and lowering the activation energy by introduction of trichloroacetimidate at the anomeric carbon.

(b) 6-Heteroaryl functions [6-(1,2,4-triazol-4-yl) and 6-(imidazol-1-yl)] were introduced into purine derivatives for regioselective N9 alkylation. The regiospecificity of alkylation mainly results from steric effects due to the coplanar conformation of the two linked …

The Importance Of A Critical Protonation State And The Fate Of The Catalytic Steps In Class A Β-Lactamases And Penicillin-Binding Proteins, Dasantila Golemi-Kotra, Samy O. Meroueh, Choonkeun Kim, Sergei B. Vakulenko, Alexey Bulychev, Ann J. Stemmler, Timothy L. Stemmler, Shahriar Mobashery

Biochemistry and Molecular Biology Faculty Publications

b-Lactamases and penicillin-binding proteins are bacterial enzymes involved in antibiotic resistance to b-lactam antibiotics and biosynthetic assembly of cell wall, respectively. Members of these large families of enzymes all experience acylation by their respective substrates at an active-site serine as the first step in their catalytic activities. A Ser-X-X-Lys sequence motif is seen in all these proteins and crystal structures demonstrate that the side chain functions of the serine and lysine are in contact with one another. Three independent methods were used in this report to address the question of the protonation state of this important lysine (Lys73) in the …

Pcr And 16s Rdna Sequencing For Identifying And Comparing Gram-Negative Bacteria, Molly Truax

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber

Faculty Publications

n- and p-type Ge nanowires were synthesized by a multistep process in which axial elongation, via vapor–liquid–solid (VLS) growth, and doping were accomplished in separate chemical vapor deposition steps. Intrinsic, single-crystal, Ge nanowires prepared by Au nanocluster-mediated VLS growth were surface-doped in situ using diborane or phosphine, and then radial growth of an epitaxial Ge shell was used to cap the dopant layer. Field-effect transistors prepared from these Ge nanowires exhibited on currents and transconductances up to 850 µA/µm and 4.9 µA/V, respectively, with device yields of >85%.

Increased Levels Of Erythrocyte Glutathione In Acute Myocardial Infarction: An Antioxidant Defence, M P. Iqbal, M Ishaq, N Mehboobali

Department of Biological & Biomedical Sciences

Objective: Glutathione (GSH) has a central role in the defence against oxidative damage. This study was carried out to investigate any change in erythrocyte GSH levels in a population of patients with acute myocardial infarction (AMI) and compare them with levels in normal healthy subjects.
Method: GSH levels were determined in erythrocytes of one hundred and seventy six patients with AMI (age: 30-70 years; 131 males and 45 females) admitted to the National Institute of Cardiovascular Diseases, Karachi. These levels were compared with eryrocyte GSH levels obtained from 95 normal healthy subjects (controls).
Results: Mean +/- SD erythrocyte GSH levels …

The Prokaryotic Selenoproteome, Gregory V. Kryukov, Vadim N. Gladyshev

Vadim Gladyshev Publications

In the genetic code, the UGA codon has a dual function as it encodes selenocysteine (Sec) and serves as a stop signal. However, only the translation terminator function is used in gene annotation programs, resulting in misannotation of selenoprotein genes. Here, we applied two independent bioinformatics approaches to characterize a selenoprotein set in prokaryotic genomes. One method searched for selenoprotein genes by identifying RNA stem–loop structures, selenocysteine insertion sequence elements; the second approach identified Sec/Cys pairs in homologous sequences. These analyses identified all or almost all selenoproteins in completely sequenced bacterial and archaeal genomes and provided a view on the …

Role Of Iron In The Mechanism Of Asbestos-Induced Apoptosis In Human Lung And Pleural Target Cells, Aleksander Baldys

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Occupational exposure to asbestos has been associated with increased incidence of pulmonary interstitial fibrosis, mesothelioma of the pleura, and bronchogenic carcinoma. Although the mechanism by which asbestos causes cancer remains unknown, iron associated with asbestos is thought to play a role in the pathogenic effects of fibers.

The aim of this research was to examine and compare the asbestos-induced signaling phenomena in relevant human lung and pleural target cells, and to determine the role of iron from asbestos fibers in these events. Exposure of human airway epithelial (A549) cells, human pleural mesothelial (MET5A) cells, and normal human small airway epithelial …

Association Study Of The Angiotensin-Converting Enzyme (Ace) Gene G2350a Dimorphism With Myocardial Infarction, M Perwaiz Iqbal, Saeed Mahmood, Naseema Mehboobali, Mohammad Ishaq, Tasnim Fatima, Saddiqa Parveen, Philippe Frossard

Department of Biological & Biomedical Sciences

The angiotensin converting enzyme (ACE) is a strong candidate gene for myocardial infarction (MI). Insertion-deletion dimorphism in intron 16 of this gene has been inconclusively found to be associated with it. Several new polymorphisms in the ACE gene have been identified and among these, a dimorphism in exon 17, ACE G2350A, has a significant effect on plasma ACE concentrations. To assess the value of genotyping the ACE G2350A dimorphism in a genetically homogeneous population, we carried out a case-control study of dimorphism G2350A for a putative association with MI among Pakistani nationals. We investigated a sample population of 370 Pakistanis, …

Identification Of An Il-17-Producing Nk1.1neg Inkt Cell Population Involved In Airway Neutrophilia, Paul B. Savage, Marie-Laure Michel, Alexandre Castro Keller, Christophe Paget, Masakazu Fujio, Francois Trottein, Chi-Huey Wong, Elke Schneider, Michael Dy, Maria C. Leite-De-Moraes

Faculty Publications

Invariant natural killer T (iNKT) cells are an important source of both T helper type 1 (Th1) and Th2 cytokines, through which they can exert beneficial, as well as deleterious, effects in a variety of inflammatory diseases. This functional heterogeneity raises the question of how far phenotypically distinct subpopulations are responsible for such contrasting activities. In this study, we identify a particular set of iNKT cells that lack the NK1.1 marker (NK1.1neg) and secrete high amounts of interleukin (IL)-17 and low levels of interferon (IFN)-{gamma} and IL-4. NK1.1neg iNKT cells produce IL-17 upon synthetic ({alpha}-galactosylceramide [{alpha}-GalCer] or PBS-57), as well …

Jnk Regulates Hipk3 Expression And Promotes Resistance To Fas-Mediated Apoptosis In Du 145 Prostate Carcinoma Cells, James Curtin, Thomas Cotter

Articles

Elevated endogenous JNK activity and resistance to Fas receptor-mediated apoptosis have recently been implicated in progression of prostate cancer and can promote resistance to apoptosis in response to chemotherapeutic drugs. In addition, JNK has been demonstrated to promote transformation of epithelial cells by increasing both proliferation and survival. Although numerous studies have reported a role for JNK in promoting Fas receptor-mediated apoptosis, there is a paucity in the literature studying the antiapoptotic function of JNK during Fas receptor-mediated apoptosis. Consequently, we have used the recently described specific JNK inhibitor SP600125 and RNA interference to inhibit endogenous JNK activity in the …

Fluorescence Detectors For Proteins And Toxic Heavy Metals, Uchenna Prince Paul

Theses and Dissertations

An inexpensive detector for proteins is described. The detection technique was based on two-photon excitation intrinsic protein fluorescence using a visible 532 nm diode-pumped nano laser as the excitation source. Proteins that exhibit intrinsic fluorescence must contain at least one tryptophan, tyrosine, or phenylalanine residue in their amino acid sequences. The detector was characterized and was found to have a detection limit of 4 micro-molar for tryptophan, 22 micro-molar for tyrosine and 500 micro-molar for phenylalanine. Bovine serum albumin, a serum protein with 3 tryptophan residues in its amino acid sequence was also used to characterize the detector. It was …

Analysis Of Clinically Important Compounds Using Electrophoretic Separation Techniques Coupled To Time-Of-Flight Mass Spectrometry, Zlatuse Durda Peterson

Theses and Dissertations

Capillary electrophoretic (CE) separations were successfully coupled to time-of-flight mass spectrometric (TOFMS) detection for the analysis of three families of biological compounds that act as mediators and/or indicators of disease, namely, catecholamines (dopamine, epinephrine, norepinephrine) and their O-methoxylated metabolites (3-methoxytyramine, norepinephrine, and normetanephrine), indolamines (serotonin, tryptophan, and 5-hydroxytryptophan), and angiotensin peptides. While electrophoretic separation techniques provided high separation efficiency, mass spectrometric detection afforded specificity unsurpassed by other types of detectors.

Both catecholamines and indolamines are present in body fluids at concentrations that make it possible for them to be determined by capillary zone electrophoresis coupled to TOFMS without employing any …

The C. Elegans Heterochronic Gene Lin-46 Affects Developmental Timing At Two Larval Stages And Encodes A Relative Of The Scaffolding Protein Gephyrin, A. S.-R. Pepper, Jill E. Mccane, Kevin Kemper, Dennis Au Yeung, Rosalind C. Lee, Victor Ambros, Eric G. Moss

Dartmouth Scholarship

The succession of developmental events in the C. elegans larva is governed by the heterochronic genes. When mutated, these genes cause either precocious or retarded developmental phenotypes, in which stage-specific patterns of cell division and differentiation are either skipped or reiterated, respectively. We identified a new heterochronic gene, lin-46, from mutations that suppress the precocious phenotypes caused by mutations in the heterochronic genes lin-14 and lin-28. lin-46 mutants on their own display retarded phenotypes in which cell division patterns are reiterated and differentiation is prevented in certain cell lineages. Our analysis indicates that lin-46 acts at a step immediately downstream …

Core Concepts In Biochemistry And Molecular Biology In An Integrated Mbbs Curriculum, M P. Iqbal

Department of Biological & Biomedical Sciences

No abstract provided.

Health Impacts Of Polychlorinated Biphenyls (Pcbs) In Aquatic Organisms, Marla Ann Fisher

Dissertations

Polychlorinated biphenyls (PCBs) are a major contaminant of global extent in water resources and aquatic biota. Due to its high lipid solubility, PCBs fail to be degraded and, therefore, continue to bioaccumulate throughout the environment and food chain. To determine the impact of PCBs on the immune system ofaged and juvenile Japanese medaka (Oryzias latipes), fish were injected with the coplanar PCB congener 126 and examined after 3 and 14 days. PCB 126 produced oxidative stress in both age groups of fish 14 days post-injection; however, juvenile medaka appeared more susceptible than aged fish. Humoral immunity, as determined by antibody …

A Subgroup Algorithm To Identify Cross-Rotation Peaks Consistent With Non-Crystallographic Symmetry, Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald

Dartmouth Scholarship

Molecular replacement (MR) often plays a prominent role in determining initial phase angles for structure determination by X-ray crystallography. In this paper, an efficient quaternion-based algorithm is presented for analyzing peaks from a cross-rotation function in order to identify model orientations consistent with proper non-crystallographic symmetry (NCS) and to generate proper NCS-consistent orientations missing from the list of cross-rotation peaks. The algorithm, CRANS, analyzes the rotation differences between each pair of cross-rotation peaks to identify finite subgroups. Sets of rotation differences satisfying the subgroup axioms correspond to orientations compatible with the correct proper NCS. The CRANS algorithm was first …