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Fractionation Of The Rice Bran Layer And Quantification Of Vitamin E, Oryzanol, Protein, And Rice Bran Saccharide, Rebecca Schramm, Alicia Abadie, Na Hua, Zhimin Xu, Marybeth Lima Dec 2007

Fractionation Of The Rice Bran Layer And Quantification Of Vitamin E, Oryzanol, Protein, And Rice Bran Saccharide, Rebecca Schramm, Alicia Abadie, Na Hua, Zhimin Xu, Marybeth Lima

Faculty Publications

Value-added processing with respect to rice milling has traditionally treated the rice bran layer as a homogenous material that contains significant concentrations of high-value components of interest for pharmaceutical and nutraceutical applications. Investigators have shown that high-value components in the rice bran layer vary from differences in kernel-thickness, bran fraction, rice variety, and environmental conditions during the growing season. The objectives of this study were to quantify the amount of rice bran removed at pre-selected milling times and to correlate the amount of rice bran removed at each milling time with the concentration of vitamin E, gamma-oryzanol, rice bran saccharide, …

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Mobile Dna Elements In Primate And Human Evolution, Jinchuan Xing, David J. Witherspoon, David A. Ray, Mark A. Batzer, Lynn B. Jorde Dec 2007

Mobile Dna Elements In Primate And Human Evolution, Jinchuan Xing, David J. Witherspoon, David A. Ray, Mark A. Batzer, Lynn B. Jorde

Faculty Publications

Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements. The causes and evolutionary consequences of mobile element insertion, which have received considerable attention during the past decade, are reviewed in this article. Because of their unique mutational mechanisms, these elements are highly useful for answering phylogenetic questions. We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the human-chimpanzee- gorilla trichotomy and New World primate phylogeny. Alu and LINE1 element insertion polymorphisms have also been analyzed in human populations to test hypotheses about …

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Shared Parasitoids In A Metacommunity: Indirect Interactions Inhibit Herbivore Membership In Local Communities, James T. Cronin Dec 2007

Shared Parasitoids In A Metacommunity: Indirect Interactions Inhibit Herbivore Membership In Local Communities, James T. Cronin

Faculty Publications

The interaction between species, mediated by a shared natural enemy (i.e., apparent competition), has been the subject of much theoretical and empirical investigation. However, we lack field experiments that assess the importance of apparent competition to metacommunity structure. Here, I conducted a series of field experiments to test whether apparent competition, mediated by shared egg parasitoids (Anagrus nigriventris and A. columbi), occurs between two abundant planthopper species (Delphacodes scolochloa and Prokelisia crocea) of the North American Great Plains. The two planthoppers feed on different plant species within prairie potholes (wet depressions) and, thus, do not interact directly. At the scale …

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From Population Sources To Sieves: The Matrix Alters Host-Parasitoid Source-Sink Structure, James T. Cronin Dec 2007

From Population Sources To Sieves: The Matrix Alters Host-Parasitoid Source-Sink Structure, James T. Cronin

Faculty Publications

Field experiments that examine the impact of immigration, emigration, or landscape structure (e.g., the composition of the matrix) on the source-sink dynamics of fragmented populations are scarce. Here, planthoppers (Prokelisia crocea) and egg parasitoids (Anagrus columbi) were released among host-plant patches that varied in structural (caged, isolated, or in a network of other patches) and functional (mudflat matrix that impedes dispersal vs. brome-grass matrix that facilitates dispersal) connectivity. Planthoppers and parasitoids on caged patches exhibited density-dependent growth rates, achieved high equilibrium densities, and rarely went extinct. Therefore, experimental cordgrass patches were classified as population sources. Because access to immigrants did …

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The Need For Proper Vouchering In Phylogenetic Studies Of Birds, A. Townsend Peterson, Robert G. Moyle, Árpád S. Nyári, Mark B. Robbins, Robb T. Brumfield, J. V. Remsen Dec 2007

The Need For Proper Vouchering In Phylogenetic Studies Of Birds, A. Townsend Peterson, Robert G. Moyle, Árpád S. Nyári, Mark B. Robbins, Robb T. Brumfield, J. V. Remsen

Faculty Publications

No abstract provided.

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Fluxes Of Iron And Manganese Across The Sediment-Water Interface Under Various Redox Conditions, Svetlana V. Pakhomova, Per O.J. Hall, Mikhail Yu Kononets, Alexander G. Rozanov, Anders Tengberg, Andrei V. Vershinin Dec 2007

Fluxes Of Iron And Manganese Across The Sediment-Water Interface Under Various Redox Conditions, Svetlana V. Pakhomova, Per O.J. Hall, Mikhail Yu Kononets, Alexander G. Rozanov, Anders Tengberg, Andrei V. Vershinin

Faculty Publications

Fluxes of dissolved forms of iron and manganese across the sediment-water interface were studied in situ in the Gulf of Finland and the Vistula Lagoon (Baltic Sea), and in the Golubaya Bay (Black Sea) from 2001 to 2005. Fluxes were measured using chamber incubations, and sediment cores were collected and sliced to assess the porewater and solid phase metal distribution at different depths. Measured and calculated benthic fluxes of manganese and iron were directed out of sediment for all sites and were found to vary between 70-4450 and 5-1000 μmole m- 2 day- 1 for manganese and iron, respectively. The …

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Impact Of Energy Intake, Physical Activity, And Population-Wide Weight Loss On Cardiovascular Disease And Diabetes Mortality In Cuba, 1980-2005, Manuel Franco, Pedro Orduñez, Benjamín Caballero, José A. Tapia Granados, Mariana Lazo, José Luís Bernal, Eliseo Guallar, Richard S. Cooper Dec 2007

Impact Of Energy Intake, Physical Activity, And Population-Wide Weight Loss On Cardiovascular Disease And Diabetes Mortality In Cuba, 1980-2005, Manuel Franco, Pedro Orduñez, Benjamín Caballero, José A. Tapia Granados, Mariana Lazo, José Luís Bernal, Eliseo Guallar, Richard S. Cooper

Faculty Publications

Cuba's economic crisis of 1989-2000 resulted in reduced energy intake, increased physical activity, and sustained population-wide weight loss. The authors evaluated the possible association of these factors with mortality trends. Data on per capita daily energy intake, physical activity, weight loss, and smoking were systematically retrieved from national and local surveys. National vital statistics from 1980-2005 were used to assess trends in mortality from diabetes, coronary heart disease, stroke, cancer, and all causes. The crisis reduced per capita daily energy intake from 2,899 calories to 1,863 calories. During the crisis period, the proportion of physically active adults increased from 30% …

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Density Gradient Enrichment Of Escherichia Coli Conditional Msba Mutants, William T. Doerrler Dec 2007

Density Gradient Enrichment Of Escherichia Coli Conditional Msba Mutants, William T. Doerrler

Faculty Publications

Insight into the mechanism of lipid transport to the outer membrane of gram-negative bacteria has been hampered by the lack of an effective genetic screen for defective mutants. This work demonstrates an enrichment of conditional mutants defective in lipopolysaccharide export by Ludox density gradient centrifugation and selection for detergent resistance. New temperature-sensitive mutants with lipid export defects were isolated with single missense mutations in msbA. The results demonstrate the power of this approach for the study of lipid export in Escherichia coli. Copyright © 2007, American Society for Microbiology. All Rights Reserved.

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Cold Seeps And Associated Communities Of The Gulf Of Mexico, Charles Fisher, Harry Roberts, Erik Cordes, Bernie Bernard Dec 2007

Cold Seeps And Associated Communities Of The Gulf Of Mexico, Charles Fisher, Harry Roberts, Erik Cordes, Bernie Bernard

Faculty Publications

No abstract provided.

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A Random Change Of Variables And Applications To The Stochastic Porous Medium Equation With Multiplicative Time Noise, S V Lototsky Dec 2007

A Random Change Of Variables And Applications To The Stochastic Porous Medium Equation With Multiplicative Time Noise, S V Lototsky

Communications on Stochastic Analysis

No abstract provided.

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Improving Protein Crystal Quality By Selective Removal Of A Ca 2+-Dependent Membrane-Insertion Loop, David B. Neau, Nathaniel C. Gilbert, Sue G. Bartlett, Adam Dassey, Marcia E. Newcomer Nov 2007

Improving Protein Crystal Quality By Selective Removal Of A Ca 2+-Dependent Membrane-Insertion Loop, David B. Neau, Nathaniel C. Gilbert, Sue G. Bartlett, Adam Dassey, Marcia E. Newcomer

Faculty Publications

Lipoxygenases (LOXs) catalyze the regiospecific and stereospecific dioxygenation of polyunsaturated membrane-embedded fatty acids. A Ca 2+-dependent membrane-binding function was localized to the amino-terminal C2-like domain of 8R-lipoxygenase (8R-LOX) from the soft coral Plexaura homomalla. The 3.2 Å crystal structure of 8R-LOX and spectroscopic data suggested that Ca2+ stabilizes two membrane-insertion loops. Analysis of the protein packing contacts in the crystal lattice indicated that the conformation of one of the two loops complicated efforts to improve the resolution of the X-ray data. A deletion mutant of 8R-LOX in which the corresponding membrane-insertion loop is absent (Δ41-45:GSLOX) was engineered. Removal of the …

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Conferred Immunity Against The H1n1 Type A Influenza Virus In Madin-Darby Canine Kidney Cells Via Cecropin B Transfection Therapy., Tomasz P. Stryjewski Nov 2007

Conferred Immunity Against The H1n1 Type A Influenza Virus In Madin-Darby Canine Kidney Cells Via Cecropin B Transfection Therapy., Tomasz P. Stryjewski

Honors Capstones

No abstract provided.

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Compressed Data Structures: Dictionaries And Data-Aware Measures, Ankur Gupta, Wing Kai Hon, Rahul Shah, Jeffrey Scott Vitter Nov 2007

Compressed Data Structures: Dictionaries And Data-Aware Measures, Ankur Gupta, Wing Kai Hon, Rahul Shah, Jeffrey Scott Vitter

Faculty Publications

In this paper, we propose measures for compressed data structures, in which space usage is measured in a data-aware manner. In particular, we consider the fundamental dictionary problem on set data, where the task is to construct a data structure for representing a set S of n items out of a universe U = {0, ..., u - 1} and supporting various queries on S. We use a well-known data-aware measure for set data called gap to bound the space of our data structures. We describe a novel dictionary structure that requires gap + O (n log (u / n) …

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Role Of Adiponectin And Inflammation In Insulin Resistance Of Mc3r And Mc4r Knockout Mice, James L. Trevaskis, Barbara Gawronska-Kozak, Gregory M. Sutton, Michele Mcneil, Jacqueline M. Stephens, Steven R. Smith, Andrew A. Butler Nov 2007

Role Of Adiponectin And Inflammation In Insulin Resistance Of Mc3r And Mc4r Knockout Mice, James L. Trevaskis, Barbara Gawronska-Kozak, Gregory M. Sutton, Michele Mcneil, Jacqueline M. Stephens, Steven R. Smith, Andrew A. Butler

Faculty Publications

Objective: To investigate the involvement of hypoadiponectinemia and inflammation in coupling obesity to insulin resistance in melanocortin-3 receptor and melanocortin-4 receptor knockout (KO) mice (Mc3/4rKO). Research Methods and Procedures: Sera and tissue were collected from 6-month-old Mc3rKO, Mc4rKO, and wild-type C57BL6J litter mates maintained on low-fat diet or exposed to high-fat diet (HFD) for 1 or 3 months. Inflammation was assessed by both real-time polymerase chain reaction analysis of macrophage-specific gene expression and immunohistochemistry. Results: Mc4rKO exhibited hypoadiponectinemia, exacerbated by HFD and obesity, previously reported in murine models of obesity. Mc4r deficiency was also associated with high levels of macrophage …

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Is A 3-Mm Intrafractional Margin Sufficient For Daily Image-Guided Intensity-Modulated Radiation Therapy Of Prostate Cancer?, Adam D. Melancon, Jennifer C. O'Daniel, Lifei Zhang, Rajat J. Kudchadker, Deborah A. Kuban, Andrew K. Lee, Rex M. Cheung, Renaud De Crevoisier, Susan L. Tucker, Wayne D. Newhauser, Radhe Mohan, Lei Dong Nov 2007

Is A 3-Mm Intrafractional Margin Sufficient For Daily Image-Guided Intensity-Modulated Radiation Therapy Of Prostate Cancer?, Adam D. Melancon, Jennifer C. O'Daniel, Lifei Zhang, Rajat J. Kudchadker, Deborah A. Kuban, Andrew K. Lee, Rex M. Cheung, Renaud De Crevoisier, Susan L. Tucker, Wayne D. Newhauser, Radhe Mohan, Lei Dong

Faculty Publications

Purpose: To determine whether a 3-mm isotropic target margin adequately covers the prostate and seminal vesicles (SVs) during administration of an intensity-modulated radiation therapy (IMRT) treatment fraction, assuming that daily image-guided setup is performed just before each fraction. Materials and methods: In-room computed tomographic (CT) scans were acquired immediately before and after a daily treatment fraction in 46 patients with prostate cancer. An eight-field IMRT plan was designed using the pre-fraction CT with a 3-mm margin and subsequently recalculated on the post-fraction CT. For convenience of comparison, dose plans were scaled to full course of treatment (75.6 Gy). Dose coverage …

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Capillary Electrophoretic Screening For The Inhibition Of Homocysteine Thiolactone-Induced Protein Oligomerization, Arther T. Gates, Mark Lowry, Kristin A. Fletcher, Abitha Murugeshu, Oleksandr Rusin, James W. Robinson, Robert M. Strongin, Isiah M. Warner Nov 2007

Capillary Electrophoretic Screening For The Inhibition Of Homocysteine Thiolactone-Induced Protein Oligomerization, Arther T. Gates, Mark Lowry, Kristin A. Fletcher, Abitha Murugeshu, Oleksandr Rusin, James W. Robinson, Robert M. Strongin, Isiah M. Warner

Faculty Publications

We report the first demonstration of rapid electrophoretic monitoring of homocysteine thiolactone-induced protein oligomerization (HTPO), a unique type of post-translational protein modification that may have clinical significance as an indicator of cardiovascular and neurovascular diseases. HTPO of the model protein bovine cytochrome c was initiated in vitro. The relative monomer and aggregate levels of the resultant protein mixtures were determined following separation using capillaries coated with the cationic polymer, poly(diallyldimethylammonium chloride). UV detection provided adequate sensitivity for the monitoring of higher order species, which exist at relatively low concentrations in the protein reaction mixture as compared to the monomelic species. …

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Sound Production And Spectral Hearing Sensitivity In The Hawaiian Sergeant Damselfish, Abudefduf Abdominalis, Karen P. Maruska, Kelly S. Boyle, Laura R. Dewan, Timothy C. Tricas Nov 2007

Sound Production And Spectral Hearing Sensitivity In The Hawaiian Sergeant Damselfish, Abudefduf Abdominalis, Karen P. Maruska, Kelly S. Boyle, Laura R. Dewan, Timothy C. Tricas

Faculty Publications

Sounds provide important signals for inter- and intraspecific communication in fishes, but few studies examine fish acoustic behavior in the context of coevolution of sound production and hearing ability within a species. This study characterizes the acoustic behavior in a reproductive population of the Hawaiian sergeant fish, Abudefduf abdominalis, and compares acoustic features to hearing ability, measured by the auditory evoked potential (AEP) technique. Sergeant fish produce sounds at close distances to the intended receiver (≤1-2 body lengths), with different pulse characteristics that are associated primarily with aggression, nest preparation and courtship-female-visit behaviors. Energy peaks of all sounds were between …

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Characterization Of Polymorphic Microsatellite Loci For The Invasive Monk Parakeet (Myiopsitta Monachus), M. A. Russello, V. Saranathan, S. Buhrman-Deever, J. Eberhard, A. Caccone Nov 2007

Characterization Of Polymorphic Microsatellite Loci For The Invasive Monk Parakeet (Myiopsitta Monachus), M. A. Russello, V. Saranathan, S. Buhrman-Deever, J. Eberhard, A. Caccone

Faculty Publications

Microsatellite loci were characterized for the monk parakeet (Myiopsitta monachus) from a GTn-enriched genomic library. Twelve of 14 microsatellite loci were polymorphic, averaging 6.7 alleles per locus across the 20 individuals genotyped. Mean expected heterozygosity was 0.72, with locus-specific values ranging from 0.53 to 0.90. An equally high multilocus probability of identity (2.48 × 10-12) was revealed for this set of loci. In addition, all 12 loci were demonstrated to cross-amplify to varying extents within three additional parrot genera suggesting their potential utility for population-level studies in a broad range of Neotropical psittacines. © 2007 The Authors.

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Tarphonomus, A New Genus Of Ovenbird (Aves: Passeriformes: Furnariidae) From South America, R. Terry Chesser, Robb T. Brumfield Oct 2007

Tarphonomus, A New Genus Of Ovenbird (Aves: Passeriformes: Furnariidae) From South America, R. Terry Chesser, Robb T. Brumfield

Faculty Publications

Tarphonomus, a new genus of ovenbird (Aves: Passeriformes: Furnariidae) from South America, is described. Species included in the new genus, formerly placed in Upucerthia, are T. certhioides and T. harterti.

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The Chlamydomonas Genome Reveals The Evolution Of Key Animal And Plant Functions, Sabeeha S. Merchant, Simon E. Prochnik, Olivier Vallon, Elizabeth H. Harris, Steven J. Karpowicz, George B. Witman, Astrid Terry, Asaf Salamov, Lillian K. Fritz-Laylin, Laurence Maréchal-Drouard, Wallace F. Marshall, Liang Hu Qu, David R. Nelson, Anton A. Sanderfoot, Martin H. Spalding, Vladimir V. Kapitonov, Qinghu Ren, Patrick Ferris, Erika Lindquist, Harris Shapiro, Susan M. Lucas, Jane Grimwood, Jeremy Schmutz, Igor V. Grigoriev, Daniel S. Rokhsar, Arthur R. Grossman, Pierre Cardol, Heriberto Cerutti, Guillaume Chanfreau, Chun Long Chen, Valérie Cognat, Martin T. Croft, Rachel Dent Oct 2007

The Chlamydomonas Genome Reveals The Evolution Of Key Animal And Plant Functions, Sabeeha S. Merchant, Simon E. Prochnik, Olivier Vallon, Elizabeth H. Harris, Steven J. Karpowicz, George B. Witman, Astrid Terry, Asaf Salamov, Lillian K. Fritz-Laylin, Laurence Maréchal-Drouard, Wallace F. Marshall, Liang Hu Qu, David R. Nelson, Anton A. Sanderfoot, Martin H. Spalding, Vladimir V. Kapitonov, Qinghu Ren, Patrick Ferris, Erika Lindquist, Harris Shapiro, Susan M. Lucas, Jane Grimwood, Jeremy Schmutz, Igor V. Grigoriev, Daniel S. Rokhsar, Arthur R. Grossman, Pierre Cardol, Heriberto Cerutti, Guillaume Chanfreau, Chun Long Chen, Valérie Cognat, Martin T. Croft, Rachel Dent

Faculty Publications

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, …

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Habitat Fragmentation, Variable Edge Effects, And The Landscape-Divergence Hypothesis, William F. Laurance, Henrique E.M. Nascimento, Susan G. Laurance, Ana Andrade, Robert M. Ewers, Kyle E. Harms, Regina C.C. Luizão, José E. Ribeiro Oct 2007

Habitat Fragmentation, Variable Edge Effects, And The Landscape-Divergence Hypothesis, William F. Laurance, Henrique E.M. Nascimento, Susan G. Laurance, Ana Andrade, Robert M. Ewers, Kyle E. Harms, Regina C.C. Luizão, José E. Ribeiro

Faculty Publications

Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world's largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: …

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Hypoxia In The Northern Gulf Of Mexico: Does The Science Support The Plan To Reduce, Mitigate, And Control Hypoxia?, Nancy N. Rabalais, R. Eugene Turner, B.K. Sen Gupta, D. F. Boesch, P. Chapman, M. C. Murrell Oct 2007

Hypoxia In The Northern Gulf Of Mexico: Does The Science Support The Plan To Reduce, Mitigate, And Control Hypoxia?, Nancy N. Rabalais, R. Eugene Turner, B.K. Sen Gupta, D. F. Boesch, P. Chapman, M. C. Murrell

Faculty Publications

We update and reevaluate the scientific information on the distribution, history, and causes of continental shelf hypoxia that supports the 2001 Action Plan for Reducing, Mitigating, and Controlling Hypoxia in the Northern Gulf of Mexico (Mississippi River/Gulf of Mexico Watershed Nutrient Task Force 2001), incorporating data, publications, and research results produced since the 1999 integrated assessment. The metric of mid-summer hypoxic area on the Louisiana-Texas shelf is an adequate and suitable measure for continued efforts to reduce nutrients loads from the Mississippi River and hypoxia in the northern Gulf of Mexico as outlined in the Action Plan. More frequent measurements …

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Requirement Of Α And Β Subunit Transmembrane Helix Separation For Integrin Outside-In Signaling, Jieqing Zhu, Christopher V. Carman, Minsoo Kim, Motomu Shimaoka, Timothy A. Springer, Bing Hao Luo Oct 2007

Requirement Of Α And Β Subunit Transmembrane Helix Separation For Integrin Outside-In Signaling, Jieqing Zhu, Christopher V. Carman, Minsoo Kim, Motomu Shimaoka, Timothy A. Springer, Bing Hao Luo

Faculty Publications

Adhesion to extracellular ligands through integrins regulates cell shape, migration, growth, and survival. How integrins transmit signals in the outside-to-in direction remains unknown. Whereas in resting integrins the α and β subunit transmembrane domains are associated, ligand binding promotes dissociation and separation of these domains. Here we address whether such separation is required for outside-in signaling. By introduction of an intersubunit disulfide bond, we generated mutant integrin αIIbβ3 with blocked transmembrane separation that binds ligand, mediates adhesion, adopts an extended conformation after ligand binding, and forms antibody-induced macroclusters on the cell surface similarly to wild type. However, the mutant integrin …

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Phylogenetic Conservatism And Antiquity Of A Tropical Specialization: Army-Ant-Following In The Typical Antbirds (Thamnophilidae), Robb T. Brumfield, Jose G. Tello, Z. A. Cheviron, Matthew D. Carling, Nanette Crochet, Kenneth V. Rosenberg Oct 2007

Phylogenetic Conservatism And Antiquity Of A Tropical Specialization: Army-Ant-Following In The Typical Antbirds (Thamnophilidae), Robb T. Brumfield, Jose G. Tello, Z. A. Cheviron, Matthew D. Carling, Nanette Crochet, Kenneth V. Rosenberg

Faculty Publications

One of the most novel foraging strategies in Neotropical birds is army-ant-following, in which birds prey upon arthropods and small vertebrates flushed from the forest floor by swarm raids of the army-ant Eciton burchellii. This specialization is most developed in the typical antbirds (Thamnophilidae) which are divisible into three specialization categories: (1) those that forage at swarms opportunistically as army-ants move through their territories (occasional followers), (2) those that follow swarms beyond their territories but also forage independently of swarms (regular followers), and (3) those that appear incapable of foraging independently of swarms (obligate followers). Although army-ant-following is one of …

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Louisiana Agriculture Fall, 2007, Lsu Agcenter Oct 2007

Louisiana Agriculture Fall, 2007, Lsu Agcenter

Louisiana Agriculture

No abstract provided.

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Split Luciferase Complementation Assay To Study Protein-Protein Interactions In Arabidopsis Protoplasts, Yukichi Fujikawa, Naohiro Kato Oct 2007

Split Luciferase Complementation Assay To Study Protein-Protein Interactions In Arabidopsis Protoplasts, Yukichi Fujikawa, Naohiro Kato

Faculty Publications

We developed a split luciferase complementation assay to study protein-protein interactions in Arabidopsis protoplasts. In this assay, the N- and C-terminal fragments of Renilla reniforms luciferase are translationally fused to bait and prey proteins, respectively. When the proteins interact, split luciferase becomes activated and emits luminescence that can be measured by a microplate luminometer. Split luciferase activity was measured by first transforming protoplasts with a DNA vector in a 96-well plate. DNA vector expressing both bait and prey genes was constructed through two independent in vitro DNA recombinant reactions, Gateway and Cre-loxP. As proof of concept, we detected the protein-protein …

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Alu Recombination-Mediated Structural Deletions In The Chimpanzee Genome, Kyudong Han, Jungnam Lee, Thomas J. Meyer, Jianxin Wang, Shurjo K. Sen, Deepa Srikanta, Ping Liang, Mark A. Batzer Oct 2007

Alu Recombination-Mediated Structural Deletions In The Chimpanzee Genome, Kyudong Han, Jungnam Lee, Thomas J. Meyer, Jianxin Wang, Shurjo K. Sen, Deepa Srikanta, Ping Liang, Mark A. Batzer

Faculty Publications

With more than 1.2 million copies, Alu elements are one of the most important sources of structural variation in primate genomes. Here, we compare the chimpanzee and human genomes to determine the extent of Alu recombination-mediated deletion (ARMD) in the chimpanzee genome since the divergence of the chimpanzee and human lineages (∼6 million y ago). Combining computational data analysis and experimental verification, we have identified 663 chimpanzee lineage-specific deletions (involving a total of ∼771 kb of genomic sequence) attributable to this process. The ARMD events essentially counteract the genomic expansion caused by chimpanzee-specific Alu inserts. The RefSeq databases indicate that …

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Conformational Control Of Selectivity In The Dienone-Phenol Rearrangement, Anne M. Sauer, William E. Crowe, Gregg Henderson, Roger A. Laine Sep 2007

Conformational Control Of Selectivity In The Dienone-Phenol Rearrangement, Anne M. Sauer, William E. Crowe, Gregg Henderson, Roger A. Laine

Faculty Publications

We have explored the dienone-phenol rearrangement of substrates where: only the p-cresol pathway is possible and relative migratory aptitudes should play no role in determining the regiochemistry of the reaction. For these substrates the selectivity of the rearrangement was found to depend on the stereochemistry of the spirocyclic intermediate formed during the course of the rearrangement. Rearrangement of one of these substrates gave-surprisingly-a single regioisomeric product. Selectivity in this case can be correlated with the relative stability of cationic intermediates, which lie on the pathway between spirocycle and final product. © 2007 Elsevier Ltd. All rights reserved.

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Solution Structure Of Recombinant Somatomedin B Domain From Vitronectin Produced In Pichia Pastoris, Magnus Kjaergaard, Henrik Gårdsvoll, Daniel Hirschberg, Steen Nielbo, Anand Mayasundari, Cynthia B. Peterson, Anna Jansson, Thomas J.D. Jørgensen, Flemming M. Poulsen, Michael Ploug Sep 2007

Solution Structure Of Recombinant Somatomedin B Domain From Vitronectin Produced In Pichia Pastoris, Magnus Kjaergaard, Henrik Gårdsvoll, Daniel Hirschberg, Steen Nielbo, Anand Mayasundari, Cynthia B. Peterson, Anna Jansson, Thomas J.D. Jørgensen, Flemming M. Poulsen, Michael Ploug

Faculty Publications

The cysteine-rich somatomedin B domain (SMB) of the matrix protein vitronectin is involved in several important biological processes. First, it stabilizes the active conformation of the plasminogen activator inhibitor (PAI-1); second, it provides the recognition motif for cell adhesion via the cognate integrins (αvβ3, α vβ5, and αIIbβ3); and third, it binds the complex between urokinase-type plasminogen activator (uPA) and its glycolipid-anchored receptor (uPAR). Previous structural studies on SMB have used recombinant protein expressed in Escherichia coli or SMB released from plasma-derived vitronectin by CNBr cleavage. However, different disulfide patterns and three-dimensional structures for SMB were reported. In the present …

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Destabilization Of Human Glycine N-Methyltransferase By H176n Mutation, Zigmund Luka, Svetlana Pakhomova, Yury Luka, Marcia E. Newcomer, Conrad Wagner Sep 2007

Destabilization Of Human Glycine N-Methyltransferase By H176n Mutation, Zigmund Luka, Svetlana Pakhomova, Yury Luka, Marcia E. Newcomer, Conrad Wagner

Faculty Publications

In the presence of moderate (2-4 M) urea concentrations the tetrameric enzyme, glycine N-methyltransferase (GNMT), dissociates into compact monomers. Higher concentrations of urea (7-8 M) promote complete denaturation of the enzyme. We report here that the H176N mutation in this enzyme, found in humans with hypermethioninaemia, significantly decreases stability of the tetramer, although H176 is located far from the intersubunit contact areas. Dissociation of the tetramer to compact monomers and unfolding of compact monomers of the mutant protein were detected by circular dichroism, quenching of fluorescence emission, size-exclusion chromatography, and enzyme activity. The values of apparent free energy of dissociation …

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