Biochemistry, Biophysics, and Structural Biology Commons^™

Mechanisms Of Cell Death Initiated In Herpes Simplex Virus Thymidine Kinase Expressing Colon Tumor Cells Treated With Ganciclovir And Ucn-01, Christina Elizabeth Ahn

Theses and Dissertations in Biomedical Sciences

Metastatic colon carcinoma is the second leading cause of death from malignancy in the United States, and development of more effective treatments is essential. Heterologous expression of Herpes Simplex Virus Thymidine Kinase (HSVtk) in combination with the prodrug, ganciclovir (GCV), has shown great promise for the genetic therapy of many cancers, but most patients have had only a partial or minimal response to the therapy. After screening a panel of two drug combinations, our laboratory has shown that the combination of GCV and the protein kinase inhibitor UCN-01 (7-hydroxystaurosporine) enhances tumor cell death more effectively than either drug alone. However …

Alterations In Uterine And Placental Sodium Pump Abundance May Contribute To The Onset Of Mouse Labor, Carlos Jacob Vance

Theses and Dissertations

Objective: Reductions in sodium pump (SP) abundance can give rise to increases in contractile force in uterine and vascular smooth muscle as well as an increased secretion in secretory cells, including potentially those of the placenta. To determine whether the mouse might serve as a model for human pregnancy in terms of the SP and to determine whether changes in SP abundance anticipate or follow labor, we studied pregnant mice over the final trimester of their pregnancy.

Study Design: C57Bl6 dams (n=46) were bred and studied during their pregnancy. Animals (n=4) were sacrificed at specific gestational time points. Other mice …

The Microbial Selenoproteome Of The Sargasso Sea, Yan Zhang, Dmitri E. Fomenko, Vadim Gladyshev

Vadim Gladyshev Publications

Background: Selenocysteine (Sec) is a rare amino acid which occurs in proteins in major domains of life. It is encoded by TGA, which also serves as the signal for termination of translation, precluding identification of selenoprotein genes by available annotation tools. Information on full sets of selenoproteins (selenoproteomes) is essential for understanding the biology of selenium. Herein, we characterized the selenoproteome of the largest microbial sequence dataset, the Sargasso Sea environmental genome project.
Results: We identified 310 selenoprotein genes that clustered into 25 families, including 101 new selenoprotein genes that belonged to 15 families. Most of these proteins were predicted …

Ion Transmission In The First Vacuum Stage Of An Inductively Coupled Plasma Mass Spectrometer, Jeffrey Harris Macedone

Theses and Dissertations

The inductively coupled plasma mass spectrometer (ICP-MS) is the instrument of choice for trace and ultra-trace elemental analysis. However, the ICP-MS suffers from matrix effects. Matrix effects occur when instrument response varies as the composition of the sample matrix is changed. Matrix effects, or non-spectroscopic interferences, limit the accuracy of routine analysis. Identification of the sources of matrix effects provide a basis for reducing or eliminating them. As inaccuracies in the ICP-MS are more severe than those in the ICP atomic emission spectrometer, the problem may be due, at least in part, to the vacuum interface used to couple the …

Nucleic Acid Sequencing Using Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.

Clean, High-Yield Preparation Of S,S- And R,S- Amino Acid Isosteres, Aslam A. Malik, Todd E. Clement, Hasan Palandoken, James Robinson Iii, Joy A. Stringer

Chemistry and Biochemistry

The present invention provides compounds and methods that can be used to convert the intermediate halomethyl ketones (HMKs), e.g., chloromethyl ketones, to the corresponding S,S- and R,S-diastereomers. More particularly, the present invention provides: (1) reduction methods; (2) inversion methods; and (3) methods involving the epoxidation of alkenes. Using the various methods of the present invention, the R,S-epoxide and the intermediary compounds can be prepared reliably, in high yields and in high purity.

Um34 In Selenocysteine Trna Is Required For The Expression Of Stress-Related Selenoproteins In Mammals, Bradley A. Carlson, Xue-Ming Xu, Vadim N. Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

Selenium is an essential micronutrient in the diet of mammals and has many health benefits. Selenium-containing proteins are responsible for most, if not all, of these benefits. This element is incorporated into protein as selenocysteine (Sec), the 21^st amino acid in the genetic code. There are two species of Sec tRNA in mammalian cells that differ by a single 2’-O-hydroxymethyl group on the ribosyl moiety at position 34 (Um34). The relationship between this modification and selenoprotein synthesis was examined in mice in which the wild type Sec tRNA gene was replaced with a mutant Sec tRNA transgene incapable of …

Variability In Lipid Profile Before And After Coronary Artery Bypass Grafting (Cabg), M Perwaiz Iqbal, Hasanat Mohammad Sharif, Naseema Mehboobali

Department of Biological & Biomedical Sciences

Objective: To investigate changes in total cholesterol, low density lipoprotein (LDL) cholesterol, high density lipoprotein (HDL) cholesterol, and triglycerides in serum of Pakistani patients before, immediately after and 5 days post CABG.
Method: Serum samples from 31 consecutive Pakistani angina patients undergoing CABG at the Aga Khan University Hospital were analyzed for total cholesterol, LDL cholesterol, HDL cholesterol and triglycerides using kit methods.
Results: Immediately after CABG, there is a significant decline in the mean levels of serum cholesterol, LDL cholesterol, HDL cholesterol and triglycerides. However, 5 days post CABG, there is a significant increase in the concentrations of total …

Arabidopsis Atspl14, A Plant-Specific Sbp-Domain Transcription Factor, Participates In Plant Development And Sensitivity To Fumonisin B1, Julie M. Stone, Xinwen Liang, Emily R. Nekl, Justin J. Stiers

Department of Biochemistry: Faculty Publications

The recessive Arabidopsis thaliana fumonisin B1-resistant (fbr6) mutant was identified by its ability to survive in the presence of a programmed cell death (PCD)-inducing fungal toxin FB1. The fbr6 mutant also displays altered plant architecture in the absence of FB1, most notably elongated petioles and enhanced leaf margin serration. These phenotypes are a result of a T-DNA insertion in the SQUAMOSA promoter binding protein (SBP) domain gene, AtSPL14. AtSPL14 encodes a plant-specific protein with features characteristic of a transcriptional regulator, including a nuclear localization signal sequence, a plant-specific DNA binding domain (the SBP box), and a protein …

Selective Rescue Of Selenoprotein Expression In Mice Lacking A Highly Specialized Methyl Group In Selenocysteine Trna, Bradley A. Carlson, Xue-Ming Xu, Vadim N. Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

Selenocysteine (Sec) is the 21st amino acid in the genetic code. Its tRNA is variably methylated on the 2’-Ohydroxyl site of the ribosyl moiety at position 34 (Um34). Herein, we identified a role of Um34 in regulating the expression of some, but not all, selenoproteins. A strain of knock-out transgenic mice was generated, wherein the Sec tRNA gene was replaced with either wild type or mutant Sec tRNA transgenes. The mutant transgene yielded a tRNA that lacked two base modifications, N⁶- isopentenyladenosine at position 37 (i⁶A37) and Um34. Several selenoproteins, including glutathione peroxidases 1 and 3, …

5-Ht1b Receptor-Mediated Presynaptic Inhibition Of Gaba Release In The Suprachiasmatic Nucleus, Jayne R. Bramley, Patricia J. Sollars, Gary E. Pickard, F. Edward Dudek

School of Veterinary and Biomedical Sciences: Faculty Publications

The suprachiasmatic nucleus (SCN) receives a dense serotonergic innervation that modulates photic input to the SCN via serotonin 1B (5-HT_1B) presynaptic receptors on retinal glutamatergic terminals. However, the majority of 5-HT_1B binding sites in the SCN are located on nonretinal terminals and most axonal terminals in the SCN are GABAergic. We therefore tested the hypothesis that 5-HT_1B receptors might also be located on SCN GABAergic terminals by examining the effects of the highly selective 5-HT_1B receptor agonist CP-93,129 on SCN miniature inhibitory postsynaptic currents (mIPSCs). Whole cell patch-clamp recordings of mIPSCs were obtained from rat …

Temperature Dependence Of The Double Layer Capacitance For The Restricted Primitive Model Of An Electrolyte Solution From A Density Functional Approach, Douglas Henderson, J. Reszko-Zygmunt, Stefan Sokolowski, Dezso Boda

Faculty Publications

We apply a different version of the density functional theory, given by Pizio, Patrykiejew, and Sokolowski [J. Chem. Phys. 121, 11957 (2004)], for a nonuniform restricted primitive model of an electrolyte solution to evaluate the temperature dependence of the capacitance of an electric double layer. We show that this theory is capable of reproducing the computer simulation data at a quantitative level. In particular, the reversal of the temperature dependence of the capacitance at low temperatures is predicted. This phenomenon has been difficult to predict from theory. Further, this theory also leads to an accurate description of the double layer …

Preparation Of 2s,3s-N-Isobutyl-N-(2-Hydroxy-3-Amino-4-Phenylbutyl)-P-Nitrobenzenesulfonylamide Hydrochloride And Other Derivatives Of 2-Hydroxy-1,3-Diamines, Aslam A. Malik, Hasan Palandoken, Joy A. Stringer, Roland P. Carlson, John Leach, Thomas G. Archibald, Robert G. Miotke

Chemistry and Biochemistry

The present invention provides a new process for the preparation of 2S,3S-N-isobutyl-N-(2-hydroxy-3-amino-4phenylbutyl)- p-nitrobenzenesulfonylamide hydrochloride, wherein this compound is prepared directly from the chloromethylalcohol. Importantly, the process of the present invention results in higher yields of 2S,3S-N-isobutyl-N-(2hydroxy -3 -amino -4-phenylbutyl) -pnitrobenzenesulfonylamide hydrochloride without sacrificing its purity. The processes of the present invention can be used to prepare not only the 2S,3S-derivative, but also the 2R,3S-, 2S,2R- and the 2R,3R-derivatives.

Two Crystal Structures Of Dihydrofolate Reductase-Thymidylate Synthase From Cryptosporidium Hominis Reveal Protein–Ligand Interactions Including A Structural Basis For Observed Antifolate Resistance, Amy C. Anderson

Dartmouth Scholarship

Cryptosporidium hominis is a protozoan parasite that causes acute gastro- intestinal illness. There are no effective therapies for cryptosporidiosis, highlighting the need for new drug-lead discovery. An analysis of the protein ligand interactions in two crystal structures of dihydrofolate reductase- thymidylate synthase 􏰀DHFR-TS) from C. hominis, determined at 2.8 and 2.87 AÊ resolution, reveals that the interactions of residues Ile29, Thr58 and Cys113 in the active site of C. hominis DHFR provide a possible structural basis for the observed antifolate resistance. A comparison with the structure of human DHFR reveals active-site differences that may be exploited for the design of …

Biochemical Screening For The Prediction Of Preeclampsia, Dileep Kumar Rohra, Nazia Qidwai

Department of Biological & Biomedical Sciences

No abstract provided.

Novel Protein-Protein Interactions Regulate The Proteolytic Activity Of The Pro- Apoptotic Serine Protease, Omi/Htra2, Supriya Singh

Electronic Theses and Dissertations

Omi/HtrA2 is a mitochondrial serine protease with high homology to the bacterial HtrA proteins. Omi promotes caspase-dependent apoptosis by binding and degrading IAPs-inhibitor of apoptosis proteins. Omi can also induce caspase-independent apoptosis but the actual mechanism is still unknown. IAP's are not the only substrates cleaved by Omi. There are at least two more known substrates of Omi, the HAX-1 and the ped/pea-15 proteins. HS1-associated protein X-1 (HAX-1) is a mitochondrial protein, degraded by Omi after induction of caspase-dependent apoptosis. Ped/pea-15 is also an anti-apoptotic protein and is cleaved by Omi after induction of caspase-independent apoptosis. The proteolytic activity of …

The Effects Of Arsenic On Selenoprotein Biosythesis, Fanta Konate

Electronic Theses and Dissertations

Arsenic contamination of drinking water is a real public health problem in certain areas of South-East Asia where chronic exposure has been correlated to higher rates of lung, skin, bladder, kidney, and liver cancer. Although arsenic carcinogenicity is well established, the mechanism by which it induces cancer is poorly understood. Recent evidence suggests that oxidative stress could be a possible mechanism for the carcinogenic effects of arsenic. Selenium, in the form of selenocysteine, is necessary for the activity of several enzymes with a role in the defense against reactive oxygen species (ROS), primarily thioredoxin reductases (TrxR) and glutathione peroxidases (Gpx). …

Appendix C. Physical Measurements And Chemical Analyses Of China Lake Water Quality, Problems In Environmental Science Course (Biology 493), Colby College, Colby Environmental Assessment Team, Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

A Watershed Analysis Of China Lake, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

The Colby Environmental Assessment Team (CEAT) investigated the water quality of China Lake, located in China and Vassalboro Maine, from June through December 2005. The group analyzed physical, chemical, and biological water quality parameters from samples taken on China Lake and from tributaries flowing into the lake. An analysis of land use patterns, especially the impact of residential, commercial, municipal, and institutional development in this watershed, enabled CEAT to study their impact on water quality trends. Data collected by CEAT in 2005 were compared to historic data from the Maine Department of Environmental Protection (MDEP) to gain a historical perspective …

Shoreline Survey Pictures Group 2, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

Rachel Road Survey Pictures Group 8, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

Greg Road Survey Pictures, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

Stream Pictures, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

China Lake Ejbg Road Survey Pictures, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

China Lake Asjb Road Survey Pictures 2005-2006, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

A Watershed Analysis Of China Lake [Presentation], Problems In Environmental Science Course (Biology 493), Colby College, Colby Environmental Assessment Team, Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

China Lake Area Pictures, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

Summer Pictures 2005, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: China Lake (2005, 1989)

No abstract provided.

Real Time Rt-Pcr For Direct Detection Of Viable Mycobacterium Avium Subspecies Paratuberculosis In Chron's Disease Patients And Association Of Map Infection With Downregulation In Interferon-Gamma Receptor (Infg1) Gene In Crohn's Disease Patients, Mounir Chehtane

Electronic Theses and Dissertations

Association of Mycobacterium avium subspecies paratuberculosis (MAP) with Crohn's disease (CD) and not with ulcerative colitis (UC), two forms of inflammatory bowel disease (IBD), has been vigorously debated in recent years. This theory has been strengthened by recent culture of MAP from breast milk, intestinal tissue and Blood from patients with active Crohn's disease. Culture of MAP from clinical samples remained challenging due to the fastidious nature of MAP including its lack of cell wall in infected patients. The advent of real time PCR has proven to be significant in infectious disease diagnostics. In this study, real time reverse transcriptase …

Expression Of Hepatitis C Viral Non-Structural 3 Antigen In Transgenic Chloroplasts, Anubhuti Bhati

Electronic Theses and Dissertations

Hepatitis C viral infection is the major cause of acute hepatitis and chronic liver disease and remains the leading cause of liver transplants (NIH). An estimated 180 million people are infected globally (WHO). There is no vaccine available to prevent hepatitis C. The treatment with antiviral drugs is expensive, accompanied with various side effects and is limited only to those at risk of developing advanced liver disease. The treatment is also effective in only about 30% to 50% of treated patients and still a high percentage of patients are resistant to therapy. Therefore, there is an urgent need for the …