Digital Commons Network^™

A Functional Link Between Housekeeping Selenoproteins And Phase Ii Enzymes, Aniruddha Sengupta, Bradley A. Carlson, James A. Weaver, Sergey V. Novoselov, Dmitri E. Fomenko, Vadim N. Gladyshev, Dolph Hatfield

Vadim Gladyshev Publications

Sec (selenocysteine) is biosynthesized on its tRNA and incorporated into selenium-containing proteins (selenoproteins) as the 21st amino acid residue. Selenoprotein synthesis is dependent on Sec tRNA and the expression of this class of proteins can be modulated by altering Sec tRNA expression. The gene encoding Sec tRNA (Trsp) is a single-copy gene and its targeted removal in liver demonstrated that selenoproteins are essential for proper function wherein their absence leads to necrosis and hepatocellular degeneration. In the present study, we found that the complete loss of selenoproteins in liver was compensated for by an enhanced expression of several phase II …

Comparative Metabolite Profiling Of Carboxylic Acids In Rat Urine By Ce-Esi Ms/Ms Through Positively Pre-Charged And 2H-Coded Derivatization, Wen-Chu Yang, Fred E. Regnier, Jiri Adamec

Department of Biochemistry: Faculty Publications

A new approach for the selective comparative metabolite profiling of carboxylic acids in rat urine was established using capillary electrophoresis-mass spectrometry (CE-MS) and a method for positively pre-charged and ²H-coded derivatization. Novel derivatizing reagents, N-alkyl-4-

aminomethylpyridinum iodide (alkyl=butyl, butyl-d9 or hexyl), containing quaternary amine and

stable isotope atoms (deuterium), were introduced for the derivatization of carboxylic acids. CE

separation in positive polarity showed high reproducibility (0.99 –1.32% RSD of migration time)

and eliminated problems with capillary coating known in CE-MS anion analyses. Essentially

complete ionization and increased hydrophobicity after the derivatization also enhanced MS

detection sensitivity (e.g. formic …

Stable Isotope-Coded Quaternization For Comparative Quantification Of Estrogen Metabolites By High-Performance Liquid Chromatography-Electrospray Ionization Mass Spectrometry, Wen-Chu Yang, Fred E. Regnier, Dan Silva, Jiri Adamec

Department of Biochemistry: Faculty Publications

A fast and sensitive LC-ESI-MS method is described for the comparative quantification of 16 estrogen metabolites based on the derivatization of estrogens with a novel derivatizing reagent, Nmethyl- nicotinic acid N-hydroxysuccinimide ester (C1-NA-NHS). The process introduces a quaternary amine to the analytes, making the analytes permanently charged regardless of the pH of the HPLC mobile phase. This quaternization resulted in a highly efficient separation of 16 estrogen metabolites in 7 minutes at a detection level below 1 ng/mL. By using a deuterated derivatizing reagent (C1-d3-NA-NHS), a complete set of deuterated standards was utilized and used as internal standards in a …

Mapping The Functional Interaction Of Sco1 And Cox2 In Cytochrome Oxidase Biogenesis, Kevin Rigby, Paul A. Cobine, Oleh Khalimonchuk, Dennis R. Winge

Department of Biochemistry: Faculty Publications

Sco1 is implicated in the copper metallation of the Cu_A site in

Cox2 of cytochrome oxidase. The structure of Sco1 in the metallated

and apo-conformers revealed structural dynamics primarily

in an exposed region designated loop 8. The structural

dynamics of loop 8 in Sco1 suggests it may be an interface for

interactions with Cox17, the Cu(I) donor and/or Cox2. A series

of conserved residues in the sequence motif ²¹⁷KKYRVYF²²³ on

the leading edge of this loop are shown presently to be important

for yeast Sco1 function. Cells harboring Y219D, R220D, V221D,

and Y222D mutant Sco1 proteins failed …

Function And Redox State Of Mitochondrial Localized Cysteine-Rich Proteins Important In The Assembly Of Cytochrome C Oxidase, Oleh Khalimonchuk, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The cytochrome c oxidase (CcO) complex of the mitochondrial respiratory chain exists within the mitochondrial inner membrane (IM). The biogenesis of the complex is a multi-faceted process requiring multiple assembly factors that function on both faces of the IM. Formation of the two copper centers of CcO occurs within the intermembrane space (IMS) and is dependent on assembly factors with critical cysteinyl thiolates. Two classes of assembly factors exist, one group being soluble IMS proteins and the second class being proteins tethered to the IM. A common motif in the soluble assembly factors is a duplicated Cx₉C sequence …

Pet191 Is A Cytochrome C Oxidase Assembly Factor In Saccharomyces Cerevisiae, Oleh Khalimonchuk, Kevin Rigby, Megan Bestwick, Fabien Pierrel, Paul A. Cobine, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The twin-Cx₉C motif protein Pet191 is essential for cytochrome c oxidase maturation. The motif Cys residues are functionally important and appear to be present in disulfide linkages within a large oligomeric complex associated with the mitochondrial inner membrane. The import of Pet191 differs from that of other twin-Cx₉C motif class of proteins in being independent of the Mia40 pathway.

Coa2 Is An Assembly Factor For Yeast Cytochrome C Oxidase Biogenesis That Facilitates The Maturation Of Cox1, Fabien Pierrel, Oleh Khalimonchuk, Paul A. Cobine, Megan Bestwick, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The assembly of cytochrome c oxidase (CcO) in yeast mitochondria is dependent on a new assembly factor designated Coa2. Coa2 was identified from its ability to suppress the respiratory deficiency of coa1 Δ and shy1 Δ cells. Coa1 and Shy1 function at an early step in maturation of the Cox1 subunit of CcO. Coa2 functions downstream of the Mss51-Coa1 step in Cox1 maturation and likely concurrent with the Shy1-related heme a₃ insertion into Cox1. Coa2 interacts with Shy1. Cells lacking Coa2 show a rapid degradation of newly synthesized Cox1. Rapid Cox1 proteolysis also occurs in shy1 Δ cells, suggesting …

Purification From Human Milk Of Matriptase Complexes With Secreted Serpins: Mechanism For Inhibition Of Matriptase Other Than Hai-1, I-Chu Tseng, Feng-Pai Chou, Sheng-Feng Su, Michael Oberst, Nandakumar Madayiputhiya, Ming-Shyue Lee, Jehng-Kang Wang, David E. Sloane, Michael Johnson, Chen-Yong Lin

Department of Biochemistry: Faculty Publications

Matriptase, a type 2 transmembrane serine protease, is predominately expressed by epithelial and carcinoma cells in which hepatocyte growth factor activator inhibitor 1 (HAI-1), a membrane-bound, Kunitz-type serine protease inhibitor, is also expressed. HAI-1 plays dual roles in the regulation of matriptase, as a conventional protease inhibitor and as a factor required for zymogen activation of matriptase. As a consequence, activation of matriptase is immediately followed by HAI-1-mediated inhibition, with the activated matriptase being sequestered into HAI-1 complexes. Matriptase is also expressed by peripheral blood leukocytes, such as monocytes and macrophages; however, in contrast to epithelial cells, monocytes and macrophages …

A Highly Conserved Family Of Inactivated Archaeal B Family Dna Polymerases, Igor Rogozin, Kira Makarova, Youri Pavlov, Eugene Koonin

Papers in Evolution

A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly separated from each other and from a small group of bacterial homologs. These findings are compatible with an ancient duplication of the DNA polymerase gene followed by inactivation and parallel loss in some of the lineages although contribution of horizontal gene transfer cannot be ruled out. The inactivated derivative of the archaeal DNA polymerase could form a complex …

Arabidopsis Drb4, Ago1, Ago7, And Rdr6 Participate In A Dcl4-Initiated Antiviral Rna Silencing Pathway Negatively Regulated By Dcl1, Feng Qu, Xiaohong Ye, Thomas Jack Morris

School of Biological Sciences: Faculty Publications

Plant RNA silencing machinery enlists four primary classes of proteins to achieve sequence-specific regulation of gene expression and mount an antiviral defense. These include Dicer-like ribonucleases (DCLs), Argonaute proteins (AGOs), dsRNA-binding proteins (DRBs), and RNA-dependent RNA polymerases (RDRs). Although at least four distinct endogenous RNA silencing pathways have been thoroughly characterized, a detailed understanding of the antiviral RNA silencing pathway is just emerging. In this report, we have examined the role of four DCLs, two AGOs, one DRB, and one RDR in controlling viral RNA accumulation in infected Arabidopsis plants by using a mutant virus lacking its silencing suppressor. Our …

Interspecific Demographic Trade-Offs And Soil-Related Habitat Associations Of Tree Species Along Resource Gradients, Sabrina E. Russo, Patrick Brown, Sylvester Tan, Stuart J. Davies

School of Biological Sciences: Faculty Publications

Summary

1. Interspecific relationships between fundamental demographic rates, often called demographic trade-offs, emerge from constraints within individuals related to morphology, physiology and resource allocation. Plant species that grow fast in high light usually have high mortality in shade, and this well-established relationship in part defines a species’ successional niche. More generally, this relationship represents a trade-off between a species’ ability to grow quickly to exploit abundant resources vs. avoiding mortality when resources are less plentiful, but few studies have described this demographic trade-off with respect to environmental factors other than light.

2. Using demographic data from 960 tree species in …

The Spectrum Of Mitochondrial Mutation Differs Across Species, Kristi L. Montooth, David M. Rand

School of Biological Sciences: Faculty Publications

Mutations are ubiquitous, and many arise during the very process of replicating and transmitting genomes. This process is the source of the genetic variation that provides the raw material for both evolutionary novelty and human disease. Mutation rates are known to vary among nucleotides, across genomic regions, and between taxa. It is conventional wisdom that animal mitochondrial DNA (mtDNA) is one genomic region that has a particularly high mutation rate. Until recently, this high rate of mutation has been predominantly inferred from high levels of mitochondrial sequence divergence between species. However, the apparently simple process of mutation and sequence divergence …

Simian Immunodeficiency Virus–Induced Intestinal Cell Apoptosis Is The Underlying Mechanism Of The Regenerative Enteropathy Of Early Infection, Qingsheng Li, Jacob D. Estes, Lijie Duan, Jose Jessurun, Stefan Pambuccian, Colleen Forster, Stephen Wietgrefe, Mary Zupancic, Timothy Schacker, Cavan Reilly, John V. Carlis, Ashley T. Haase

Qingsheng Li Publications

The enteropathic manifestations of the human immunodeficiency virus (HIV) and the simian immunodeficiency virus (SIV) in late infection are usually due to infection by other microbes, but in early infection the viruses themselves cause an enteropathy by heretofore undetermined mechanisms. Here we report that SIV induces massive apoptosis of intestinal epithelial cells lining the small and large bowel, thus identifying apoptosis as the driving force behind the regenerative pathology of early infection. We found that apoptosis of gut epithelium paralleled the previously documented apoptosis and massive depletion of CD4 T cells in gut lamina propria, triggered by established mechanisms of …

Molecular Evolution Of Cytochrome B In High- And Low-Altitude Deer Mice (Genus Peromyscus), E.J. Gering, J. C. Opazo, Jay F. Storz

Jay F. Storz Publications

Patterns of amino-acid polymorphism in human mitochondrial genes have been interpreted as evidence for divergent selection among populations that inhabit climatically distinct environments. If similar patterns are mirrored in other broadly distributed mammalian species, then adaptive modifications of mitochondrial protein function may be detected in comparisons among locally adapted populations of a single wide-ranging species, or among closely related species that have adapted to different environments. Here, we test for evidence of positive selection on cytochrome b variation within and among species of the ecologically diverse rodent genus Peromyscus. We used likelihood-based comparisons of synonymous and nonsynonymous substitution rates …

The Fha Domain Proteins Dawdle In Arabidopsis And Snip1 In Humans Act In Small Rna Biogenesis, Bin Yu, Binglian Zheng, Lijuan Ji, David Chevalier, Manu Agarwal, Vanitharani Ramachandran, Wanxiang Li, Thierry Lagrange, John C. Walker, Xuemei Chen

Bin Yu Publications

Proteins containing the forkhead-associated domain (FHA) are known to act in biological processes such as DNA damage repair, protein degradation, and signal transduction. Here we report that DAWDLE (DDL), an FHA domain-containing protein in Arabidopsis, acts in the biogenesis of miRNAs and endogenous siRNAs. Unlike mutants of genes known to participate in the processing of miRNA precursors, such as dcl1, hyponastic leaves1, and serrate, ddl mutants show reduced levels of pri-miRNAs as well as mature miRNAs. Promoter activity of MIR genes, however, is not affected by ddl mutations. DDL is an RNA binding protein and is able …

Presidential Address: Nothing Succeeds Like Excess, Steven A. Nadler

Harold W. Manter Laboratory of Parasitology: Faculty Publications

To the members of the American Society of Parasitologists, I offer my appreciation for the opportunity to serve as your president. When I was notified of my successful election as an officer, it brought to mind that famous remark by Adlai Stevenson who said, ‘‘In America, anybody can be president. That’s one of the risks you take.’’ So, what I initially perceived as somewhat of a risky venture, proved to be a more valuable and interesting experience than I anticipated. Let’s hope that my presidential address has a similar outcome.

Muscleworms, Parelaphostrongylus Andersoni (Nematoda: Protostrongylidae), Discovered In Columbia White-Tailed Deer From Oregon And Washington: Implications For Biogeography And Host Associations, Ingrid M. Asmundsson, Jack A. Mortenson, Eric P. Hoberg

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Parelaphostrongylus andersoni is considered a characteristic nematode infecting white-tailed deer (Odocoileus virginianus). Host and geographic distribution for this parasite, however, remain poorly defined in the region of western North America. Fecal samples collected from Columbia white-tailed deer (O. v. leucurus) in a restricted range endemic to Oregon and Washington, USA, were examined for dorsal-spined larvae characteristic of many protostrongylid nematodes. Multilocus DNA sequence data (internal transcribed spacer 2 and cytochrome c oxidase subunit 1) established the identity and a new record for P. andersoni in a subspecies of white-tailed deer previously unrecognized as hosts. Populations of …

The Application Of Fast-Nmr For The Identification Of Novel Drug Discovery Targets, Robert Powers, Kelly A. Mercier, Jennifer C. Copeland

Robert Powers Publications

The continued success of genome sequencing projects has resulted in a wealth of information, but 40-50% of identified genes correspond to hypothetical proteins or proteins of unknown function. The Functional Annotation Screening Technology by NMR (FAST-NMR) screen was developed to assign a biological function for these unannotated proteins with a structure solved by the Protein Structure Initiative. FAST-NMR is based on the premise that a biological function can be described by a similarity in binding sites and ligand interactions with proteins of known function. The resulting co-structure and functional assignment may provide a starting point for …

Wind Through The Buffalo Grass: A Lakota Story Cycle, Paul A. Johnsgard

Paul Johnsgard Collection

Wind Through the Buffalo Grass: A Lakota Story Cycle is a narrative history of the Pine Ridge Lakota tribe of South Dakota, following its history from 1850 to the present day through actual historical events and through the stories of four fictional Lakota children, each related by descent and separated from one another by two generations.

The ecology of the Pine Ridge region, especially its mammalian and avian wildlife, is woven into the stories of the children. Illustrated by the author, the book includes drawings of Pine Ridge wildlife, regional maps, and Native American pictorial art. Appendices include a listing …

Evidence That The Nijmegen Breakage Syndrome Protein, An Early Sensor Of Double-Strand Dna Breaks (Dsb), Is Involved In Hiv-1 Post-Integration Repair By Recruiting The Ataxia Telangiectasia-Mutated Kinase In A Process Similar To, But Distinct From, Cellular Dsb Repair., Johanna A Smith, Feng-Xiang Wang, Hui Zhang, Kou-Juey Wu, Kevin Jon Williams, René Daniel

Kimmel Cancer Center Faculty Papers

Retroviral transduction involves integrase-dependent linkage of viral and host DNA that leaves an intermediate that requires post-integration repair (PIR). We and others proposed that PIR hijacks the host cell double-strand DNA break (DSB) repair pathways. Nevertheless, the geometry of retroviral DNA integration differs considerably from that of DSB repair and so the precise role of host-cell mechanisms in PIR remains unclear. In the current study, we found that the Nijmegen breakage syndrome 1 protein (NBS1), an early sensor of DSBs, associates with HIV-1 DNA, recruits the ataxia telangiectasia-mutated (ATM) kinase, promotes stable retroviral transduction, mediates efficient integration of viral DNA …

Tax Reform And Charitable Giving, Seth H. Giertz

Department of Economics: Faculty Publications

Of the $240.7 billion donated to U.S. charities in 2003, 75 percent was from individuals. Of that total, $145.7 billion was taken as itemized deductions on federal income tax returns. In addition, non-itemizers and non-filers contributed $33.0 billion – contributions that received no special tax treatment. Under current law, only taxpayers who itemize may deduct from Adjusted Gross Income (AGI) their charitable donations in determining taxable income. In recent years, a number of different proposals have been put forth that would alter the tax treatment of giving by individuals. Some plans would extend a variant of the charitable deduction to …

Reef Foraminifera As Bioindicators Of Coral Reef Health: Low Isles Reef, Northern Great Barrier Reef, Australia, Jonathan D. Schueth, Tracy D. Frank

Department of Earth and Atmospheric Sciences: Faculty Publications

Declining water quality associated with changes in land use over the past century is considered a significant environmental threat to the health of coral platforms of the Great Barrier Reef, Australia, in particular for those situated in nearshore areas of the wet tropics. Of these reefs, perhaps the most well known is Low Isles Reef, which has been studied since 1928. Decline in scleractinian coral cover and increased abundances of soft-bodied corals and macroalgae since the 1950’s have led researchers to speculate that the reef is being affected by increased nutrient and sediment fluxes from nearby rivers. The Foraminifera in …

Corporate Social Responsibility For Solving The Housing Problem For The Poor In South Africa, Ayman Ahmed Ezzat Othman, Basheera Mia

Architectural Engineering

No abstract provided.

Incorporating Value And Risk Management Principles In Developing Low-Income Housing Projects, Ayman Ahmed Ezzat Othman

Architectural Engineering

The construction industry is concerned with satisfying its customers’ needs through delivering projects that achieve their objectives and meet their expectations on time, within budget and as specified. Despite the several housing programmes constructed by government authorities, there is a real housing problem for the poor. This problem is attributed to a number of reasons. Amongst them, the inability of the low-incomers to cover the cost of supplied houses and the lack of the constructed projects to achieve users’ satisfaction. This highlighted the need to develop innovative and creative solutions that can deliver housing projects that achieve the satisfaction of …

Contributions Of Ibn Al-Nafis 1210-1288 Ad To The Progress Of Medicine And Urology. A Study And Translations From His Medical Works, Rabie E. Abdel-Halim

Saudi Medical Journal

This primary-source study of 4 medical works of the 13th century Muslim scholar Ibn Al-Nafis confirmed that his Kitab Al-Mujaz Fi Al-Tibb was authored as an independent book meant to be a handbook for medical students and practitioners not as an epitome of Kitab Al-Qanun of Ibn Sina as thought by recent historians. His huge medical encyclopedia, Al-Shamil, represents a wave of intense scientific activity that spread among the scholars of Cairo and Damascus following the massive destruction of books by Hulako9s Army during the devastation of Baghdad in 1258. Like his predecessors in the Islamic Era, Ibn Al-Nafis critically …

Determination Of The Effects Of Extremely Low Frequency Electromagnetic Fields On The Percentages Of Peripheral Blood Leukocytes And Histology Of Lymphoid Organs Of The Mouse, Aynur E. Cicekcibasi, Ilhami Celik, Ahmet Salbacak, Yasemin Ozkan, Nilsel Okudan, Mustafa Buyukmumcu

Saudi Medical Journal

OBJECTIVE: To determine the effects of very weak, extremely low frequency (50 Hz) electromagnetic field (ELF-EMF) on the relative spleen weight, lymphoid organ histology, peripheral blood leukocyte and alpha-naphthyl acetate esterase positive (ANAE- positive) lymphocyte percentages of the mouse. METHODS: The study was carried out in Scientific Research and Application Center of Selcuk University, Konya, Turkey in 2005. A total of 120 Swiss albino mice were divided into 6 groups (20 in each group). The experimental animals were exposed to 1, 2, 3, 4 and 5 uT flux intensities (rms) of EMF at 50 Hz for 40 days. RESULTS: In …

Safety Profile Of Parenteral Ketamine And Lignocaine Infiltration In Pediatric Operations, David O. Osifo, Kennedy N. Emeagui, Sylvester E. Aghahowa

Saudi Medical Journal

OBJECTIVE: To study the safety and benefits of parenteral ketamine and lignocaine infiltration among pediatric surgical patients with co-morbidities that would preclude the use of general anesthesia requiring endotracheal intubation/face mask in a developing country. METHODS: This prospective study was undertaken at the Leadeks Medical Centre, Benin City Edo State, Nigeria between January 2002 and December 2006. Patients requiring surgery were safely operated even in the presence of co-morbidity. RESULTS: A total of 416 children were recruited and they were aged 6 days to 16 years (mean 12 -/+ 2.04 years) with a male/female ratio of 1:1.1. Appendectomy (33.2%), herniotomy …

Ileal-Conduit Following Cystectomy, Single-Institution Revision Of Indications And Outcome, Hassan A. Abol-Enein, Ausama S. Abdul-Muhsin, Yousuf M. Alhallaq

Saudi Medical Journal

OBJECTIVE: To revise indications, case fatality ratio, and postoperative early and late complications of ileal conduit as a method of urinary diversion. METHODS: This is a retrospective study in which 200 patients underwent an ileal conduit from August 1994 to December 2000 in Mansoura Urology and Nephrology Center, Mansoura, Egypt. Preoperative criteria of patient selection, peroperative findings, and postoperative follow-up data were reviewed. RESULTS: In 200 patients aged 29-75 years, with a mean age of 55.84 -/+ 8.91 years, the ileal conduit was chosen as a method of urinary diversion, due to one of the following patient or surgical factors; …

Evaluating The Trace Elements In Preoperative And Postoperative Duration Of Hydatid Surgery, Gurhan Sakman, Cem K. Parsak, Ismail S. Koltas, Gulsah Seydaoglu, Husnu Sonmez, Ismail Hanta

Saudi Medical Journal

OBJECTIVE: To evaluate the preoperative and postoperative values of serum levels of zinc, magnesium, and copper in patients with cystic echinococcosis (CE). METHODS: This study was conducted on patients with CE between 2000-2005 at the Faculty of Medicine, University of Cukurova, Adana, Turkey. Serum levels of zinc, copper, and magnesium of 85 patients with CE were measured both before and one year after the operation. Patients with liver CE (85 patients, 48 males) and healthy adults (40 adults, 17 males) as the control group were enrolled in the study. RESULTS: When compared with the control group, the mean serum levels …

Comparison Of The Clinical And Pathological Features Between Patients With Recurrent Metastatic Breast Carcinoma And Patients With Initially Metastatic Breast Carcinoma, Birsen K. Saydam, Gamze Goksel, Esra Korkmaz, Murat Kapkac, Necmettin Ozdemir, Canfeza Sezgin, Ruchan Uslu

Saudi Medical Journal

OBJECTIVE: To compare initial metastatic breast carcinoma (MBC) with recurrent MBC and assess their biologic phenotypes and clinical behaviors. METHODS: A comparison of clinical and biological characteristics and median overall survival times were assessed in the 251 patients with MBC at the Division of Medical Oncology, Ege University School of Medicine, and the Division of Radiation Oncology, Tepecik Government Hospital, Izmir, Turkey between 1995 and 2004. Hormone receptors, c-erbB-2, Ki-67, and p53 expressions were performed by immunohistochemistry. RESULTS: Out of 251 MBC patients, 206 patients had recurrent MBC, and 45 had initial MBC. Regarding survival, there was no difference between …