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The 1.85 Å Structure Of An 8r-Lipoxygenase Suggests A General Model For Lipoxygenase Product Specificity, David B. Neau, Nathaniel C. Gilbert, Sue G. Bartlett, William Boeglin, Alan R. Brash, Marcia E. Newcomer Aug 2009

The 1.85 Å Structure Of An 8r-Lipoxygenase Suggests A General Model For Lipoxygenase Product Specificity, David B. Neau, Nathaniel C. Gilbert, Sue G. Bartlett, William Boeglin, Alan R. Brash, Marcia E. Newcomer

Faculty Publications

Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active eicosanoids derived from arachidonic acid. A mechanistic understanding of substrate recognition, when lipoxygenases that recognize the same substrate generate different products, can be used to help guide the design of enzyme-specific inhibitors. We report here the 1.85 A ° resolution structure of an 8R-lipoxygenase from Plexaura homomalla, an enzyme with a sequence ∼40% identical to that of human 5-LOX. The structure reveals a U-shaped channel, defined by invariant amino acids, that would allow substrate access to the catalytic iron. We demonstrate that mutations within the channel …

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An Efficient And Economic Asymmetric Synthesis Of (+)-Nootkatone, Tetrahydronootkatone, And Derivatives, Anne M. Sauer, William E. Crowe, Gregg Henderson, Roger A. Laine Aug 2009

An Efficient And Economic Asymmetric Synthesis Of (+)-Nootkatone, Tetrahydronootkatone, And Derivatives, Anne M. Sauer, William E. Crowe, Gregg Henderson, Roger A. Laine

Faculty Publications

Image Persented A facile route to enantiomerically pure (+)-nootkatone and derivatives has been established through conjunctive stereoselective Grignard/anionic oxy-Cope (AOC) reactions. © 2009 American Chemical Society.

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Variable Temperature Sensitivity Of Soil Organic Carbon In North American Forests, Cinzia Fissore, Christian P. Giardina, Christopher W. Swanston, Gary M. King, Randall K. Kolka Aug 2009

Variable Temperature Sensitivity Of Soil Organic Carbon In North American Forests, Cinzia Fissore, Christian P. Giardina, Christopher W. Swanston, Gary M. King, Randall K. Kolka

Faculty Publications

We investigated mean residence time (MRT) for soil organic carbon (SOC) sampled from paired hardwood and pine forests located along a 22 °C mean annual temperature (MAT) gradient in North America. We used acid hydrolysis fractionation, radiocarbon analyses, long-term laboratory incubations (525-d), and a three-pool model to describe the size and kinetics of the acid insoluble C (AIC), active and slow SOC fractions in soil. We found that active SOC was 2 ± 0.2% (mean ± SE) of total SOC, with an MRT of 33 ± 6 days that decreased strongly with increasing MAT. In contrast, MRT for slow SOC …

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Coordination Of Ribosomal Protein And Ribosomal Rna Gene Expression In Response To Tor Signaling, Li Juan Xiao, Anne Grove Aug 2009

Coordination Of Ribosomal Protein And Ribosomal Rna Gene Expression In Response To Tor Signaling, Li Juan Xiao, Anne Grove

Faculty Publications

Cells grow in response to nutrients or growth factors, whose presence is detected and communicated by elaborate signaling pathways. Protein kinases play crucial roles in processes such as cell cycle progression and gene expression, and misregulation of such pathways has been correlated with various diseased states. Signals intended to promote cell growth converge on ribosome biogenesis, as the ability to produce cellular proteins is intimately tied to cell growth. Part of the response to growth signals is therefore the coordinate expression of genes encoding ribosomal RNA (rRNA) and ribosomal proteins (RP). A key player in regulating cell growth is the …

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Mechanistic Investigation Of N-Homocysteinylation-Mediated Protein-Gold Nanoconjugate Assembly, Arther T. Gates, Leonard Moore, Monica R. Sylvain, Christina M. Jones, Mark Lowry, Bilal El-Zahab, James W. Robinson, Robert M. Strongin, Isiah M. Warner Aug 2009

Mechanistic Investigation Of N-Homocysteinylation-Mediated Protein-Gold Nanoconjugate Assembly, Arther T. Gates, Leonard Moore, Monica R. Sylvain, Christina M. Jones, Mark Lowry, Bilal El-Zahab, James W. Robinson, Robert M. Strongin, Isiah M. Warner

Faculty Publications

Herein we report the use of protein-gold nanoconjugate (PGNs) as probes for elucidating mechanistic events involved in protein homocystamide detection with gold nanoparticles (GNPs), as was previously reported by our laboratory. Three different PGN probes are synthesized by direct adsorption of cytochrome c, albumin, or human serum onto citrate-capped GNPs. The PGNs are subsequently purified and treated to confer N-homocysteinylation. Individual PGN systems are evaluated to assess the effect of modification on (1) surface plasmon resonance (SPR), (2) protein structural conformation, and (3) assembly-association. The degree of PGN assembly and colorimetric signal observed postmodification varies based on the type of …

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Metabolic Depression Is Delayed And Mitochondrial Impairment Averted During Prolonged Anoxia In The Ghost Shrimp, Lepidophthalmus Louisianensis (Schmitt, 1935), Jeremy D. Holman, Steven C. Hand Aug 2009

Metabolic Depression Is Delayed And Mitochondrial Impairment Averted During Prolonged Anoxia In The Ghost Shrimp, Lepidophthalmus Louisianensis (Schmitt, 1935), Jeremy D. Holman, Steven C. Hand

Faculty Publications

Lepidophthalmus louisianensis burrows deeply into oxygen-limited estuarine sediments and is subjected to extended anoxia at low tides. Large specimens (> 2 g) have a lethal time for 50% mortality (LT50) of 64 h under anoxia at 25 °C. Small specimens (< 1 g) have a significantly higher LT50 of 113 h, which is the longest ever reported for a crustacean. Whole body lactate levels rise dramatically under anoxia and exceed 120 μmol g.f.w.- 1 by 72 h. ATP, ADP, and AMP do not change during 48 h of anoxia, but arginine phosphate declines by over 50%. Thus arginine phosphate may help stabilize the ATP pool. Surprisingly, when compared to the aerobic resting rate, ATP production under anoxia declines only moderately during the first 12 h, and drops to only about 30% between 12 and 48 h. Finally, after 48 h of anoxia, a major metabolic depression to less than 5% occurs. Downregulation of metabolism is delayed in L. louisianensis compared to many invertebrates that exhibit facultative anaerobiosis. Bioenergetic constraints as a result of eventual metabolic depression lead to ionic disturbances like calcium overload and compromised membrane potential of mitochondria. Because these phenomena trigger apoptosis in mammalian species, we evaluated the susceptibility of ghost shrimp mitochondria to opening of the mitochondrial permeability transition pore (MPTP) and associated damage. Energized mitochondria isolated from hepatopancreas possess a pronounced capacity for calcium uptake. Exogenous calcium does not stimulate opening of the MPTP, which potentially could reduce cell death during prolonged anoxia. © 2009 Elsevier B.V. All rights reserved.

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A Link Between Aurora Kinase And Clp1/Cdc14 Regulation Uncovered By The Identification Of A Fission Yeast Borealin-Like Protein, K. Adam Bohnert, Jun Song Chen, Dawn M. Clifford, Craig W. Vander Kooi, Kathleen L. Gould Aug 2009

A Link Between Aurora Kinase And Clp1/Cdc14 Regulation Uncovered By The Identification Of A Fission Yeast Borealin-Like Protein, K. Adam Bohnert, Jun Song Chen, Dawn M. Clifford, Craig W. Vander Kooi, Kathleen L. Gould

Faculty Publications

The chromosomal passenger complex (CPC) regulates various events in cell division. This complex is composed of a catalytic subunit, Aurora B kinase, and three nonenzymatic subunits, INCENP, Survivin, and Borealin. Together, these four subunits interdependently regulate CPC function, and they are highly conserved among eukaryotes. However, a Borealin homologue has never been characterized in the fission yeast, Schizosaccharomyces pombe. Here, we isolate a previously uncharacterized S. pombe protein through association with the Cdc14 phosphatase homologue, Clp1/Flp1, and identify it as a Borealin-like member of the CPC. Nbl1 (novel Borealin-like 1) physically associates with known CPC components, affects the kinase activity …

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Binding Of Pseudomonas Aeruginosa Apobacterioferritin-Associated Ferredoxin To Bacterioferritin B Promotes Heme Mediation Of Electron Delivery And Mobilization Of Core Mineral Iron, Saroja K. Weeratunga, Casey E. Gee, Scott Lovell, Yuhong Zeng, Carrie L. Woodin, Mario Rivera Aug 2009

Binding Of Pseudomonas Aeruginosa Apobacterioferritin-Associated Ferredoxin To Bacterioferritin B Promotes Heme Mediation Of Electron Delivery And Mobilization Of Core Mineral Iron, Saroja K. Weeratunga, Casey E. Gee, Scott Lovell, Yuhong Zeng, Carrie L. Woodin, Mario Rivera

Faculty Publications

The bfrB gene from Pseudomonas aeruginosa was cloned and expressed in Escherichia coli. The resultant protein (BfrB), which assembles into a 445.3 kDa complex from 24 identical subunits, binds 12 molecules of heme axially coordinated by two Met residues. BfrB, isolated with 5-10 iron atoms per protein molecule, was reconstituted with ferrous ions to prepare samples with a core mineral containing 600 ± 40 ferric ions per BfrB molecule and approximately one phosphate molecule per iron atom. In the presence of sodium dithionite or in the presence of P. aeruginosa ferredoxin NADP reductase (FPR) and NADPH, the heme in BfrB …

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Dna Methylation Analysis Of The Mammalian Peg3 Imprinted Domain, Jennifer M. Huang, Joomyeong Kim Aug 2009

Dna Methylation Analysis Of The Mammalian Peg3 Imprinted Domain, Jennifer M. Huang, Joomyeong Kim

Faculty Publications

In this study, we performed the first systematic survey of DNA methylation status of the CpG islands of the PEG3 (Paternally expressed gene 3) imprinted domain in the mouse, cow, and human genomes. Previous studies have shown that the region surrounding the first exon of PEG3 contains a differentially methylated CpG island. In addition, we have discovered two previously unreported differentially methylated regions (DMR): one in the promoter region of mouse Zim3 and another in the promoter region of human USP29. In the cow, the Peg3-CpG island was the only area that showed DMR status. We have also examined the …

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Functional Complementation Of The Arabidopsis Thaliana Psbo1 Mutant Phenotype With An N-Terminally His6-Tagged Psbo-1 Protein In Photosystem Ii, Haijun Liu, Laurie K. Frankel, Terry M. Bricker Aug 2009

Functional Complementation Of The Arabidopsis Thaliana Psbo1 Mutant Phenotype With An N-Terminally His6-Tagged Psbo-1 Protein In Photosystem Ii, Haijun Liu, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

The Arabidopsis thaliana mutant psbo1 has recently been described and characterized. Loss of expression of the PsbO-1 protein leads to a variety of functional perturbations including elevated levels of the PsbO-2 protein and defects on both the oxidizing- and reducing-sides of Photosystem II. In this communication, two plant lines were produced using the psbo1 mutant as transgenic host, which contained an N-terminally histidine6-tagged PsbO-1 protein. This protein was expressed and correctly targeted into the thylakoid lumen. Immunological analysis indicated that different levels of expression of the modified PsbO-1 protein were obtained in different transgenic plant lines and that the level …

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Phylogeny And Phylogenetic Classification Of The Antbirds, Ovenbirds, Woodcreepers, And Allies (Aves: Passeriformes: Infraorder Furnariides), Robert G. Moyle, R. Terry Chesser, Robb T. Brumfield, Jose G. Tello, Daniel J. Marchese, Joel Cracraft Aug 2009

Phylogeny And Phylogenetic Classification Of The Antbirds, Ovenbirds, Woodcreepers, And Allies (Aves: Passeriformes: Infraorder Furnariides), Robert G. Moyle, R. Terry Chesser, Robb T. Brumfield, Jose G. Tello, Daniel J. Marchese, Joel Cracraft

Faculty Publications

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier …

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Application Of Ground Penetrating Radar In Detecting The Hazards And Risks Of Termites And Ants In Soil Levees, Xiuhao Yang, Gregg Henderson, Lixin Mao, Ahmad Evans Aug 2009

Application Of Ground Penetrating Radar In Detecting The Hazards And Risks Of Termites And Ants In Soil Levees, Xiuhao Yang, Gregg Henderson, Lixin Mao, Ahmad Evans

Faculty Publications

A ground penetrating radar (GPR) technique was used to detect Formosan subterranean termite (Coptoterrnesfonnosanus) and red imported fire ant (Solenopsis invicta) hazards and risks (targets) in a soil levee at the London Avenue Canal in New Orleans, LA. To make this assessment, GPR signal scans were examined for features produced by termite or ant activities and potential sources of food and shelter such as nests, tree roots, and voids (tunnels). The total scanned length of the soil levee was 4,125 m. The average velocity and effective depth of the radar penetration was 0.080 m/ns and 0.61 m, respectively. Four hundred …

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Sperm Motility Initiation And Duration In A Euryhaline Fish, Medaka (Oryzias Latipes), H. Yang, T. R. Tiersch Aug 2009

Sperm Motility Initiation And Duration In A Euryhaline Fish, Medaka (Oryzias Latipes), H. Yang, T. R. Tiersch

Faculty Publications

The medaka, Oryzias latipes, is a well-recognized fish model for biomedical research. An understanding of gamete characteristics is necessary for experimental manipulations such as artificial fertilization and sperm cryopreservation. The goal of this study was to investigate sperm characteristics of motility initiation, duration, and retention in medaka. First, motility was initiated by osmolality values ranging from 25 to 686 mOsm/kg, which included deionized water and hypotonic, isotonic, and hypertonic Hanks' balanced salt solution. The percentage of motile sperm was >80% when osmolality was /kg and decreased as osmolality increased. This is different from most fish with external fertilization in which …

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Purification And Thermodynamic Analysis Of The Stability Of Hiv-1 Reverse Transcriptase In The Presence Of Efavirenz, Chantal A. Sanmiguel Aug 2009

Purification And Thermodynamic Analysis Of The Stability Of Hiv-1 Reverse Transcriptase In The Presence Of Efavirenz, Chantal A. Sanmiguel

Honors Capstones

No abstract provided.

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Positional Identification Of Variants Of Adamts16 Linked To Inherited Hypertension, Bina Joe, Yasser Saad, Norman H. Lee, Bryan C. Frank, Ovokeraye H. Achinike, Truong V. Luu, Kathirvel Gopalakrishnan, Edward J. Toland, Phyllis Farms, Shane Yerga-Woolwine, Ezhilarasi Manickavasagam, John P. Rapp, Michael R. Garrett, David Coe, Suneel S. Apte, Tuomo Rankinen, Louis Pérusse, Georg B. Ehret, Santhi K. Ganesh, Richard S. Cooper, Ashley O'Connor, Treva Rice, Alan B. Weder, Aravinda Chakravarti, Dabeeru C. Rao, Claude Bouchard Jul 2009

Positional Identification Of Variants Of Adamts16 Linked To Inherited Hypertension, Bina Joe, Yasser Saad, Norman H. Lee, Bryan C. Frank, Ovokeraye H. Achinike, Truong V. Luu, Kathirvel Gopalakrishnan, Edward J. Toland, Phyllis Farms, Shane Yerga-Woolwine, Ezhilarasi Manickavasagam, John P. Rapp, Michael R. Garrett, David Coe, Suneel S. Apte, Tuomo Rankinen, Louis Pérusse, Georg B. Ehret, Santhi K. Ganesh, Richard S. Cooper, Ashley O'Connor, Treva Rice, Alan B. Weder, Aravinda Chakravarti, Dabeeru C. Rao, Claude Bouchard

Faculty Publications

A previously reported blood pressure (BP) quantitative trait locus on rat Chromosome 1 was isolated in a short congenic segment spanning 804.6 kb. The 804.6 kb region contained only two genes, LOC306664 and LOC306665. LOC306664 is predicted to translate into A Disintegrin-like and Metalloproteinase with Thrombospondin Motifs-16 (Adamts16). LOC306665 is a novel gene. All predicted exons of both LOC306664 and LOC306665 were sequenced. Non-synonymous variants were identified in only one of these genes, LOC306664. These variants were naturally existing polymorphisms among inbred, outbred and wild rats. The full-length rat transcript of Adamts16 was detected in multiple tissues. Similar to ADAMTS16 …

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Yy1'S Role In Dna Methylation Of Peg3 And Xist, Jeong Do Kim, Keunsoo Kang, Joomyeong Kim Jul 2009

Yy1'S Role In Dna Methylation Of Peg3 And Xist, Jeong Do Kim, Keunsoo Kang, Joomyeong Kim

Faculty Publications

Unusual clusters of YY1 binding sites are located within several differentially methylated regions (DMRs), including Xist, Nespas and Peg3, which all become methylated during oogenesis. In this study, we performed conditional YY1 knockdown (KD) to investigate YY1's roles in DNA methylation of these DMRs. Reduced levels of YY1 during spermatogenesis did not cause any major change in these DMRs although the same YY1 KD caused hypermethylation in these DMRs among a subset of aged mice. However, YY1 KD during oogenesis resulted in the loss of DNA methylation on Peg3 and Xist, but there were no changes on Nespas and H19. …

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Modulation Of Lung Inflammation By Vessel Dilator In A Mouse Model Of Allergic Asthma, Xiaoqin Wang, Weidong Xu, Xiaoyuan Kong, Dongqing Chen, Gary Hellermann, Terry A. Ahlert, Joseph D. Giaimo, Stephania A. Cormier, Xu Li, Richard F. Lockey, Subhra Mohapatra, Shyam S. Mohapatra Jul 2009

Modulation Of Lung Inflammation By Vessel Dilator In A Mouse Model Of Allergic Asthma, Xiaoqin Wang, Weidong Xu, Xiaoyuan Kong, Dongqing Chen, Gary Hellermann, Terry A. Ahlert, Joseph D. Giaimo, Stephania A. Cormier, Xu Li, Richard F. Lockey, Subhra Mohapatra, Shyam S. Mohapatra

Faculty Publications

Background: Atrial natriuretic peptide (ANP) and its receptor, NPRA, have been extensively studied in terms of cardiovascular effects. We have found that the ANP-NPRA signaling pathway is also involved in airway allergic inflammation and asthma. ANP, a C-terminal peptide (amino acid 99-126) of pro-atrial natriuretic factor (proANF) and a recombinant peptide, NP73-102 (amino acid 73-102 of proANF) have been reported to induce bronchoprotective effects in a mouse model of allergic asthma. In this report, we evaluated the effects of vessel dilator (VD), another N-terminal natriuretic peptide covering amino acids 31-67 of proANF, on acute lung inflammation in a mouse model …

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Orientation Of Grasshopper Sparrow And Eastern Meadowlark Nests In Relation To Wind Direction, Ashley M. Long, William E. Jensen, Kimberly A. With Jul 2009

Orientation Of Grasshopper Sparrow And Eastern Meadowlark Nests In Relation To Wind Direction, Ashley M. Long, William E. Jensen, Kimberly A. With

Faculty Publications

Orientation of the entrances of bird nests may be especially important in grasslands, where protective cover from solar radiation and wind is minimal. We examined orientation patterns of nest-dome entrances in two grassland bird species, the Grasshopper Sparrow (Ammodramus savannarum) and the Eastern Meadowlark (Sturnella magna). We noted how these patterns changed over the nesting season and how they related to prevailing wind direction. We found that Grasshopper Sparrow (n = 333) and Eastern Meadowlark (n = 272) nests were oriented nonrandomly, toward the northeast (ā = 33.4° and 52.9°, respectively). Prevailing wind in the study region was approximately from …

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An Indole-Containing Dauer Pheromone Component With Unusual Dauer Inhibitory Activity At Higher Concentrations, Rebecca A. Butcher, Justin R. Ragains, Jon Clardy Jul 2009

An Indole-Containing Dauer Pheromone Component With Unusual Dauer Inhibitory Activity At Higher Concentrations, Rebecca A. Butcher, Justin R. Ragains, Jon Clardy

Faculty Publications

In Caenorhabdltls elegans, the dauer pheromone, which consists of a number of derivatives of the 3,6-dideoxysugar ascarylose, is the primary cue for entry into the stress-resistant, "nonaging" dauer larval stage. Here, using activity-guided fractionation and NMR-based structure elucidation, a structurally novel, indole-3-carboxyl-modified ascaroside is identified that promotes dauer formation at low nanomolar concentrations but inhibits dauer formation at higher concentrations. © 2009 American Chemical Society.

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Decoupling Development And Energy Flow During Embryonic Diapause In The Cricket, Allonemobius Socius, Julie A. Reynolds, Steven C. Hand Jul 2009

Decoupling Development And Energy Flow During Embryonic Diapause In The Cricket, Allonemobius Socius, Julie A. Reynolds, Steven C. Hand

Faculty Publications

Respiration rate increases 6.3-fold during 15days of post-oviposition development in embryos of the Southern ground cricket, Allonemobius socius. This ontogenetic increase in metabolism of non-diapause insects is blocked during diapause, such that metabolic rate is only 36% of the rate measured for 15 days developing embryos. Surprisingly, however, there is not an acute metabolic depression during diapause entry at the point when developmental ceases (4-5days post-oviposition), as measured by blockage of morphological change and DNA proliferation. The results indicate a decoupling of developmental arrest from metabolism. Both non-diapause and diapause embryos have unusually high [AMP]:[ATP] ratios and low [ATP]:[ADP] ratios …

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Louisiana Agriculture Summer, 2009 Jul 2009

Louisiana Agriculture Summer, 2009

Louisiana Agriculture

No abstract provided.

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Decomposition In Tropical Forests: A Pan-Tropical Study Of The Effects Of Litter Type, Litter Placement And Mesofaunal Exclusion Across A Precipitation Gradient, Jennifer S. Powers, Rebecca A. Montgomery, E. Carol Adair, Francis Q. Brearley, Saara J. Dewalt, Camila T. Castanho, Jerome Chave, Erika Deinert, Jörg U. Ganzhorn, Matthew E. Gilbert, José Antonio González-Iturbe, Sarayudh Bunyavejchewin, H. Ricardo Grau, Kyle E. Harms, Ankila Hiremath, Silvia Iriarte-Vivar, Eric Manzane, Alexandre A. De Oliveira, Lourens Poorter, Jean Baptiste Ramanamanjato, Carl Salk, Amanda Varela, George D. Weiblen, Manuel T. Lerdau Jul 2009

Decomposition In Tropical Forests: A Pan-Tropical Study Of The Effects Of Litter Type, Litter Placement And Mesofaunal Exclusion Across A Precipitation Gradient, Jennifer S. Powers, Rebecca A. Montgomery, E. Carol Adair, Francis Q. Brearley, Saara J. Dewalt, Camila T. Castanho, Jerome Chave, Erika Deinert, Jörg U. Ganzhorn, Matthew E. Gilbert, José Antonio González-Iturbe, Sarayudh Bunyavejchewin, H. Ricardo Grau, Kyle E. Harms, Ankila Hiremath, Silvia Iriarte-Vivar, Eric Manzane, Alexandre A. De Oliveira, Lourens Poorter, Jean Baptiste Ramanamanjato, Carl Salk, Amanda Varela, George D. Weiblen, Manuel T. Lerdau

Faculty Publications

Litter decomposition recycles nutrients and causes large ?uxes of carbon dioxide into the atmosphere. It is typically assumed that climate, litter quality and decomposer communities determine litter decay rates, yet few comparative studies have examined their relative contributions in tropical forests. 2. We used a short-term litterbag experiment to quantify the effects of litter quality, placement and mesofaunal exclusion on decomposition in 23 tropical forests in 14 countries. Annual precipitation varied among sites (7605797 mm). At each site, two standard substrates (Raphia farinifera and Laurus nobilis) were decomposed in ?ne- and coarse-mesh litterbags both above and below ground for approximately …

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Genome-Wide Mapping Of Boundary Element-Associated Factor (Beaf) Binding Sites In Drosophila Melanogaster Links Beaf To Transcription, Nan Jiang, Eldon Emberly, Olivier Cuvier, Craig M. Hart Jul 2009

Genome-Wide Mapping Of Boundary Element-Associated Factor (Beaf) Binding Sites In Drosophila Melanogaster Links Beaf To Transcription, Nan Jiang, Eldon Emberly, Olivier Cuvier, Craig M. Hart

Faculty Publications

Insulator elements play a role in gene regulation that is potentially linked to nuclear organization. Boundary element-associated factors (BEAFs) 32A and 32B associate with hundreds of sites on Drosophila polytene chromosomes. We hybridized DNA isolated by chromatin immunoprecipitation to genome tiling microarrays to construct a genome-wide map of BEAF binding locations. A distinct difference in the association of 32A and 32B with chromatin was noted. We identified 1,820 BEAF peaks and found that more than 85% were less than 300 bp from transcription start sites. Half are between head-to-head gene pairs. BEAF-associated genes are transcriptionally active as judged by the …

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Embryonic Diapause Highlighted By Differential Expression Of Mrnas For Ecdysteroidogenesis, Transcription And Lipid Sparing In The Cricket Allonemobius Socius, Julie A. Reynolds, Steven C. Hand Jul 2009

Embryonic Diapause Highlighted By Differential Expression Of Mrnas For Ecdysteroidogenesis, Transcription And Lipid Sparing In The Cricket Allonemobius Socius, Julie A. Reynolds, Steven C. Hand

Faculty Publications

Embryos of the ground cricket, Allonemobius socius, enter diapause 4-5days post-oviposition and overwinter in this dormant state that is characterized by developmental arrest. Suppressive subtractive hybridization and quantitative real-time PCR reveal eight candidate genes in pre-diapause embryos that show promise as regulators of diapause entry, when compared with embryos not destined for diapause. Identifications are based both on the magnitude/consistency of differential mRNA abundances and the predicted functions of their products when placed in context of the physiological and biochemical events of diapause characterized in our companion paper. The proteins CYP450, AKR and RACK1 (associated with ecdysteroid synthesis and signaling) …

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Volunteerism And The Fight Against Hiv/Aids In Post-Katrina Louisiana, Lindsay Elizabeth Jarrell Jul 2009

Volunteerism And The Fight Against Hiv/Aids In Post-Katrina Louisiana, Lindsay Elizabeth Jarrell

Honors Capstones

No abstract provided.

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The Effect Of Ambiguous Data On Phylogenetic Estimates Obtained By Maximum Likelihood And Bayesian Inference, Alan R. Lemmon, Jeremy M. Brown, Kathrin Stanger-Hall, Emily Moriarty Lemmon Jun 2009

The Effect Of Ambiguous Data On Phylogenetic Estimates Obtained By Maximum Likelihood And Bayesian Inference, Alan R. Lemmon, Jeremy M. Brown, Kathrin Stanger-Hall, Emily Moriarty Lemmon

Faculty Publications

Although an increasing number of phyiogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum, likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes confounding factors, we provide the first clear understanding of 1 mechanism, by which ambiguous data can mislead phylogenetic analyses. We find that in both ML and Bayesian frameworks, among-site rate variation can interact with, ambiguous data to produce misleading estimates of topology and branch, lengths. Furthermore, …

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Findsite: A Combined Evolution/Structure-Based Approach To Protein Function Prediction, Jeffrey Skolnick, Michal Brylinski Jun 2009

Findsite: A Combined Evolution/Structure-Based Approach To Protein Function Prediction, Jeffrey Skolnick, Michal Brylinski

Faculty Publications

A key challenge of the post-genomic era is the identification of the function(s) of all the molecules in a given organism. Here, we review the status of sequence and structure-based approaches to protein function inference and ligand screening that can provide functional insights for a significant fraction of the ∼50% of ORFs of unassigned function in an average proteome. We then describe FINDSITE, a recently developed algorithm for ligand binding site prediction, ligand screening and molecular function prediction, which is based on binding site conservation across evolutionary distant proteins identified by threading. Importantly, FINDSITE gives comparable results when high-resolution experimental …

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Local Conformations And Competitive Binding Affinities Of Single-And Double-Stranded Primer-Template Dna At The Polymerization And Editing Active Sites Of Dna Polymerases, Kausiki Datta, Neil P. Johnson, Vince J. Licata, Peter H. Von Hippel Jun 2009

Local Conformations And Competitive Binding Affinities Of Single-And Double-Stranded Primer-Template Dna At The Polymerization And Editing Active Sites Of Dna Polymerases, Kausiki Datta, Neil P. Johnson, Vince J. Licata, Peter H. Von Hippel

Faculty Publications

In addition to their capacity for template-directed 5′ → 3′ DNA synthesis at the polymerase (pol) site, DNA polymerases have a separate 3′ → 5′ exonuclease (exo) editing activity that is involved in assuring the fidelity of DNA replication. Upon misincorporation of an incorrect nucleotide residue, the 3′ terminus of the primer strand at the primer-template (P/T) junction is preferentially transferred to the exo site, where the faulty residue is excised, allowing the shortened primer to rebind to the template strand at the pol site and incorporate the correct dNTP. Here we describe the conformational changes that occur in the …

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The Psbp Protein, But Not The Psbq Protein, Is Required For Normal Thylakoid Architecture In Arabidopsis Thaliana, Xiaoping Yi, Stefan R. Hargett, Laurie K. Frankel, Terry M. Bricker Jun 2009

The Psbp Protein, But Not The Psbq Protein, Is Required For Normal Thylakoid Architecture In Arabidopsis Thaliana, Xiaoping Yi, Stefan R. Hargett, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

Interfering RNA was used to suppress the expression of the genes At1g06680 and At2g30790 in Arabidopsis thaliana, which encode the PsbP-1 and PsbP-2 proteins, respectively, of Photosystem II. A phenotypic series of transgenic plants was recovered that expressed intermediate and low amounts of PsbP. Earlier we had documented significant alterations in a variety of Photosystem II parameters in these plant lines [Yi, X., Liu, H., Hargett, S. R., Frankel, L. K., Bricker, T. M. (2007). The PsbP protein is required for photosystem II complex assembly/stability and photoautotrophy in Arabidopsis thaliana. J. Biol. Chem. 34, 24833-24841]. In this communication, we document …

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Complex Segregation Analysis Of Pedigrees From The Gilda Radner Familial Ovarian Cancer Registry Reveals Evidence For Mendelian Dominant Inheritance, Bamidele O. Tayo, Richard A. Dicioccio, Yulan Liang, Maurizio Trevisan, Richard S. Cooper, Shashikant Lele, Lara Sucheston, Steven M. Piver, Kunle Odunsi Jun 2009

Complex Segregation Analysis Of Pedigrees From The Gilda Radner Familial Ovarian Cancer Registry Reveals Evidence For Mendelian Dominant Inheritance, Bamidele O. Tayo, Richard A. Dicioccio, Yulan Liang, Maurizio Trevisan, Richard S. Cooper, Shashikant Lele, Lara Sucheston, Steven M. Piver, Kunle Odunsi

Faculty Publications

Background: Familial component is estimated to account for about 10% of ovarian cancer. However, the mode of inheritance of ovarian cancer remains poorly understood. The goal of this study was to investigate the inheritance model that best fits the observed transmission pattern of ovarian cancer among 7669 members of 1919 pedigrees ascertained through probands from the Gilda Radner Familial Ovarian Cancer Registry at Roswell Park Cancer Institute, Buffalo, New York. Methodology/Principal Findings: Using the Statistical Analysis for Genetic Epidemiology program, we carried out complex segregation analyses of ovarian cancer affection status by fitting different genetic hypothesis-based regressive multivariate logistic models. …

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