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University of Nebraska - Lincoln

2006

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Articles 31 - 52 of 52

Full-Text Articles in Chemistry

Protein–Protein Interactions Of Tandem Affinity Purification-Tagged Protein Kinases In Rice, Jai S. Rohila, Mei Chen, Shuo Chen, Johann Chen, Ronald Cerny, Chris Dardick, Patrick Canlas, Xia Xu, Michael Gribskov, Siddhartha Kanrar, Jian-Kang Zhu, P C. Ronald, Michael E. Fromm Apr 2006

Protein–Protein Interactions Of Tandem Affinity Purification-Tagged Protein Kinases In Rice, Jai S. Rohila, Mei Chen, Shuo Chen, Johann Chen, Ronald Cerny, Chris Dardick, Patrick Canlas, Xia Xu, Michael Gribskov, Siddhartha Kanrar, Jian-Kang Zhu, P C. Ronald, Michael E. Fromm

Ronald Cerny Publications

Forty-one rice cDNAs encoding protein kinases were fused to the tandem affinity purification (TAP) tag and expressed in transgenic rice plants. The TAP-tagged kinases and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by mass spectrometry. Ninety-five percent of the TAP-tagged kinases were recovered. Fifty-six percent of the TAP-tagged kinases were found to interact with other rice proteins. A number of these interactions were consistent with known protein complexes found in other species, validating the TAP-tag method in rice plants. Phosphorylation sites were identified on four of the kinases that interacted with either …

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A Comparative Genomic Analysis Of Chlorella Nc64a Virus Ny-2a And Chlorella Pbi Virus Mt325 From The Family Phycodnaviridae, Lisa A. Fitzgerald Mar 2006

A Comparative Genomic Analysis Of Chlorella Nc64a Virus Ny-2a And Chlorella Pbi Virus Mt325 From The Family Phycodnaviridae, Lisa A. Fitzgerald

Department of Chemistry: Dissertations, Theses, and Student Research

The family Phycodnaviridae consists of a morphologically similar but genetically diverse group of large dsDNA viruses which infect both fresh and marine water eukaryotic algae. Two viruses, the 370 kb Chlorella NC64A virus NY-2A and the 313 kb Chlorella Pbi virus MT325, from the family Phycodnaviridae, genus Chlorovirus, were sequenced, analyzed, and compared to the prototype chlorella virus PBCV-1. The NY-2A genome, the largest chlorella viral genome sequenced to date, contains 886 open reading frames (ORFs) of 65 codons or larger and encodes 404 putative proteins and 7 tRNAs. The MT325 genome, the smallest chlorella viral genome sequenced to date, …

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Electrolytic Deposition Of Coatings For Prosthetic Metals And Alloys, Jody G. Redepenning Mar 2006

Electrolytic Deposition Of Coatings For Prosthetic Metals And Alloys, Jody G. Redepenning

Chemistry Department: Faculty Publications

An article coated with an electrolytically deposited biocompatible composite layer useful as an internal prosthetic device is disclosed. The bio-compatible composite coating that is electrolytically deposited onto the article comprises hydroxyapatite and chitosan. The introduction of chitosan into the crystal matrix of brushite/hydroxyapatite significantly improves the adhesive and chemical and mechanical stability properties of the coating.
United States Patent Number 7,014,749 B2

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Rapid, Sequence-Specific Detection Of Unpurified Pcr Amplicons Via A Reusable, Electrochemical Sensor, Rebecca Lai, Eric T. Hagally, Sang-Ho Lee, H. T. Soh, Kevin W. Plaxco, Alan J. Heeger Mar 2006

Rapid, Sequence-Specific Detection Of Unpurified Pcr Amplicons Via A Reusable, Electrochemical Sensor, Rebecca Lai, Eric T. Hagally, Sang-Ho Lee, H. T. Soh, Kevin W. Plaxco, Alan J. Heeger

Rebecca Lai Publications

We report an electrochemical method for the sequence-specific detection of unpurified amplification products of the gyrB gene of Salmonella typhimurium. Using an asymmetric PCR and the electrochemical E-DNA detection scheme, single-stranded amplicons were produced from as few as 90 gene copies and, without subsequent purification, rapidly identified. The detection is specific; the sensor does not respond when challenged with control oligonucleotides based on the gyrB genes of either Escherichia coli or various Shigella species. In contrast to existing sequence-specific optical- and capillary electrophoresis- based detection methods, the E-DNA sensor is fully electronic and requires neither cumbersome, expensive optics nor …

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Fabrication Of Nanopillars By Nanosphere Lithography, Chin Li Cheung, R. J. Nikolic, C. E. Reinhardt, T. F. Wang Mar 2006

Fabrication Of Nanopillars By Nanosphere Lithography, Chin Li Cheung, R. J. Nikolic, C. E. Reinhardt, T. F. Wang

Barry Chin Li Cheung Publications

A low cost nanosphere lithography method for patterning and generation of semiconductor nanostructures provides a potential alternative to the conventional top-down fabrication techniques. Forests of silicon pillars of sub-500 nm diameter and with an aspect ratio up to 10 were fabricated using a combination of the nanosphere lithography and deep reactive ion etching techniques. The nanosphere etch mask coated silicon substrates were etched using oxygen plasma and a timemultiplexed “Bosch” process to produce nanopillars of different length, diameter and separation. Scanning electron microscopy data indicate that the silicon etch rates with the nanoscale etch masks decrease linearly with increasing aspect …

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Supplemental Materials For "Distinct Ceramide Synthases Regulate Polarized Growth In The Filamentous Fungus Aspergillus NidulansD", Shaojie Li, Liangcheng Du, Gary Yuen, Steven D. Harris Mar 2006

Supplemental Materials For "Distinct Ceramide Synthases Regulate Polarized Growth In The Filamentous Fungus Aspergillus NidulansD", Shaojie Li, Liangcheng Du, Gary Yuen, Steven D. Harris

Liangcheng Du Publications

Four figures not included in the print edition of the above-referenced article, that was published in Molecular Biology of the Cell, Vol. 17, 1218–1227 (March 2006). :

Figure 1 - barA mutants are resistant to the effects of HPLC-purified HSAF.

Figure 2 - Alignment of Lag1 homologues.

Figure 3 - Alignments of BasA homologues.

Figure 4 - Growth defects of lagA mutants.

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Distinct Ceramide Synthases Regulate Polarized Growth In The Filamentous Fungus Aspergillus NidulansD, Shaojie Li, Liangcheng Du, Gary Yuen, Steven D. Harris Mar 2006

Distinct Ceramide Synthases Regulate Polarized Growth In The Filamentous Fungus Aspergillus NidulansD, Shaojie Li, Liangcheng Du, Gary Yuen, Steven D. Harris

Liangcheng Du Publications

In filamentous fungi, the stabilization of a polarity axis is likely to be a pivotal event underlying the emergence of a germ tube from a germinating spore. Recent results implicate the polarisome in this process and also suggest that it requires localized membrane organization. Here, we employ a chemical genetic approach to demonstrate that ceramide synthesis is necessary for the formation of a stable polarity axis in the model fungus Aspergillus nidulans. We demonstrate that a novel compound (HSAF) produced by a bacterial biocontrol agent disrupts polarized growth and leads to loss of membrane organization and formin localization at …

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A Formal [3,3]-Sigmatropic Rearrangement Route To Quaternary Α-Vinyl Amino Acids: Use Of Allylic N-Pmp Trifluoroacetimidates, David B. Berkowitz, Bin Wu, Huijie Li Mar 2006

A Formal [3,3]-Sigmatropic Rearrangement Route To Quaternary Α-Vinyl Amino Acids: Use Of Allylic N-Pmp Trifluoroacetimidates, David B. Berkowitz, Bin Wu, Huijie Li

David Berkowitz Publications

Pd(II)-mediated rearrangement of allylic N-PMP (p-methoxyphenyl) trifluoroacetimidates provides the first formal sigmatropic route to quaternary, α-vinylic amino acids, potential suicide substrates for PLP-enzymes. The amino acid side chains enter via transition metal-mediated C-C bond constructions, including (i) Cu(I)-mediated conjugate addition (Ala); (ii) Pd(0)/AsPh3-mediated Stille coupling (Allyl-Gly, Phe, DOPA, m-Tyr) and (iii) Pd(0)/Pt-Bu3-mediated Negishi coupling (Leu). In the synthesis of the DOPA decarboxylase inactivator, α-vinyl-m-tyrosine, the new N-PMP trifluoroacetimidate rearranges much more efficiently than the corresponding trichloroacetimidate.

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Future Of Semiconductor Based Thermal Neutron Detectors, R. J. Nikolić, Chin Li Cheung, C. E. Reinhardt, T. F. Wang Feb 2006

Future Of Semiconductor Based Thermal Neutron Detectors, R. J. Nikolić, Chin Li Cheung, C. E. Reinhardt, T. F. Wang

Barry Chin Li Cheung Publications

Thermal neutron detectors have seen only incremental improvements over the last decades. In this paper we overview the current technology of choice for thermal neutron detection – 3He tubes, which suffer from, moderate to poor fieldability, and low absolute efficiency. The need for improved neutron detection is evident due to this technology gap and the fact that neutrons are a highly specific indicator of fissile material. Recognizing this need, we propose to exploit recent advances in microfabrication technology for building the next generation of semiconductor thermal neutron detectors for national security requirements, for applications requiring excellent fieldability of small …

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Rhodium-Catalyzed Asymmetric Hydrogenation Using Self-Assembled Chiral Bidentate Ligands, James M. Takacs, Kittichai Chaiseeda, Shin A. Moteki, D. Sahadeva Reddy, Di Wu, Kusumlata Chandra Feb 2006

Rhodium-Catalyzed Asymmetric Hydrogenation Using Self-Assembled Chiral Bidentate Ligands, James M. Takacs, Kittichai Chaiseeda, Shin A. Moteki, D. Sahadeva Reddy, Di Wu, Kusumlata Chandra

James Takacs Publications

The chirality-directed self-assembly of bifunctional subunits around a structural metal-typically, zinc(II)-is used to form a heteroleptic complex in which a second set of ligating groups are suitably disposed to bind a second metal, forming a heterobimetallic catalyst system. We find that subtle changes in the structural backbone (i.e., ligand scaffold) of such chiral bidentate self-assembled ligands (SALs) can be used to manipulate the ligand topography and chiral environment around catalytic metal; thus, the scaffold can be optimized to maximize asymmetric induction. Using this combinatorial strategy for ligand synthesis, a preliminary study was carried out in which a library of 110 …

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A Topology-Constrained Distance Network Algorithm For Protein Structure Determination From Noesy Data, Yuanpeng Janet Huang, Roberto Tejero, Robert Powers, Gaetano T. Montelione Feb 2006

A Topology-Constrained Distance Network Algorithm For Protein Structure Determination From Noesy Data, Yuanpeng Janet Huang, Roberto Tejero, Robert Powers, Gaetano T. Montelione

Robert Powers Publications

This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology- constrained distance network analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DYANA. The minimum input for AutoStructure includes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStructure can also analyze homodimeric proteins when X-filtered NOESY experiments are available. The quality …

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Changes In Dna Bending And Flexing Due To Tethered Cations Detected By Fluorescence Resonance Energy Transfer, Sarah L. Williams, Laura K. Parkhurst, Lawrence J. Parkhurst Feb 2006

Changes In Dna Bending And Flexing Due To Tethered Cations Detected By Fluorescence Resonance Energy Transfer, Sarah L. Williams, Laura K. Parkhurst, Lawrence J. Parkhurst

Lawrence Parkhurst Publications

Local DNA deformation arises from an interplay among sequence-related base stacking, intrastrand phosphate repulsion, and counterion and water distribution, which is further complicated by the approach and binding of a protein. The role of electrostatics in this complex chemistry was investigated using tethered cationic groups that mimic proximate side chains. A DNA duplex was modified with one or two centrally located deoxyuracils substituted at the 5-position with either a flexible 3-aminopropyl group or a rigid 3-aminopropyn-1-yl group. End-to-end helical distances and duplex flexibility were obtained from measurements of the time-resolved Fö̈rster resonance energy transfer between 5’- and 3’-linked dye pairs. …

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A Bidomain Nonribosomal Peptide Synthetase Encoded By Fum14 Catalyzes The Formation Of Tricarballylic Esters In The Biosynthesis Of Fumonisins, Kathia Zaleta-Rivera, Chunping Xu, Fengan Yu, Robert A. E. Butchko, Robert H. Proctor, Maria E. Hidalgo-Lara, Ashraf S. Raza, Patrick Dussault, Liangcheng Du Feb 2006

A Bidomain Nonribosomal Peptide Synthetase Encoded By Fum14 Catalyzes The Formation Of Tricarballylic Esters In The Biosynthesis Of Fumonisins, Kathia Zaleta-Rivera, Chunping Xu, Fengan Yu, Robert A. E. Butchko, Robert H. Proctor, Maria E. Hidalgo-Lara, Ashraf S. Raza, Patrick Dussault, Liangcheng Du

Patrick Dussault Publications

Fumonisins are a group of polyketide-derived mycotoxins produced by Fusarium Verticillioides, a filamentous fungus infecting corn and contaminating food and feeds. Fumonisins contain two tricarballylic esters that are critical for toxicity. Here, we present genetic and biochemical data for the esterification mechanism. FUM14 in F. Verticillioides has been deleted by homologous recombination, and the resultant mutant lost the ability to produce fumonisins. Two new metabolites, HFB3 and HFB4, which are biosynthetic precursors of fumonisins lacking the tricarballylic esters, were detected in the mutant. The results suggest that FUM14 is required for the esterification of fumonisins. FUM14 …

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Structures And Relative Stability Of Medium-Sized Silicon Clusters. Iv. Motif Based Low-Lying Clusters Si21–Si30, Soohaeng Yoo, Xiao Cheng Zeng Feb 2006

Structures And Relative Stability Of Medium-Sized Silicon Clusters. Iv. Motif Based Low-Lying Clusters Si21–Si30, Soohaeng Yoo, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Structures and relative stability of four families of low-lying silicon clusters in the size range of Sin(n=21–30) are studied, wherein two families of the clusters show prolate structures while the third one shows near-spherical structures. The prolate clusters in the first family can be assembled by connecting two small-sized magic clusters Sin(n=6, 7, 9, or 10) via a fused-puckered-hexagonal-ring Si9 unit (a fragment of bulk diamond silicon), while those in the second family can be constructed on the basis of a structural motif consisting of a puckered-hexagonal-ring Si6 unit (also …

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Global Characterization Of Porcine Intrauterine Proteins During Early Pregnancy, Jean-Patrick R. Kayser, Jong G. Kim, Ronald Cerny, Jeffrey L. Vallet Jan 2006

Global Characterization Of Porcine Intrauterine Proteins During Early Pregnancy, Jean-Patrick R. Kayser, Jong G. Kim, Ronald Cerny, Jeffrey L. Vallet

Ronald Cerny Publications

Total protein secreted in the intrauterine lumen increases between day 10 and 13 post-estrus in both cyclic and pregnant gilts. The objective of this experiment was to identify those intrauterine proteins whose secretion changes during this time period. Sixteen mature gilts were either mated (day 0) or remained cyclic and were slaughtered at either day 10 or day 13 (n = 4 per status by day). At slaughter, each uterine horn was flushed with 20 ml Minimal Essential Medium. Flushings were dialyzed extensively against distilled water. A 0.5 ml aliquot of each was lyophilized, subjected to two-dimensional PAGE, and protein …

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Direct Detection Of Double-Stranded Dna: Molecular Methods And Applications For Dna Diagnostics, Indraneel Ghosh, Cliff I. Stains, Aik T. Ooi, David J. Segal Jan 2006

Direct Detection Of Double-Stranded Dna: Molecular Methods And Applications For Dna Diagnostics, Indraneel Ghosh, Cliff I. Stains, Aik T. Ooi, David J. Segal

Cliff Stains Publications

Methodologies to detect DNA sequences with high sensitivity and specificity have tremendous potential as molecular diagnostic agents. Most current methods exploit the ability of single-stranded DNA (ssDNA) to base pair with high specificity to a complementary molecule. However, recent advances in robust techniques for recognition of DNA in the major and minor groove have made possible the direct detection of double-stranded DNA (dsDNA), without the need for denaturation, renaturation, or hybridization. This review will describe the progress in adapting polyamides, triplex DNA, and engineered zinc finger DNA-binding proteins as dsDNA diagnostic systems. In particular, the sequence-enabled reassembly (SEER) method, involving …

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Negative Impact Of Noise On The Principal Component Analysis Of Nmr Data, Steven M. Halouska, Robert Powers Jan 2006

Negative Impact Of Noise On The Principal Component Analysis Of Nmr Data, Steven M. Halouska, Robert Powers

Chemistry Department: Faculty Publications

Principal component analysis (PCA) is routinely applied to the study of NMR based metabolomic data. PCA is used to simplify the examination of complex metabolite mixtures obtained from biological samples that may be composed of hundreds or thousands of chemical components. PCA is primarily used to identify relative changes in the concentration of metabolites to identify trends or characteristics within the NMR data that permits discrimination between various samples that differ in their source or treatment. A common concern with PCA of NMR data is the potential over emphasis of small changes in high concentration metabolites that would over-shadow signifi …

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Stability Of Warfarin Solutions For Drug–Protein Binding Measurements: Spectroscopic And Chromatographic Studies, Annette C. Moser, Charles A. Kingsbury, David S. Hage Jan 2006

Stability Of Warfarin Solutions For Drug–Protein Binding Measurements: Spectroscopic And Chromatographic Studies, Annette C. Moser, Charles A. Kingsbury, David S. Hage

Chemistry Department: Faculty Publications

Warfarin is commonly used in drug–protein binding studies as a displacement marker for Sudlow site I on the protein human serum albumin (HSA). This study examined the stability of aqueous warfarin solutions prepared for such experiments. This was investigated using NMR spectroscopy and affinity chromatography. It was found by 1H NMR that warfarin underwent a slow first-order conversion in aqueous solution. The rate of this reaction increased with temperature, giving rate constants at pH 7.4 of 0.0086 h−1 at 25 °C and 0.041 h−1 at 37 °C. It was concluded from further 1H and 13C NMR studies, along …

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Sequence-Enabled Reassembly (Seer) Peptides For The Detection Of Dna Sequences, Aik T. Ooi, Cliff I. Stains, Jason R. Porter, Indraneel Ghosh, David J. Segal Jan 2006

Sequence-Enabled Reassembly (Seer) Peptides For The Detection Of Dna Sequences, Aik T. Ooi, Cliff I. Stains, Jason R. Porter, Indraneel Ghosh, David J. Segal

Cliff Stains Publications

By combining custom zinc finger (ZF) DNA-binding technology [1,2] with protein fragment complementation [3], we have developed a technology, designated SEER (Sequence-Enabled Reassembly), that has the potential to “see” or detect genetic information within a living cell (Figure 1). These agents consist of two inactive parts of signal-generating peptides that have the ability to recognize specific DNA sequences. The two parts bind near each other in the presence of a user-defined DNA target site and generate a fluorescent signal. Two prototype SEER systems have been constructed, based on the reassembly of green fluorescent protein (SEERGFP) [4] and the enzyme β-lactamase …

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The Elastic Constants And Related Properties Of The Energetic Material Cyclotrimethylene Trinitramine (Rdx) Determined By Brillouin Scattering, James J. Haycraft, Lewis L. Stevens, Craig J. Eckhardt Jan 2006

The Elastic Constants And Related Properties Of The Energetic Material Cyclotrimethylene Trinitramine (Rdx) Determined By Brillouin Scattering, James J. Haycraft, Lewis L. Stevens, Craig J. Eckhardt

Craig J. Eckhardt Publications

The acoustic phonons of cyclotrimethylene trinitramine (RDX) have been studied using Brillouin scattering. The analysis of the acoustic-phonon velocities allowed determination of the complete stiffness tensor for this energetic material. The results are compared to other recent experimental and theoretical determinations of the RDX elastic constants, bulk moduli, and shear moduli. The observed ordering of elastic constants, C11>C22>C33, is qualitatively associated with a (001) cleavage plane and molecular packing. This interpretation is further corroborated by the linear compressibilities plotted in three crystallographic planes, and a comparison to recent theoretical and experimental hydrostatic compression studies …

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A Minimum-Impact Method For Measuring Corrosion Rate Of Steel-Hulled Shipwrecks In Seawater, Matthew A. Russell, David L. Conlin, Larry E. Murphy, Donald L. Johnson, Brent M. Wilson, James D. Carr Jan 2006

A Minimum-Impact Method For Measuring Corrosion Rate Of Steel-Hulled Shipwrecks In Seawater, Matthew A. Russell, David L. Conlin, Larry E. Murphy, Donald L. Johnson, Brent M. Wilson, James D. Carr

Chemistry Department: Faculty Publications

Current research on USS Arizona is focused on a minimum-impact technique for calculating corrosion rate of the battleship’s steel hull by analysing physical and chemical properties of marine encrustation covering the exposed hull. An equation is derived that allows concretion thickness, density, and total iron content to be used to calculate corrosion rate of steel hull plate.

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Isotope Sourcing Of Prehistoric Willow And Tule Textiles Recovered From Western Great Basin Rock Shelters And Caves: Proof Of Concept, Larry V. Benson, E. M. Hattori, H. E. Taylor, S. R. Poulson, E. A. Jolie Jan 2006

Isotope Sourcing Of Prehistoric Willow And Tule Textiles Recovered From Western Great Basin Rock Shelters And Caves: Proof Of Concept, Larry V. Benson, E. M. Hattori, H. E. Taylor, S. R. Poulson, E. A. Jolie

United States Geological Survey: Staff Publications

Isotope and trace-metal analyses were used to determine the origin of plants used to manufacture prehistoric textiles (basketry and matting) from archaeological sites in the western Great Basin. Research focused on strontium (87Sr/86Sr) and oxygen (18O/16O) isotope ratios of willow (Salix sp.) and tule (Schoenoplectus sp.), the dominant raw materials in Great Basin textiles. The oxygen-isotope data indicated that the willow and tule used to produce the textiles were harvested from the banks of rivers or in marshes characterized by flowing water and not from lakes or sinks. The strontium-isotope …

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