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Dur3 Is The Major Urea Transporter In Candida Albicans And Is Co-Regulated With The Urea Amidolyase Dur1,2, Dhammika H. M. L. P Navarathna, Aditi Das, Joachim Morschhauser, Kenneth W. Nickerson, David D. Roberts

Kenneth Nickerson Papers

Hemiascomycetes, including the pathogen Candida albicans, acquire nitrogen from urea using the urea amidolyase Dur1,2, whereas all other higher fungi use primarily the nickel-containing urease. Urea metabolism via Dur1,2 is important for resistance to innate host immunity in C. albicans infections. To further characterize urea metabolism in C. albicans we examined the function of seven putative urea transporters. Gene disruption established that Dur3, encoded by orf 19.781, is the predominant transporter. [¹⁴C]Urea uptake was energy-dependent and decreased approximately sevenfold in a dur3D mutant. DUR1,2 and DUR3 expression was strongly induced by urea, whereas the other putative transporter genes …

Use Of Nape Tags For Marking Offspring Of Precocial Waterbirds, Todd W. Arnold, Daizaburo Shizuka, Bruce E. Lyon, Jeffrey T. Pelayo, Katherine R. Mehl, Joshua J. Traylor, Wendy L. Reed, Courtney L. Amundson

Papers in Ornithology

Individualized markers that allow organisms to be identified without recapture are invaluable for studies of survival, movement, and behavior. Nape tags consisting of brass safety pins with unique combinations of two or three colored plastic beads were used to mark 5,868 American Coot (Fulica americana) chicks and 331 Ruddy Duck (Oxyura jamaicensis), 157 King Eider (Somateria spectabilis) and 664 White-winged Scoter (Melanitta fusca deglandi) ducklings. These markers allowed for documentation of parent-offspring interactions, post-hatching survival, brood movements and brood-mixing behaviors. Nape tags were inexpensive, easy to make, easy to observe with binoculars …

Sparrows Use Multiple Status Signals In Winter Social Flocks, Alexis S. Chaine, Kris A. Tjernell, Daizaburo Shizuka, Bruce E. Lyon

Papers in Ornithology

Status signals are thought to reduce the potential costs of social conflict over resources by advertising social status to other group members and reducing unnecessary contests between individuals of differing abilities. Nearly all studies of status signals to date have focused on single signaling traits, and most studies that have investigated multiple traits did not examine whether different traits are used in different contexts, as is required for them to function as multiple signals. We examined the role of gold and black crown patches of wintering golden-crowned sparrows, Zonotrichia atricapilla, in determining social dominance during experimentally staged encounters between unfamiliar …

Maize Cellulosic Biofuels: Soil Carbon Loss Can Be A Hidden Cost Of Residue Removal, Amy Kochsiek, Johannes Knops

School of Biological Sciences: Faculty Publications

Second generation biofuels, like cellulosic ethanol, have potential as important energy sources that can lower fossil fuel carbon emissions without affecting global food commodity prices. Agricultural crop residues, especially maize, have been proposed for use as biofuel, but the net greenhouse warming effect of the gained fossil fuel carbon offset needs to account for any ecosystem carbon losses caused by the large-scale maize residue removal. Using differential 13C isotopic ratios between residue and soil in an incubation experiment, we found that removal of residue increased soil organic matter decomposition by an average of 16%, or 540–800 kg carbon ha -1. …

Arabidopsis G-Protein Interactome Reveals Connections To Cell Wall Carbohydrates And Morphogenesis, Karsten Klopffleisch, Nguyen Phan, Kelsey Augustin, Robert S. Bayne, Katherine S. Booker, Jose R. Botella, Nicholas C. Carpita, Tyrell Carr, Jin-Gui Chen, Thomas Ryan Cooke, Arwen Frick-Cheng, Erin J. Friedman, Brandon Fulk, Michael G. Hahn, Kun Jiang, Lucia Jorda, Lydia Kruppe, Chenggang Liu, Justine Lorek, Maureen C. Mccann, Antonio Molina, Etsuko N. Moriyama, M. Shahid Mukhtar, Yashwanti Mudgil, Sivakumar Pattathil, John Schwarz, Steven Seta, Matthew Tan, Ulrike Temp, Yuri Trusov, Daisuke Urano, Bastian Welter, Jing Yang, Ralph Panstruga, Joachim F. Uhrig, Alan M. Jones

School of Biological Sciences: Faculty Publications

The heterotrimeric G-protein complex is minimally composed of Ga, Gb, and Gc subunits. In the classic scenario, the G-protein complex is the nexus in signaling from the plasma membrane, where the heterotrimeric G-protein associates with heptahelical G-protein-coupled receptors (GPCRs), to cytoplasmic target proteins called effectors. Although a number of effectors are known in metazoans and fungi, none of these are predicted to exist in their canonical forms in plants. To identify ab initio plant G-protein effectors and scaffold proteins, we screened a set of proteins from the G-protein complex using two-hybrid complementation in yeast. After deep and exhaustive interrogation, we …

Environmental And Genetic Perturbations Reveal Different Networks Of Metabolic Regulation, Anthony J. Greenberg, Sean R. Hacket, Lawrence G. Harshman, Andrew G. Clark

School of Biological Sciences: Faculty Publications

Progress in systems biology depends on accurate descriptions of biological networks. Connections in a regulatory network are identified as correlations of gene expression across a set of environmental or genetic perturbations. To use this information to predict system behavior, we must test how the nature of perturbations affects topologies of networks they reveal. To probe this question, we focused on metabolism of Drosophila melanogaster. Our source of perturbations is a set of crosses among 92 wild-derived lines from five populations, replicated in a manner permitting separate assessment of the effects of genetic variation and environmental fluctuation. We directly assayed activities …

Orientational Imaging In Polar Polymers By Piezoresponse Force Microscopy, Pankaj Sharma, Dong Wu, Shashi Poddar, Timothy J. Reece, Stephen Ducharme, Alexei Gruverman

Stephen Ducharme Publications

We report orientational imaging of the polarization distribution in nanostructured ferroelectric copolymer of polyvinylidene fluoride-trifluoroethylene (PVDF-TrFE) and collagen fibrils using vertical and lateral modes of piezoresponse force microscopy (PFM). In PVDF-TrFE, detection of azimuthal variations in the lateral PFM signal is attributed to the alignment of the molecular chains along different directions. Local switching in PVDF-TrFE is shown to proceed via 120 degrees or 180 degrees rotation of dipoles around the molecular chain, depending upon the strength of the applied electric field. Analysis of the vertical and lateral PFM signals in collagen reveals polar anisotropy of the electromechanical properties along …

Mammalia, Didelphimorphia, Didelphidae, Monodelphis Kunsi Pine, 1975: Distribution Extension And First Record For Eastern Amazonia, Donald Gettinger, Thiago Carvalho Modesto, Helena De Godoy Bergallo, Fernanda Martins-Hatano

Harold W. Manter Laboratory of Parasitology: Faculty Publications

We review the distributional records of Monodelphis kunsi, which occurs from eastern Bolivia, Paraguay, and northern Argentina into central Brazil. We report specimens of M. kunsi collected in the Carajás National Forest in eastern Pará, Brazil (06°03’00” S, 50°15’00” W), extending the known species range 430 km northward, into the eastern edge of Amazonia. This is the first record for the state of Pará, and the first certain record for the Amazon Region. Two adult males and one subadult female were deposited in the Museu Nacional, Rio de Janeiro.

Erection Of Ibirhynchus Gen. Nov. (Acanthocephala: Polymorphidae), Based On Molecular And Morphological Data, Martin Garcia-Varela, Gerardo Pérez-Ponce De León, Francisco J. Aznar, Steven A. Nadler

Harold W. Manter Laboratory of Parasitology: Faculty Publications

The genus Southwellina is composed of 3 described species, i.e., S. hispida (the type species), S. dimorpha, and S. macracanthus. All 3 are endoparasites of fish-eating birds that have worldwide distributions. Morphologically, the genus is characterized by possessing a short and compact trunk, 2 fields of spines in the anterior region of the trunk (in at least 1 sex), a short cylindrical proboscis (sometimes with a swollen region armed with numerous longitudinal rows of hooks), a double-walled proboscis receptacle, and 4 tubular cement glands in males. In the current study, specimens identified as S. dimorpha were collected from …

Helminths Of Squirrels (Sciuridae) From Mongolia, David S. Tinnin, Sumiya Ganzorig, Scott Lyell Gardner

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Two species of ground squirrels, Urocitellus undulatus and Spermophilus alashanicus, were collected and examined for parasites from two localities in Mongolia in 1999. A total of 24 individuals of U. undulatus were examined resulting in a total of six taxa of helminths found, including: Ascaris tarbagan, Physaloptera massino, Streptopharagus kutassi, Anoplocephaloides transversaria, Hymenolepis suslica, and Moniliformis sp. This represents four new species records and an additional host record for the country. Two individuals of S. alashanicus were examined and found to be uninfected.

Description Of Scottnema Lindsayae Timm, 1971 (Rhabditida: Cephalobidae) From Taylor Valley, Antarctica And Its Phylogenetic Relationship, Sven Boström, Oleksandr Holovachov, Steven A. Nadler

Harold W. Manter Laboratory of Parasitology: Faculty Publications

The endemic Antarctic nematode Scottnema lindsayae is described from specimens collected in Taylor Valley, McMurdo Dry Valleys, Victoria Land. The recently collected material is compared with the original description and other subsequent descriptions of the species. A more complete scanning electron microscopy (SEM) study of the species is presented. The phylogenetic position of S. lindsayae is inferred using a secondary structure-based alignment of a partial sequence of nuclear Large Subunit (LSU) ribosomal DNA. Phylogenetic trees were inferred using base-paired substitution models implemented in PHASE 2 software and Bayesian inference, and show S. lindsayae as the sister group to Stegelletina taxa.

Monophyly Of Clade Iii Nematodes Is Not Supported By Phylogenetic Analysis Of Complete Mitochondrial Genome Sequences, Joong-Ki Park, Tahera Sultana, Sang-Hwa Lee, Seokha Kang, Hyong Kyu Kim, Gi-Sik Min, Keeseon S. Eom, Steven A. Nadler

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Abstract Background: The orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide nematode phylogenetic hypotheses have mainly been based on nuclear rDNA sequences, but more recently complete mitochondrial (mtDNA) gene sequences have provided another source of molecular information to evaluate relationships. Although there is much agreement between nuclear rDNA and mtDNA phylogenies, relationships among certain major clades are different. In this study we report that mtDNA sequences do not support the monophyly of Ascaridida, Oxyurida and Spirurida (clade III) in contrast to results for nuclear rDNA. Results from …

Soil Moisture: A Central And Unifying Theme In Physical Geography, Rezaul Mahmood

School of Natural Resources: Faculty Publications

No abstract provided.

Land Use/Land Cover Changes And Climate: Modeling Analysis And Observational Evidence, Roger A. Pielke Sr., Andy Pitman, Dev Niyogi, Rezaul Mahmood, Clive Mcalpine, Faisal Hossain, Kees Klein Goldewijk, Udaysankar S. Nair, Richard Betts, Souleymane Fall, Markus Reichstein, Pavel Kabat, Nathalie De Noblet

School of Natural Resources: Faculty Publications

This article summarizes the changes in landscape structure because of human land management over the last several centuries, and using observed and modeled data, documents how these changes have altered biogeophysical and biogeochemical surface fluxes on the local, mesoscale, and regional scales. Remaining research issues are presented including whether these landscape changes alter large-scale atmospheric circulation patterns far from where the land use and land cover changes occur. We conclude that existing climate assessments have not yet adequately factored in this climate forcing. For those regions that have undergone intensive human landscape change, or would undergo intensive change in the …

Effects Of Solution Chemistry And Aging Time On Prion Protein Adsorption And Replication Of Soil-Bound Prions, Samuel E. Saunders, Qi Yuan, Jason C. Bartz, Shannon L. Bartelt-Hunt

Department of Civil and Environmental Engineering: Faculty Publications

Prion interactions with soil may play an important role in the transmission of chronic wasting disease (CWD) and scrapie. Prions are known to bind to a wide range of soil surfaces, but the effects of adsorption solution chemistry and long-term soil binding on prion fate and transmission risk are unknown. We investigated HY TME prion protein (PrP^Sc) adsorption to soil minerals in aqueous solutions of phosphate buffered saline (PBS), sodium chloride, calcium chloride, and deionized water using western blotting. The replication efficiency of bound prions following adsorption in these solutions was also evaluated by protein misfolding cyclic amplification …

An Inexpensive High-Throughput Nmr Tube Cleaning Apparatus, Bo Zhang, James Hodgson, Walter Hancock, Robert Powers

Robert Powers Publications

Large scale Nuclear Magnetic Resonance (NMR) tube cleaning is currently a bottleneck in high throughput NMR ligand affinity screens. Expensive alternatives include discarding the NMR tubes after a single use (~$2 to $8/tube), using commercial NMR tube cleaners (~$15K) or abandoning NMR tubes for flow probe technology (~$75K). Instead, we describe a relatively inexpensive (~ $400) and easily constructed apparatus that can clean 180 NMR tubes an hour while using a modest amount of solvent. The application of this apparatus significantly shortens the time to recycle NMR tubes while avoiding cross contaminations and tube damage.

Bacterial Protein Structures Reveal Phylum Dependent Divergence, Matthew D. Shortridge, Thomas Triplet, Peter Revesz, Mark A. Griep, Robert Powers

Robert Powers Publications

Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against …

A Correlation Between Protein Function And Ligand Binding Profiles, Matthew D. Shortridge, Michael Bokemper, Jennifer C. Copeland, Jaime L. Stark, Robert Powers

Robert Powers Publications

We report that proteins with the same function bind the same set of small molecules from a standardized chemical library. This observation led to a quantifiable and rapidly adaptable method for protein functional analysis using experimentally-derived ligand binding profiles. Ligand binding is measured using a high-throughput NMR ligand affinity screen with a structurally diverse chemical library. The method was demonstrated using a set of 19 proteins with a range of functions. A statistically significant similarity in ligand binding profiles was only observed between the two functionally identical albumins and between the five functionally similar amylases. This new approach is independent …

Nmr Analysis Of A Stress Response Metabolic Signaling Network, Bo Zhang, Steven M. Halouska, Charles E. Schiaffo, Marat R. Sadykov, Greg A. Somerville, Robert Powers

Robert Powers Publications

We previously hypothesized that Staphylococcus epidermidis senses a diverse set of environmental and nutritional factors associated with biofilm formation through a modulation in the activity of the tricarboxylic acid (TCA) cycle. Herein, we report our further investigation of the impact of additional environmental stress factors on TCA cycle activity and provide a detailed description of our NMR methodology. S. epidermidis wild-type strain 1457 was treated with stressors that are associated with biofilm formation, a sub-lethal dose of tetracycline, 5% NaCl, 2% glucose and autoinducer-2 (AI-2). As controls and to integrate our current data with our previous study, 4% ethanol stress …

Systematic Revision Of The Northern Short-Tailed Shrew, Blarina Brevicauda (Say), Wm. David Webster, Nancy D. Moncrief, Jerry R. Choate, Hugh H. Genoways

University of Nebraska State Museum: Mammalogy Papers

Short-tailed shrews, genus Blarina, are common inhabitants of a variety of terrestrial habitats in most of eastern North America. Of the 4 species currently recognized, the northern short-tailed shrew, Blarina brevicauda (Say, 1823), is the most widely distributed, occurring from southern Canada southward to the central Great Plains and the Appalachian Mountains into Georgia and Alabama and along the East Coast as far south as southeastern North Carolina. It has been more than 65 years since geographic variation within this species has been studied. Accordingly, the objectives of this study were to examine geographic variation in Blarina brevicauda and …

In Memoriam: Robert Katz (1917–2011), M. P. R. Waligorski, Francis A. Cucinotta

Robert Katz Publications

Bob Katz will be well remembered for his enthusiasm and strong personality. In a scientific dispute, few indeed could match his wit or his sense of humor or survive the cutting logic of his arguments. To those who had appreciation for his science and his personality, he was truly a great scientist and a master teacher. There are many people around the world who will remember Bob Katz for what he offered them and for the way he showed them what truth in science is.

The Katz Model, developed at that time for solid-state detectors and for cell cultures, relates …

A Study Of 131iodine Labeling Of Indomethacin, Its In Vivo Biological Distribution In Lewis-Bearing Lung Cancer, And Its Induction Of Apoptosis In Lung Cancer., Jiu-Bo Cai, Cai-Xia Zhang, Jia-Wen Luo, Dong Wang

Saudi Medical Journal

OBJECTIVES: To study the synthesis of 131iodine (I) labeled histamine-indomethacin (His-IN), its in vivo distribution in Lewis-bearing mice, and its effects on suppression of Lewis lung cancer growth and induction of apoptosis. METHODS: The present study was carried out in the Experimental Research Center, Sheng Jing Hospital of China Medical University Hospital, Shenyang China between December 2008 and October 2009. Chemical synthesis of His-IN was carried out. Ninety-five C57 mice were allocated into 12 groups, and a series of experiments including the in vivo biological distribution of 131I-His-IN in C57 mice bearing Lewis lung cancer was explored, and the therapeutic …

Thinking About The Future Cognitive Remediation Therapy—What Works And Could We Do Better?, Til Wykes, William D. Spaulding

Department of Psychology: Faculty Publications

This article reviews progress in the development of effective cognitive remediation therapy (CRT) and its translational process. There is now enough evidence that cognitive difficulties experienced by people with schizophrenia can change and that the agenda for the next generation of studies is to increase these effects systematically through cognitive remediation. We examine the necessary steps and challenges of moving CRT to treatment dissemination. Theories which have been designed to explain the effects of cognitive remediation, are important but we conclude that they are not essential for dissemination which could progress in an empirical fashion. One apparent barrier is that …

Human Fatty Acid Transport Protein 2a/Very Long Chain Acyl-Coa Synthetase 1 (Fatp2a/Acsvl1) Has A Preference In Mediating The Channeling Of Exogenous N-3 Fatty Acids Into Phosphatidylinositol, Elaina M. Melton, Ronald Cerny, Paul A. Watkins, Concetta C. Dirusso, Paul N. Black

Ronald Cerny Publications

The trafficking of fatty acids across the membrane and into downstream metabolic pathways requires their activation to CoA thioesters. Members of the fatty acid transport protein/ very long chain acyl-CoA synthetase (FATP/Acsvl) family are emerging as key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis.We have expressed two naturally occurring splice variants of human FATP2 (Acsvl1) in yeast and 293T-REx cells and addressed their roles in fatty acid transport, activation, and intracellular trafficking. Although both forms (FATP2a (Mr 70,000) and FATP2b (Mr 65,000 and lacking exon3, which encodes part of the …

Overexpression Of Galnac-Transferase Galnac-T3 Promotes Pancreatic Cancer Cell Growth, Keisuke Taniuchi, Ronald Cerny, Aki Tanouchi, Kimitoshi Kohno, Norihiro Kotani, Koichi Honke, Toshiji Saibara, Michael A. Hollingsworth

Ronald Cerny Publications

O-linked glycans of secreted and membrane bound proteins play an important role in the pathogenesis of pancreatic cancer by modulating immune responses, inflammation, and tumorigenesis. A critical aspect of O-glycosylation, the position at which proteins are glycosylated with N-acetyl-galactosamine on serine and threonine residues, is regulated by the substrate specificity of UDP-GalNAc: polypeptide N-acetylgalactosaminyl-transferases (GalNAc-Ts). Thus, GalNAc-Ts regulate the first committed step in O-glycosylated protein biosynthesis, determine sites of O-glycosylation on proteins, and are important for understanding normal and carcinoma-associated O-glycosylation. We have found that one of these enzymes, GalNAc-T3, is overexpressed in …

Identification And Characterization Of The Anti-Methicillin-Resistant Staphylococcus Aureus Wap-8294a2 Biosynthetic Gene Cluster From Lysobacter Enzymogenes Oh11, Wei Zhang, Yaoyao Li, Guoliang Qian, Yan Wang, Haotong Chen, Yue-Zhong Li, Fengquan Liu, Yuemao Shen, Liangcheng Du

Department of Chemistry: Faculty Publications

Lysobactor enzymogenes strain OH11 is an emerging biological control agent of fungal and bacterial diseases. We recently completed its genome sequence and found it contains a large number of gene clusters putatively responsible for the biosynthesis of nonribosomal peptides and polyketides, including the previously identified antifungal dihydromaltophilin (HSAF). One of the gene clusters contains two huge open reading frames, together encoding 12 modules of nonribosomal peptide synthetases (NRPS). Gene disruption of one of the NRPS led to the disappearance of a metabolite produced in the wild type and the elimination of its antibacterial activity. The metabolite and antibacterial activity were …

Characterizing Rna Dynamics At Atomic Resolution Using Solution-State Nmr Spectroscopy, Jameson R. Bothe, Evgenia N. Nikolova, Catherine D. Eichhorn, Jeetender Chugh, Alexandar L. Hansen, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering.

Energy And Climate Implications For Agricultural Nutrient Use Efficiency, Adam J. Liska, Richard K. Perrin

Adam Liska Papers

Energy and climate change are beginning to dominate the global political agenda and will drive policy formation that will shape the future of agriculture. Energy issues threaten national security and economic stability, as well as access to low-cost nutrient inputs for agriculture. Climate change has the potential to cause serious disruption to agricultural productivity. Paradoxically, nutrient use in agriculture to increase crop yields has the potential to negatively impact climate. This chapter will discuss recent and future energy and climate trends, the relationships between agricultural nutrient use efficiency and biofuels, and how global land limitations will shape agriculture in the …

Effect Of Distillers Grains Moisture And Inclusion Level In Livestock Diets On Greenhouse Gas Emissions In The Corn-Ethanol-Livestock Life Cycle, Virgil R. Bremer, Andrea K. Watson, Adam J. Liska, Galen Erickson, Kenneth Cassman, Kathryn J. Hanford, Terry Klopfenstein

Adam Liska Papers

A model was previously developed (Biofuel Energy Systems Simulator; www. bess.unl.edu) to predict greenhouse gas (GHG) emissions and net energy yield when ethanol is produced from corn. The model also predicts feedlot cattle, dairy cattle, and swine performance and feed replacement value of ethanol coproducts. Updated equations that predict performance of feedlot cattle fed 0 to 40% of dietary DM as corn wet (WDGS), modified (MDGS), or dry (DDGS) distillers grains plus solubles replacing dry-rolled and high-moisture corn were developed and incorporated into the model. Equations were derived from pen-level performance for 20 finishing studies evaluating WDGS, 4 evaluating MDGS, …

Chromatographic Analysis Of Drug Interactions In The Serum Proteome, David S. Hage, Jeanethe A. Anguizola, Abby J. Jackson, Ryan Matsuda, Efthimia Papastavros, Erika Pfaunmiller, Zenghan Tong, John Vargas-Badilla, Michelle J. Yoo, Xiwei Zheng

David Hage Publications

The binding of drugs with serum proteins and binding agents such as human serum albumin, a1-acid glycoprotein, and lipoproteins is an important process in determining the activity and fate of many pharmaceuticals in the body. A variety of techniques have been used to study drug interactions with serum proteins, but there is still a need for faster or better methods for such work. High-performance liquid chromatography (HPLC) is one tool that has been utilized in many formats for these types of measurements. Advantages of using HPLC for this application include its speed and precision, its ability to be automated, its …