Digital Commons Network^™

Structure And Function Of Pseudomonas Aeruginosa Protein Pa1324 (21–170), Kelly A. Mercier, John R. Cort, Michael A. Kennedy, Erin E. Lockert, Shuisong Ni, Matthew D. Shortridge, Robert Powers

Robert Powers Publications

Pseudomonas aeruginosa is the prototypical biofilm-forming gram-negative opportunistic human pathogen. P. aeruginosa is causatively associated with nosocomial infections and with cystic fibrosis. Antibiotic resistance in some strains adds to the inherent difficulties that result from biofilm formation when treating P. aeruginosa infections. Transcriptional profiling studies suggest widespread changes in the proteome during quorum sensing and biofilm development. Many of the proteins found to be upregulated during these processes are poorly characterized from a functional standpoint. Here, we report the solution NMR structure of PA1324, a protein of unknown function identified in these studies, and provide a putative biological functional assignment …

1H, 13C, And 15N Nmr Assignments For The Bacillus Subtilis Yndb Start Domain, Kelly A. Mercier, Geoffrey A. Mueller, Thomas B. Acton, Rong Xiao, Gaetano T. Montelione, Robert Powers

Robert Powers Publications

The steroidogenic acute regulatory-related lipid transfer (START) domain is found in both eukaryotes and prokaryotes, with putative functions including signal transduction, transcriptional regulation, GTPase activation and thioester hydrolysis. Here we report the near complete ¹H, ¹⁵N and ¹³C backbone and side chain NMR resonance assignments for the Bacillus subtilis START domain protein yndB.

Paleohydrology Of Kangerlussuaq (Søndre Strømfjord), West Greenland During The Last ~8,000 Years, Frank Aebly, Sherilyn C. Fritz

Department of Earth and Atmospheric Sciences: Faculty Publications

Major fluctuations of hydroclimate in West Greenland are recorded in paleoshoreline terraces that encircle several lakes near Kangerlussuaq, Greenland (67°01’N, 50°40’W). Geomorphic and stratigraphic analyses were used to construct a lake-level curve for Hunde Sø, a large closed-basin lake in this region. Changes in lake volume associated with lake-level fluctuations were calculated, and a water-balance model was used to determine the primary factors influencing lake volume and the changes in those factors necessary to affect reconstructed lake-level change. Sensitivity tests suggest that mean annual precipitation and the relative proportion of summer versus winter precipitation are the primary climate drivers of …

Recent Occurrence Of An American Black Bear In Nebraska, Justin D. Hoffman, Sam Wilson, Hugh H. Genoways

University of Nebraska State Museum: Mammalogy Papers

We report on a young male, cinnamon-phase American black bear (Ursus americanus) that was collected in northwestern Nebraska on May 12, 2008. This specimen represents the first black bear taken in Nebraska since 1907. Cranial characteristics and mass of the individual indicated a 15–16-month old bear. This bear may have dispersed from the Laramie Mountains in southeastern Wyoming along the North Platte River into western Nebraska. This record adds to the growing number of cases where large carnivores are reinvading previously occupied territory in the Great Plains. These reinvasions potentially have broad ecological implications to local prey populations …

Increased Susceptibility Of Spinal Muscular Atrophy Fibroblasts To Camptothecin Is P53-Independent., Chia-Yen Wu, Ilsa Gómez-Curet, Vicky L Funanage, Mena Scavina, Wenlan Wang

Department of Pediatrics Faculty Papers

BACKGROUND: Deletion or mutation(s) of the survival motor neuron 1 (SMN1) gene causes spinal muscular atrophy (SMA). The SMN protein is known to play a role in RNA metabolism, neurite outgrowth, and cell survival. Yet, it remains unclear how SMN deficiency causes selective motor neuron death and muscle atrophy seen in SMA. Previously, we have shown that skin fibroblasts from SMA patients are more sensitive to the DNA topoisomerase I inhibitor camptothecin, supporting a role for SMN in cell survival. Here, we examine the potential mechanism of camptothecin sensitivity in SMA fibroblasts.

RESULTS: Camptothecin treatment reduced the DNA relaxation activity …

The Effects Of N-Acetylcysteine On Intestinal Ischemia/Reperfusion Injury In Rats, Suleyman Ayvaz, Burhan Aksu, Mustafa Inan, Hafize Uzun, Seval Aydin, Selcuk Bilgi, Hasan C. Umit, Mehmet Pul

Saudi Medical Journal

OBJECTIVE: To evaluate the effects of N-acetylcysteine NAC on the injury of intestinal ischemia-reperfusion. METHODS: Forty-eight Wistar-Albino rats were divided into 6 groups: as control, ischemia, ischemia-reperfusion, ischemia + N-acetylcysteine, ischemia-reperfusion + N-acetylcysteine IRN, and reperfusion + N-acetylcysteine RN. Histopathologic examination was performed to all groups. In the tissue and plasma, and erythrocyte samples, malondialdehyde, superoxide dismutase, glutathione, and nitric oxide NO levels were evaluated. The present study was carried out in Trakya and Istanbul University, Edirne, Turkey between December 2002 and July 2003. RESULTS: The most severe histopathological damage was seen in the intestinal ischemia-reperfusion group, and this damage …

The Protective Effect Of Ng-Nitro-L-Arginine Methyl Ester And Insulin On Nitric Oxide Inhibition And Pathology In Experimental Diabetic Rat Liver, Hilmi Ozden, Neslihan Tekin, Fahrettin Akyuz, Firdevs Gurer, Mehmet C. Ustuner, Fulya Kucuk, Gul Guven, Faik Yaylak

Saudi Medical Journal

OBJECTIVE: To determine on protective role of NG-nitro-L-arginine methyl ester L-NAME, and insulin on the liver in streptozotocin STZ induced diabetic rats. METHODS: This study was performed in the Department of Biochemistry, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey in 2007. Forty male Wistar albino rats were divided into 5 groups. These were untreated, diabetic control, STZ+insulin, STZ+L-NAME and STZ+insulin+L-NAME induced groups. The STZ was intraperitonally injected into 3 groups, and includes insulin, L-NAME, and their joint administrations as protective agents. The blood glucose and nitric oxide NO levels were determined. The tissue samples were obtained at the end …

Characterization And Resistance Mechanisms Of Cisplatin-Resistant Human Hepatocellular Carcinoma Cell Line, Jun-Xia Yang, Ying Luo, Hong-Mei Qiu, Wei-Xue Tang

Saudi Medical Journal

OBJECTIVE: To study the biological characteristics and resistant mechanisms of the cisplatin-resistant human hepatocellular carcinoma HCC cell line. METHODS: The study took place in the Department of Pharmacology, Chongqing Medical University, Chongqing, China, between April 2005 and November 2007. A resistant HCC cell line QGY/CDDP was established by stepwise increasing cisplatin CDDP concentration and intermittent administration. Drug-chemo sensitivity was detected by 3-4,5-dimethylthiazol-2yl-2,5- diphenyltetrazolium bromide MTT assay. Cell doubling time was determined by cell counting, and cell cycle analysis was performed by flow cytometric FCM assay. Intracellular platinum accumulation was detected by atomic absorption spectrometry and the expression of P-glycoprotein P-gp …

Effect Of Human Platelet-Derived Growth Factor-Bb On Attachment Of Periodontal Ligament Cells On Root Surfaces, Sema Becerik, Sule Sonmez, Bilge H. Sen, Ismet Deliloglu-Gurhan, Evren Evrenosoglu

Saudi Medical Journal

OBJECTIVE: To evaluate the effects of platelet-derived growth factor-BB PDGF-BB on the attachment of human periodontal ligament cells HPLCs on the root surfaces demineralized with different agents. METHODS: We performed this study at Ege University, Izmir, Turkey between 2005 and 2006. Eighty root slices were subjected to one of following treatments after root planing: 1 only root planing, 2 Platelet derived growth factor-BB PDGF-BB, 3 citric acid demineralization, 4 citric acid demineralization + PDGF-BB, 5 tetracycline hydrochloric acid T-HCl demineralization, 6 T-HCl demineralization + PDGF-BB, 7 ethylenediamine tetra-acetic acid EDTA demineralization, and 8 EDTA demineralization + PDGF-BB. Human periodontal ligament …

Distribution Of Abo Blood Groups And Rhesus Factor In Southwest Saudi Arabia, Mohammed A. Sarhan, Kamel A. Saleh, Saad M. Bin-Dajem

Saudi Medical Journal

OBJECTIVE: To document the distribution of the ABO and rhesus Rh blood groups in a random sample of Saudi students from the King Khalid University, Abha, Kingdom of Saudi Arabia, and to compare our results from that of other studies in the Kingdom and elsewhere. METHODS: The subjects included in this study were 944 males from thesouthwest region of Saudi Arabia including Aseer, Jizan, and Najran regions. The ABO blood groups and Rh factor from 944 Saudi males were determined. The frequency of ABO blood groups and Rh status were calculated separately. This study was carried out at King Khalid …

Primary Retroperitoneal Mucinous Cystadenoma, Malak Abedalthagafi, Patrick G. Jackson, Metin Ozdemirli

Saudi Medical Journal

Primary mucinous neoplasms of the retroperitoneum, including mucinous cystadenocarcinomas, mucinous borderline tumors, and mucinous cystadenomas are uncommon tumors found exclusively in women. Since the retroperitoneum does not contain mucinous epithelium, the origin, and histogenesis of these tumors remain unclear. It is speculated that these tumors can arise from teratomas, supernumerary ovaries, or mucinous metaplasia of the retroperitoneal mesothelium. We describe a case of a primary mucinous cystadenoma of the retroperitoneum in a 44 year-old female that presented as a palpable abdominal mass. There was no evidence of recurrence 16 months after complete laparoscopic excision of the tumor. The morphology and …

A Practical Information Technology Program, Bijan Mashaw

Journal of International Technology and Information Management

This paper discusses the challenges facing business in the 21 st century and the dramatic changes in the use of computers and application development process. These challenges, as well as the increase of global economy, coupled with the demand for the business technology workers indicate the need for redesigning the Information System Curriculum. The proposed framework for an Information Technology (IT) Program in this paper offers a pragmatic curriculum model to accommodate the needs and challenges of the 21st century. The framework provides a fundamental IT education for the graduates of such a curriculum, as well as allowing an area …

Emotional Reactivity Across Individuals With Varying Trauma And Substance Dependence Histories, Alicia K. Klanecky, Dennis E. Mcchargue

Department of Psychology: Faculty Publications

Background—Research has reported a high rate of substance dependence in traumatized individuals who do not develop PTSD (TWP). While past studies have failed to consistently demonstrate that TWP individuals experience PTSD symptoms, findings have indicated that TWP and a history of substance dependence aside from nicotine dependence (SDH) are linked to affect disruption.

Aims—The present study explored positive and negative affective mechanisms across four groups with varying SDH and TWP including TWP + SDH, TWP only, SDH only, or no history. Researchers hypothesized that adults (n = 78) would be more emotionally reactive to an experimentally-induced negative mood compared to …

Androgen-Stimulated Udp-Glucose Dehydrogenase Expression Limits Prostate Androgen Availability Without Impacting Hyaluronan Levels, Qin Wei, Robert Galbenus, Ashraf Raza, Ronald Cerny, Melanie A. Simpson

Ronald Cerny Publications

UDP-glucose dehydrogenase (UGDH) oxidizes UDP-glucose to UDP-glucuronate, an essential precursor for production of hyaluronan (HA), proteoglycans, and xenobiotic glucuronides. High levels of HA turnover in prostate cancer are correlated with aggressive progression. UGDH expression is high in the normal prostate even though HA accumulation is virtually undetectable. Thus, its normal role in the prostate may be to provide precursors for glucuronosyltransferase enzymes, which inactivate and solubilize androgens by glucuronidation. In this report, we quantified androgen dependence of UGDH, glucuronosyltransferase, and HA synthase expression. Androgen dependent and independent human prostate cancer cell lines were used to test the effects of UGDH …

A New Peroxide Fragmentation: Efficient Chemical Generation Of 1O2 In Organic Media, Patrick Dussault, Prasanta Ghorai

Department of Chemistry: Faculty Publications

Monoactivated derivatives of 1,1-dihydroperoxides undergo an unprecedented base-promoted fragmentation to efficiently generate singlet oxygen (¹O₂) in anhydrous organic solvents.

Structural And Functional Similarity Between The Bacterial Type Iii Secretion System Needle Protein Prgi And The Eukaryotic Apoptosis Bcl-2 Proteins, Matthew D. Shortridge, Robert Powers

Department of Chemistry: Faculty Publications

Background: Functional similarity is challenging to identify when global sequence and structure similarity is low. Activesites or functionally relevant regions are evolutionarily more stable relative to the remainder of a protein structure and provide an alternative means to identify potential functional similarity between proteins. We recently developed the FASTNMR methodology to discover biochemical functions or functional hypotheses of proteins of unknown function by experimentally identifying ligand binding sites. FAST-NMR utilizes our CPASS software and database to assign a function based on a similarity in the structure and sequence of ligand binding sites between proteins of known and unknown function.

Methodology/Principal …

A Multi-Step Nmr Screen For The Identification And Evaluation Of Chemical Leads For Drug Discovery, Kelly A. Mercier, Matthew D. Shortridge, Robert Powers

Department of Chemistry: Faculty Publications

A multi-step NMR based screening assay is described for identifying and evaluating chemical leads for their ability to bind a target protein. The multi-step NMR assay provides structure-related information while being an integral part of a structure based drug discovery and design program. The fundamental principle of the multi-step NMR assay is to combine distinct 1D and 2D NMR techniques, in such a manner, that the inherent strengths and weakness associated with each technique is complementary to each other in the screen. By taking advantage of the combined strengths of 1D and 2D NMR experiments, it is possible to minimize …

Bess: BIofuel ENergy SYstems SImulator: Life Cycle Energy & Emissions Analysis Model For Corn-Ethanol Biofuel Production Systems -- User’S Guide For The Bess Model, Adam Liska, Haishun Yang, Daniel T. Walters, Kenneth Cassman, Terry Klopfenstein, Galen Erickson, Virgil R. Bremer, Richard K. Koelsch, Dan Kenney, Patrick Tracy

Adam Liska Papers

The BESS model is a software tool to calculate the energy efficiency, greenhouse gas (GHG) emissions, and natural resource requirements of corn–to-ethanol biofuel production systems. The model provides a “cradle-to-grave” analysis of the production life cycle of biofuels from the creation of material inputs to finished products, producing an inventory of distributed GHG emissions from fossil fuels and a few key indirect emissions in the production life cycle. The model parameters can be set by the user to achieve the highest accuracy in evaluating a single corn-ethanol biorefinery and its surrounding feedstock crop production zone. The model equations and summary …

Energy Gradients In Combined Fragment Molecular Orbital And Polarizable Continuum Model (Fmo/Pcm) Calculation, Hui Li, Dmitri G. Federov, Takeshi Nagata, Kazuo Kitaura, Jan H. Jensen, Mark S. Gordon

Hui Li Publications

The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6-31G* level) is used to optimize the solution structure of the 304-atom Trp-cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the a-helix, b-turn and the extended form in solution are elucidated for polyalanine.

Crystallization And Crystal-Packing Studies Of Chlorella Virus Deoxyuridine Triphosphatase, Kohei Homma, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an aminoterminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P213 crystals with unit-cell parameter a = 106.65 A . In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but …

Ecological Genomics Of Nematode Community Interactions: Model And Non-Model Approaches, Michael A. Herman, Joseph D. Coolon, Kenneth L. Jones, Timothy Todd

School of Biological Sciences: Faculty Publications

The effects of human-induced environmental change are evident at multiple levels of biological organization. To date, most environmental change studies have focused on effects at the ecosystem, community, and organismal levels. However, the ultimate controls of biological responses are located in the genome. Thus, genetic and genomic studies of organismal responses to environmental changes are necessary. Recent advances in genome analysis now make such analyses possible. In this chapter we describe a research approach and program that can begin to span this gap by using genome-enabled approaches to characterize organismal changes and then employing a genetically tractable model organism to …