Molecular Genetics Commons^™

Coupling Coherence Distinguishes Structure Sensitivity In Protein Electron Transfer, Tatiana Prytkova, Igor V. Kurnikov, David Beratan

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates. This two-regime paradigm provides a unified description of electron transfer rates in 26 ruthenium-modified heme and blue-copper proteins, as well as in numerous photosynthetic proteins.

Evaluation Of Genetic Diversity In Wild Chironomid Populations Using Rapd And Hemoglobin Protein As Molecular Biomarkers, Virendrasinh N. Jadeja

Seton Hall University Dissertations and Theses (ETDs)

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Chlamydia Trachomatis Detection In Cervical Preservcyt Specimens From An Irish Urban Female Population, Helen Keegan, Fergus Ryan, Alison Malkin, M. Griffin, Helen Lambkin

Articles

Objective: The aim of this study was to determine the prevalence of cervical Chlamydia trachomatis infection by polymerase chain reaction (PCR) in urban women undergoing routine cervical cytological screening and to investigate the relationship with age, cytology, smoking status and concurrent human papillomavirus (HPV) infection. Methods: A total of 996 women (age range 16–69 years) attending general practitioners for routine liquid-based cervical smear screening in the Dublin area were recruited in the study of prevalence of C. trachomatis. Informed consent was obtained and liquid-based cytology (LBC) specimens were sent for cytological screening. DNA was extracted from residual LBC and tested …

Flavin Charge Transfer Transitions Assist Dna Photolyase Electron Transfer, Spiros S. Skourtis, Tatiana Prytkova, David Beratan

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

This contribution describes molecular dynamics, semi-empirical and ab-initio studies of the primary photo-induced electron transfer reaction in DNA photolyase. DNA photolyases are FADH−-containing proteins that repair UV-damaged DNA by photo-induced electron transfer. A DNA photolyase recognizes and binds to cyclobutatne pyrimidine dimer lesions of DNA. The protein repairs a bound lesion by transferring an electron to the lesion from FADH−, upon photo-excitation of FADH− with 350–450 nm light. We compute the lowest singlet excited states of FADH− in DNA photolyase using INDO/S configuration interaction, time-dependent density-functional, and time-dependent Hartree-Fock methods. The calculations identify the lowest singlet excited state of FADH− …

Alternative Exon Usage Selectively Determines Both Tissue Distribution And Subcellular Localization Of The Acyl-Coa Thioesterase 7 Gene Products., Mary Hunt, Sinead Greene, Kjell Hultenby, L. Thomas Svensson, Susanna Engberg, Stefan E H Alexson

Articles

Acyl-CoA thioesterases (ACOTs) catalyze the hydrolysis of acyl-CoAs to free fatty acids and coenzyme A. Recent studies have demonstrated that one gene named Acot7, reported to be mainly expressed in brain and testis, is transcribed in several different isoforms by alternative usage of first exons. Strongly decreased levels of ACOT7 activity and protein in both mitochondria and cytosol was reported in patients diagnosed with fatty acid oxidation defects, linking ACOT7 function to regulation of fatty acid oxidation in other tissues. In this study, we have identified five possible first exons in mouse Acot7 (Acot7a-e) and show that all five first …

An In Vitro Model Of Ovarian Cancer: Studying The Effects Of Talc And Pycnogenol®, Amber Renée Buz'zard

Loma Linda University Electronic Theses, Dissertations & Projects

Ovarian cancer is the sixth most common cancer and accounts for more deaths than any other cancer of the female reproductive system. The American Cancer Society has suggested that poor diet, talc and industrial pollutants may increase the risk of developing ovarian cancer. Talc is ubiquitous and concern is raised about its safety, role as a possible carcinogen and known ability to cause irritation and inflammation. Due to the silent nature of ovarian cancer, chemoprevention is a high priority. The most useful chemopreventive compounds will inhibit, delay or reverse carcinogenesis, and can be taken for long periods of time with …

The Fat Cadherin Acts Through The Hippo Tumor-Suppressor Pathway To Regulate Tissue Size, Maria Willecke, Fisun Hamaratoglu, Madhuri Kango-Singh, Ryan Udan, Chiao-Lin Chen, Chunyao Tao, Xinwei Zhang, Georg Halder

Biology Faculty Publications

Background: The Hippo tumor-suppressor pathway has emerged as a key signaling pathway that controls tissue size in Drosophila. Merlin, the Drosophila homolog of the human Neurofibromatosis type-2 (NF2) tumor-suppressor gene, and the related protein Expanded are the most upstream components of the Hippo pathway identified so far. However, components acting upstream of Expanded and Merlin, such as transmembrane receptors, have not yet been identified.

Results: Here, we report that the protocadherin Fat acts as an upstream component in the Hippo pathway. Fat is a known tumor-suppressor gene in Drosophila, and fat mutants have severely overgrown imaginal discs. We …

Lobe And Serrate Are Required For Cell Survival During Early Eye Development In Drosophila, Amit Singh, Xiao Shi, Kwang-Wook Choi

Biology Faculty Publications

Organogenesis involves an initial surge of cell proliferation, leading to differentiation. This is followed by cell death in order to remove extra cells. During early development, there is little or no cell death. However, there is a lack of information concerning the genes required for survival during the early cell-proliferation phase. Here, we show that Lobe (L) and the Notch (N) ligand Serrate (Ser), which are both involved in ventral eye growth, are required for cell survival in the early eye disc. We observed that the loss-of-ventral-eye phenotype in L or Ser mutants is due to …

The Role Of Mapks In B Cell Receptor-Induced Down-Regulation Of Egr-1 In Immature B Lymphoma Cells, Jiyuan Ke, Murali Gururajan, Anupam Kumar, Alan Simmons, Lilia Turcios, Ralph Lakshman Chelvarajan, David M. Cohen, David L. Wiest, John G. Monroe, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Cross-linking of the B cell receptor (BCR) on the immature B lymphoma cell line BKS-2 induces growth inhibition and apoptosis accompanied by rapid down-regulation of the immediate-early gene egr-1. In these lymphoma cells, egr-1 is expressed constitutively and has a prosurvival role, as Egr-1-specific antisense oligonucleotides or expression of a dominant-negative inhibitor of Egr-1 also prevented the growth of BKS-2 cells. Moreover, enhancement of Egr-1 protein with phorbol 12-myristate 13-acetate or an egr-1 expression vector rescued BKS-2 cells from BCR signal-induced growth inhibition. Nuclear run-on and mRNA stability assays indicated that BCR-derived signals act at the transcriptional level to …

Expression Of The Primary Carbohydrate Component Of The Bordetella Bronchiseptica Biofilm Matrix Is Dependent On Growth Phase But Independent Of Bvg Regulation, Yasuhiko Irie, Andrew Preston, Ming H. Yuk

Biology Faculty Publications

We previously showed that the Bvg virulence control system regulates biofilm formation in Bordetella bronchiseptica (Y. Irie, S. Mattoo, and M. H. Yuk, J. Bacteriol. 186:5692-5698, 2004). Analyses of the extracellular components of B. bronchiseptica biofilm matrix revealed that the major sugar component in the matrix was xylose, and linkage analysis indicated a majority of it to be in a 4-linked polymeric form. The production of xylose was independent of Bvg regulation but instead was dependent on bacterial growth phase. In addition, N-acetyl-glucosamine in the matrix was found to be important for the initial development of the biofilm. These …

Synergism Of Gingipains In Endothelial Cell Adhesion Disruption And Apoptosis, Shaun Michellee Sheets

Loma Linda University Electronic Theses, Dissertations & Projects

The presence of Porphyromonas gingivalisin the periodontal pocket and the high levels of gingipain activity detected in gingival crevicular fluid could implicate a role for gingipains in the destruction of the highly vascular periodontal tissue. To explore the effects of these proteases on endothelial cells, we exposed bovine coronary artery endothelial cells (BCAEC) and human microvascular endothelial cells (HMVEC) to gingipain-active extracellular protein preparations and/or purified gingipains from P. gingivalis. Treated cells exhibited a rapid loss of cell adhesion properties that was followed by apoptotic cell death. Cleavage of N- and VE-cadherin and integrin (31 was observed in immunoblots …

Evaluating Genetic Viability Of Pronghorn In Wind Cave National Park, Jonathan A. Jenks, Christopher N. Jacques, Jaret D. Sievers, Robert W. Klaver, R. Terry Bowyer, Daniel E. Roddy

The Prairie Naturalist

The pronghorn (Antilocapra americana) was reintroduced into Wind Cave National Park, South Dakota, in 1914 and thus, has inhabited the Park for almost a century. A decline in the population has raised concern for the continued existence of pronghorn inside Wind Cave National Park. Historically, pronghorn numbers reached greater than 300 individuals in the 1960's but declined to about 30 individuals by 2002. The primary objective of our study was to evaluate genetic characteristics of pronghorn to determine if reduced heterozygosity contributed to the decline of pronghorn in Wind Cave National Park. Microsatellite DNA was collected from 75 …

Membrane Organization And Multimeric Interactions Of The Aer Receptor In E. Coli, Divya Dashrathkumar Amin

Loma Linda University Electronic Theses, Dissertations & Projects

Escherichia coli swims toward niches ideal for generating maximum energy by monitoring the environment with the aerotaxis sensor, Aer. This receptor has an N-terminal PAS domain, which is a sensor module present in a variety of proteins from all kingdoms of life (including humans). To date, the mechanism of signaling from a PAS sensor domain to a single signaling receiver domain has not been resolved. In Aer, the PAS sensor is separated from the signaling region by a membrane anchor. Most "transmembrane prediction" programs forecast a single membrane span for this membrane anchor, but such a topology is inconsistent our …

Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome Structure At 1.5 A˚ And Cytochrome Interaction With Metal Complexes, Mrunalini Pattarkine, J J. Tanner, C A. Bottoms, Y H. Lee, Judy D. Wall

Faculty Works

The structure of the type I tetraheme cytochrome c3 from Desulfovibrio desulfuricans G20 was determined to 1.5 A˚ by X-ray crystallography. In addition to the oxidized form, the structure of the molybdate-bound form of the protein was determined from oxidized crystals soaked in sodium molybdate. Only small structural shifts were obtained with metal binding, consistent with the remarkable structural stability of this protein. In vitro experiments with pure cytochrome showed that molybdate could oxidize the reduced cytochrome, although not as rapidly as U(VI) present as uranyl acetate. Alterations in the overall conformation and thermostability of the metal-oxidized protein were investigated …

Cloning And Overexpression Of Imp/Osta, An Essential Escherichia Coli Outer Membrane Protein With A Possible Role In Lipid Transport, Leslie Lekatz

Honors Capstones

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

Influence Of Human Papillomavirus 16 E6 On Trail-Mediated Apoptosis, Theodore O. Garnett

Loma Linda University Electronic Theses, Dissertations & Projects

Viruses have developed sophisticated strategies to evade host defenses and facilitate the production and spread of progeny. HPV 16, whose immune evasion activities can contribute to cervical cancer, is a prime example of such a virus. In this study, we examined the influence of HPV 16 E6 on TRAIL-induced FADD-dependent and -independent pathways in two cellular models: HCT116 colon carcinoma cells and U2OS osteosarcoma cells. We show that transfection of the HPV 16 E6 oncogene into HCT116 cells provides protection from TRAIL-mediated apoptosis. Additionally, we demonstrate that the protection provided by E6 is dose-dependent because higher levels of E6 provide …

H2-M3-Restricted Cd8+ T Cells Are Not Required For Mhc Class Ib-Restricted Immunity Against Listeria Monocytogenes, Sarah E. F. D'Orazio, Christine A. Shaw, Michael N. Starnbach

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Studies using major histocompatibility complex (MHC)-Ia–deficient mice have shown that MHC-Ib–restricted CD8⁺ T cells can clear infections caused by intracellular pathogens such as Listeria monocytogenes. M3-restricted CD8⁺ T cells, which recognize short hydrophobic N-formylated peptides, appear to comprise a substantial portion of the MHC-Ib–restricted T cell response in the mouse model of L. monocytogenes infection. In this study, we isolated formyltransferase (fmt) mutant strains of L. monocytogenes that lacked the ability to add formyl groups to nascent polypeptides. These fmt mutant Listeria strains did not produce antigens that could be recognized by M3-restricted T …

Displacement Of Histones At Promoters Of Saccharomyces Cerevisiae Heat Shock Genes Is Differentially Associated With Histone H3 Acetylation, Tamara Y. Erkina, Alexander M. Erkine

Scholarship and Professional Work – COPHS

Chromatin remodeling at promoters of activated genes spans from mild histone modifications to outright displacement of nucleosomes in trans. Factors affecting these events are not always clear. Our results indicate that histone H3 acetylation associated with histone displacement differs drastically even between promoters of such closely related heat shock genes as HSP12, SSA4, and HSP82. The HSP12 promoter, with the highest level of histone displacement, showed the highest level of H3 acetylation, while the SSA4 promoter, with a lower histone displacement, showed only modest H3 acetylation. Moreover, for the HSP12 promoter, the level of acetylated H3 …

Overexpression And Purification Of The Oat (Avena Fatua) Protein Afn1 And Construction Of A Pmal/Afn1 Expression Plasmid, Tenzin D. Tsewang

Undergraduate Research Symposium (UGRS)

Abscisic acid (ABA) is an important phytohormone with regulatory roles in many physiological processes. ABA expression is induced by environmental stresses such as drought and it is known to be an inhibitor of seed germination. A wild oat (Avena fatua) called AFN1 has been hypothesized to initiate the early stages of germination as its mRNA accumulates in nondormant seed embryos during imbibition. The polypeptide sequence of AFN1 suggests that it is an ABA glucosyl transferase. Glucosylation by AFN1 and thereby inactivation of ABA could lead to seed germination. In order to understand the role of AFN1 in germination, an ample …

Characterization Of The Wheat Grain Pkaba1-Interacting Protein Tawd40, Natalie Wayne

Undergraduate Research Symposium (UGRS)

Abscisic acid (ABA)-mediated gene expression is a critical component of plant responses to this important hormone, which affects plant growth, development, and responses to environmental stresses. Plant responses to ABA are mediated by a number of factors including PKABA1, an ABA induced protein kinase involved in ABA-suppressed gene expression in cereal grains, and TaWD40, which has previously been shown to physically interact with PKABA1. A full-length 1.9 kb TaWD40 cDNA, CK210682, was sequenced as part of this project. Based on the deduced protein sequence, it is thought that TaWD40 may belong to the family of E3 ubiquitin ligases, possibly targeting …

Characterization Of 35 Microsatellite Loci In The Pacific Lion-Paw Scallop (Nodipecten Subnodosus) And Their Cross-Species Amplification In Four Other Scallops Of The Pectinidae Family, Ana M. Ibarra, Jessica Lynn Petersen, Thomas R. Famula, Bernie May

Department of Animal Science: Faculty Publications

Four microsatellite-enriched DNA libraries yielded 35 microsatellite loci from 100 primer pairs designed for Pacific lion-paw scallop, Nodipecten subnodosus. The number of alleles ranged from four to 28. Three of the 35 loci were not in Hardy–Weinberg equilibrium and linkage disequilibrium was found for one pair of loci. These microsatellites will be used to analyze the population structure of the species in Mexico’s Baja Peninsula to propose management strategies for scallop aquaculture development. Twenty-six primer pairs cross-amplified in Nodipecten nodosus, whereas none (Argopecten ventricosus) or few cross-amplified in the Argopecten species.

Generation And Characterization Of An Allelic Series Of Ets1 Gene Targeted Mice: Thymomegaly, Microsplenia And Defective Homeostatic Proliferation Of Peripheral Lymphocytes Of Ets1Δvii But Not Ets1s->A Mice, Frank O. Bartel

MUSC Theses and Dissertations

Ets1 is a member of the ETS transcription factor family with demonstrated roles in cell proliferation, migration, and survival. Alternative splicing of exon VII results in two distinct protein isoforms: full length Ets1 and Ets1ΔVII. These isoforms bear key distinctions regarding protein-protein interactions, DNA binding kinetics and transcriptional target specificity. Targeted disruption of both Ets1 isoforms (Ets1 null) in mice results in increased perinatal lethality, loss of detectable NK and NKT cell activity, and differentiation, proliferation and survival defects in B- and T-Iymphocytes. To further delineate the individual roles of Ets1 isoforms in vivo we have generated an allelic series …

Eye Development At The Houston "Fly Meeting", Amit Singh

Biology Faculty Publications

Meeting report: The 47th Annual Drosophila Research Conference or "Fly Meeting" took place at Houston, Texas, USA from March 29th- April 2nd, 2006, under the aegis of the Genetics Society of America. The Fly Meeting provides an excellent opportunity for fly researchers to present their work and to get a snapshot of recent developments and upcoming trends in their research field. The fruit fly, Drosophila melanogaster, is a very versatile model to study growth, patterning, neural development, evolution, systemetics and various other facets of biomedical science. The topics presented in the meeting covered a very broad spectrum of fly research. …

Empirical Analysis Of The Str Profiles Resulting From Conceptual Mixtures, David R. Paoletti, Travis E. Doom, Carissa M. Krane, Michael L. Raymer, Dan E. Krane

Biology Faculty Publications

Samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors can be challenging and associated uncertainties can have dramatic effects on the interpretation of testing results. Using an FBI genotypes dataset, containing complete genotype information from the 13 Combined DNA Index System (CODIS) loci for 959 individuals, all possible mixtures of three individuals were exhaustively and empirically computed. Allele sharing between pairs of individuals in the original dataset, a randomized dataset and datasets of generated cousins and siblings was evaluated as were the number of loci that were necessary to reliably …

Cpg Oligodeoxynucleotides Stimulate Cord Blood Mononuclear Cells To Produce Immunoglobulins., Cheri D Landers, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

CpG oligodeoxynucleotides (ODNs) stimulate adult B cells leading to cellular proliferation and immunoglobulin production. It is unknown if CpG-ODNs similarly stimulate neonatal human B cells. Neonates have immature immune responses and are poorly responsive to thymus independent antigens such as polysaccharides. We determined umbilical cord cells' response to CpG-ODNs. Adult and umbilical cord B cells produced similar amounts of IgM (adult 1371 +/- 352 vs. cord 1873 +/- 1084 ng/ml) in response to CpG-ODN stimulation. Although CpG-ODN was able to stimulate adult IgG and IgA production, cord cells produced less IgG (153 +/- 58 vs. 10 +/- 2.5 ng/ml) and …

Atypical Pkciota Contributes To Poor Prognosis Through Loss Of Apical-Basal Polarity And Cyclin E Overexpression In Ovarian Cancer, Astrid M. Eder, Xiaomei Sui, Daniel G. Rosen, Laura K. Nolden, Kwai Wa Cheng, John P. Lahad, Madhuri Kango-Singh, Karen H. Lu, Carla L. Warneke, Edward N. Atkinson, Isabelle Bedrosian, Khandan Keyomarsi, Wen-Lin Kuo, Joe W. Gray, Jerry C. P. Yin, Jinsong Liu, Georg Halder, Gordon B. Mills

Biology Faculty Publications

We show that atypical PKCι, which plays a critical role in the establishment and maintenance of epithelial cell polarity, is genomically amplified and overexpressed in serous epithelial ovarian cancers. Furthermore, PKCι protein is markedly increased or mislocalized in all serous ovarian cancers. An increased PKCι DNA copy number is associated with decreased progression-free survival in serous epithelial ovarian cancers. In a Drosophila in vivo epithelial tissue model, overexpression of persistently active atypical PKC results in defects in apical-basal polarity, increased Cyclin E protein expression, and increased proliferation. Similar to the Drosophila model, increased PKCι proteins levels are associated with …

C-Jun N-Terminal Kinase (Jnk) Is Required For Survival And Proliferation Of B-Lymphoma Cells, Murali Gururajan, Roger Chui, Anbu K. Karuppannan, Jiyuan Ke, C. Darrell Jennings, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Several primary murine and human B lymphomas and cell lines were found to constitutively express high levels of the activated form of c-jun N-terminal kinase (JNK), a member of the mitogen-activated protein (MAP) kinase family. Proliferation of murine B lymphomas CH31, CH12.Lx, BKS-2, and WEHI-231 and the human B lymphomas BJAB, RAMOS, RAJI, OCI-Ly7, and OCI-Ly10 was strongly inhibited by SP600125, an anthrapyrazolone inhibitor of JNK, in a dose-dependent manner. The lymphoma cells underwent apoptosis and arrested at the G2/M phase of cell cycle. Furthermore, JNK-specific small interfering RNA (siRNA) inhibited the growth of both murine and human B lymphomas. …

Group 13 Hox Proteins Interact With The Mh2 Domain Of R-Smads And Modulate Smad Transcriptional Activation Functions Independent Of Hox Dna Binding Capability, Thomas M. Williams, Melissa E. Williams, Joanne H. Heaton, Thomas D. Gelehrter, Jeffrey W. Innis

Biology Faculty Publications

Interactions with co-factors provide a means by which HOX proteins exert specificity. To identify candidate protein interactors of HOXA13, we created and screened an E11.5–E12.5, distal limb bud yeast two-hybrid prey library. Among the interactors, we isolated the BMP-signaling effector Smad5, which interacted with the paralogous HOXD13 but not with HOXA11 or HOXA9, revealing unique interaction capabilities of the AbdB-like HOX proteins. Using deletion mutants, we determined that the MH2 domain of Smad5 is necessary for HOXA13 interaction.

This is the first report demonstrating an interaction between HOX proteins and the MH2 domain of Smad proteins. HOXA13 and HOXD13 …

The Cell Cycle–Regulated Genes Of Schizosaccharomyces Pombe, Anna Oliva, Adan Rosebrock, Francisco Ferrezuelo, Haiying Chen, Saumyadipta Pyne, Steve Skiena, Bruce Futcher, Janet Leatherwood

Department of Molecular Genetics and Microbiology Faculty Publications

Many genes are regulated as an innate part of the eukaryotic cell cycle, and a complex transcriptional network helps enable the cyclic behavior of dividing cells. This transcriptional network has been studied in Saccharomyces cerevisiae (budding yeast) and elsewhere. To provide more perspective on these regulatory mechanisms, we have used microarrays to measure gene expression through the cell cycle of Schizosaccharomyces pombe (fission yeast). The 750 genes with the most significant oscillations were identified and analyzed. There were two broad waves of cell cycle transcription, one in early/mid G2 phase, and the other near the G2/M transition. The early/mid G2 …

Mechanisms Of Virulence Regulation In Porphyromonas Gingivalis W83, Elaine Ann-Marie Vanterpool

Loma Linda University Electronic Theses, Dissertations & Projects

The expression of extracellular proteolytic activities is highly regulated in both prokaryotic and eukaryotic systems. This regulation can occur at multiple levels including expression of the protease genes, secretion, processing of an inactive secreted precursor to its active form and/or the posttranslational glycosylation of the proteins. These regulatory mechanisms are vital to ensure that expression is tightly controlled. Porphyromonas gingivalis has been associated with adult periodontitis and in the development of many systematic diseases. The major virulence factors of P. gingivalis, the gingipains, are responsible for pathogenesis including degradation of complement and immunoglobulin, inactivation of cytokines and their receptors, …