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A Functional Type I Topoisomerase From Pseudomonas Aeruginosa, Teesta Jain, Benjamin J. Roper, Anne Grove Mar 2009

A Functional Type I Topoisomerase From Pseudomonas Aeruginosa, Teesta Jain, Benjamin J. Roper, Anne Grove

Faculty Publications

Background: Pseudomonas aeruginosa encodes a putative topoisomerase with sequence similarity to the eukaryotic type IB topoisomerase from Vaccinia virus. Residues in the active site are conserved, notably Tyr292 which would be predicted to form the transient covalent bond to DNA. Results: The gene encoding the P. aeruginosa topoisomerase I was cloned and expressed in E. coli. The enzyme relaxes supercoiled DNA, while a mutant containing a Tyr292 to Phe substitution at the active site was found to be catalytically inert. This is consistent with the role of Tyr in forming the covalent intermediate. Like Vaccinia topoisomerase, the P. aeruginosa topoisomerase …

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Faculty Senate Resolution 09-03, Louisiana State University And Agricultural & Mechanical College Mar 2009

Faculty Senate Resolution 09-03, Louisiana State University And Agricultural & Mechanical College

LSU Faculty Senate Publications

Faculty Senate Resolution on a rational pay scale at LSU; failed, not adopted.

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A Genome Wide Survey Of Snp Variation Reveals The Genetic Structure Of Sheep Breeds, James W. Kijas, David Townley, Brian P. Dalrymple, Michael P. Heaton, Jillian F. Maddox, Annette Mcgrath, Peter Wilson, Roxann G. Ingersoll, Russell Mcculloch, Sean Mcwilliam, Dave Tang, John Mcewan, Noelle Cockett, V. Hutton Oddy, Frank W. Nicholas, Herman Raadsma, Wes Barris, Steve C. Bishop, David Coltman, Allan Crawford, André Eggen, Georg Erhardt, Robert Forage, Olivier Hanotte, Peter Hunt, Han Jianlin, Kui Li, Paolo Ajmone Marsan, James E. Miller, Josephine Pemberton, Laurent Schibler Mar 2009

A Genome Wide Survey Of Snp Variation Reveals The Genetic Structure Of Sheep Breeds, James W. Kijas, David Townley, Brian P. Dalrymple, Michael P. Heaton, Jillian F. Maddox, Annette Mcgrath, Peter Wilson, Roxann G. Ingersoll, Russell Mcculloch, Sean Mcwilliam, Dave Tang, John Mcewan, Noelle Cockett, V. Hutton Oddy, Frank W. Nicholas, Herman Raadsma, Wes Barris, Steve C. Bishop, David Coltman, Allan Crawford, André Eggen, Georg Erhardt, Robert Forage, Olivier Hanotte, Peter Hunt, Han Jianlin, Kui Li, Paolo Ajmone Marsan, James E. Miller, Josephine Pemberton, Laurent Schibler

Faculty Publications

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population …

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Supplemental Irrigation Increases Seedling Performance And Diversity In A Tropical Forest, C. E.Timothy Paine, Kyle E. Harms, Jess Ramos Mar 2009

Supplemental Irrigation Increases Seedling Performance And Diversity In A Tropical Forest, C. E.Timothy Paine, Kyle E. Harms, Jess Ramos

Faculty Publications

Diversity is positively correlated with water availability at global, continental and regional scales. With the objective of better understanding the mechanisms that drive these relationships, we investigated the degree to which variation in water availability affects the performance (recruitment, growth and survival) of juvenile trees. Precipitation was supplemented throughout two dry seasons in a seasonal moist forest in south-eastern Peru. Supplementing precipitation by 160 mm mo1, we increased soil moisture by 17%. To generate seedling communities of known species composition, we sowed 3840 seeds of 12 species. We monitored the fates of the 554 seedlings recruited from the sown seeds, …

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Growth-Regulated Expression Of A Bacteriocin, Produced By The Sweet Potato Pathogen Streptomyces Ipomoeae, That Exhibits Interstrain Inhibition, Jing Wang, Kevin L. Schultyp, Gregg S. Pettis Mar 2009

Growth-Regulated Expression Of A Bacteriocin, Produced By The Sweet Potato Pathogen Streptomyces Ipomoeae, That Exhibits Interstrain Inhibition, Jing Wang, Kevin L. Schultyp, Gregg S. Pettis

Faculty Publications

Certain strains of the bacterial sweet potato pathogen Streptomyces ipomoeae produce the bacteriocin ipomicin, which inhibits other sensitive strains of the same species. Within the signal-sequence-encoding portion of the ipomicin structural gene ipoA exists a single rare TTA codon, which is recognized in Streptomyces bacteria by the temporally accumulating bldA leucyl tRNA. In this study, ipomicin was shown to stably accumulate in culture supernatants of 5. ipomoeae in a growth-regulated manner that did not coincide with the pattern of ipoA expression. Similar growth-regulated production of ipomicin in Streptomyces coelicolor containing the cloned ipoA gene was found to be directly dependent …

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An Alternative Pathway For Alu Retrotransposition Suggests A Role In Dna Double-Strand Break Repair, Deepa Srikanta, Shurjo K. Sen, Charles T. Huang, Erin M. Conlin, Ryan M. Rhodes, Mark A. Batzer Mar 2009

An Alternative Pathway For Alu Retrotransposition Suggests A Role In Dna Double-Strand Break Repair, Deepa Srikanta, Shurjo K. Sen, Charles T. Huang, Erin M. Conlin, Ryan M. Rhodes, Mark A. Batzer

Faculty Publications

The Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies have suggested that, in addition to TPRT, L1 elements occasionally utilize an alternative endonuclease-independent pathway for genomic integration. To determine whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available primate genomes (human, chimpanzee and rhesus macaque) for endonuclease-independent recently integrated or lineage specific Alu insertions. We recovered twenty-three examples of such insertions and show that these insertions …

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Microarray Analysis Of Femaleand Larval-Specific Gene Expression In The Horn Fly (Diptera: Muscidae), Felix D. Guerrero, Scot E. Dowd, Yan Sun, Leonel Saldivar, Graham B. Wiley, Simone L. Macmil, Fares Najar, Bruce A. Roe, Lane D. Foil Mar 2009

Microarray Analysis Of Femaleand Larval-Specific Gene Expression In The Horn Fly (Diptera: Muscidae), Felix D. Guerrero, Scot E. Dowd, Yan Sun, Leonel Saldivar, Graham B. Wiley, Simone L. Macmil, Fares Najar, Bruce A. Roe, Lane D. Foil

Faculty Publications

The horn My, Haematobia irritans L., is an obligate blood-feeding parasite of cattle, and control of this pest is a continuing problem because the fly is becoming resistant to pesticides. Dominant conditional lethal gene systems are being studied as population control technologies against agricultural pests. One of the components of these systems is a female-specific gene promoter that drives expression of a lethality-inducing gene. To identify candidate genes to supply this promoter, microarrays were designed from a horn fly expressed sequence tag (EST) database and probed to identify female-specific and larval-specific gene expression. Analysis of dye swap experiments found 432 …

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Reduced Adipose Tissue Oxygenation In Human Obesity Evidence For Rarefaction, Macrophage Chemotaxis, And Inflammation Without An Angiogenic Response, Magdalena Pasarica, Olga R. Sereda, Leanne M. Redman, Diana C. Albarado, David T. Hymel, Laura E. Roan, Jennifer C. Rood, David H. Burk, Steven R. Smith Mar 2009

Reduced Adipose Tissue Oxygenation In Human Obesity Evidence For Rarefaction, Macrophage Chemotaxis, And Inflammation Without An Angiogenic Response, Magdalena Pasarica, Olga R. Sereda, Leanne M. Redman, Diana C. Albarado, David T. Hymel, Laura E. Roan, Jennifer C. Rood, David H. Burk, Steven R. Smith

Faculty Publications

OBJECTIVE-Based on rodent studies, we examined the hypothesis that increased adipose tissue (AT) mass in obesity without an adequate support of vascularization might lead to hypoxia, macrophage infiltration, and inflammation. RESEARCH DESIGN AND METHODS-Oxygen partial pressure (AT pO 2) and AT temperature in abdominal AT (9 lean and 12 overweight/obese men and women) was measured by direct insertion of a polarographic Clark electrode. Body composition was measured by dual-energy X-ray absorptiometry, and insulin sensitivity was measured by hyperinsulinemic-euglycemic clamp. Abdominal subcutaneous tissue was used for staining, quantitative RT-PCR, and chemokine secretion assay. RESULTS-AT pO 2 was lower in overweight/obese subjects …

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Food Entrainment Of Circadian Gene Expression Altered In Pparα-/- Brown Fat And Heart, Brian Chun Kim Goh Mar 2009

Food Entrainment Of Circadian Gene Expression Altered In Pparα-/- Brown Fat And Heart, Brian Chun Kim Goh

Honors Capstones

No abstract provided.

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Normans And Saxons: Southern Race Mythology And The Intellectual History Of The American Civil War., James David Miller Mar 2009

Normans And Saxons: Southern Race Mythology And The Intellectual History Of The American Civil War., James David Miller

Civil War Book Review

How Southerners Viewed Race

Ritchie Devon Watson, Jr.’s longstanding interest in the culture, history, and literature of the white South is reflected in previous publications such as The Cavalier in Virginia Fiction (1985) and Yeoman Versus Cavalier (1993). In Normans a....

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Breeding And Non-Breeding Survival Of Lesser Prairie-Chickens Tympanuchus Pallidicinctus In Texas, Usa, Eddie K. Lyons, Bret A. Collier, Nova J. Silvy, Roel R. Lopez, Benjamin E. Toole, Ryan S. Jones, Stephen J. Demaso Mar 2009

Breeding And Non-Breeding Survival Of Lesser Prairie-Chickens Tympanuchus Pallidicinctus In Texas, Usa, Eddie K. Lyons, Bret A. Collier, Nova J. Silvy, Roel R. Lopez, Benjamin E. Toole, Ryan S. Jones, Stephen J. Demaso

Faculty Publications

Lesser prairie-chickens Tympanuchus pallidicinctus have declined throughout their range because of loss or fragmen-tation of habitat from conversion of native prairie to agricultural cropland, exacerbated by overgrazing and drought. We used data from radio-marked lesser prairie-chickens to determine whether differences in survival ex-isted between populations occurring in two areas dominated by different vegetation types (sand sagebrush Artemisia filifolia vs shinnery oak Quercus havardii) in the Texas Panhandle from 2001 through 2005. We used a model-selec-tion approach to evaluate potential generalities in lesser prairie-chicken survival. Our results indicated that survival of lesser prairie-chickens differed between breeding and non-breeding periods, and between …

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Redox Control Of The Dna Damage-Inducible Protein Ding Helicase Activity Via Its Iron-Sulfur Cluster, Binbin Ren, Xuewu Duan, Huangen Ding Feb 2009

Redox Control Of The Dna Damage-Inducible Protein Ding Helicase Activity Via Its Iron-Sulfur Cluster, Binbin Ren, Xuewu Duan, Huangen Ding

Faculty Publications

The Escherichia coli DNA damage-inducible protein DinG, a member of the superfamily 2 DNA helicases, has been implicated in the nucleotide excision repair and recombinational DNA repair pathways. Combining UV-visible absorption, EPR, and enzyme activity measurements, we demonstrate here that E. coli DinG contains a redox-active [4Fe-4S] cluster with a mid-point redox potential (Em) of -390 ± 23 mV (pH 8.0) and that reduction of the [4Fe-4S] cluster reversibly switches off the DinG helicase activity. Unlike the [4Fe-4S] cluster in E. coli dihydroxyacid dehydratase, the DinG [4Fe-4S] cluster is stable, and the enzyme remains fully active after exposure to 100-fold …

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Rapid Headward Erosion Of Marsh Creeks In Response To Relative Sea Level Rise, Zoe J. Hughes, Duncan M. Fitzgerald, Carol A. Wilson, Steve C. Pennings, Kazimierz Wiçski, Amala Mahadevan Feb 2009

Rapid Headward Erosion Of Marsh Creeks In Response To Relative Sea Level Rise, Zoe J. Hughes, Duncan M. Fitzgerald, Carol A. Wilson, Steve C. Pennings, Kazimierz Wiçski, Amala Mahadevan

Faculty Publications

Tidal creeks in Cape Romain, South Carolina, are extending rapidly onto the established marsh platform producing an unusual morphology, which remains selfsimilar in time. A time-series of aerial photographs establishes that these channels are headward eroding at an approximate rate of 1.9 m/yr. The rapid rate of headward erosion suggests that the marsh platform is in disequilibrium and unable to keep pace with high local relative sea level rise (RSLR 〉3.2mm/yr) through accretionary processes. Biological feedbacks play a strong role in the morphological development of the creeks. Dieback of vegetation coupled with intense burrowing by crabs produces a bare and …

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Quantitative And Fingerprint Analyses Of Chinese Sweet Tea Plant (Rubus Suavissimus S. Lee), Guixin Chou, Shun Jun Xu, Dong Liu, Yee Koh Gar, Jian Zhang, Zhijun Liu Feb 2009

Quantitative And Fingerprint Analyses Of Chinese Sweet Tea Plant (Rubus Suavissimus S. Lee), Guixin Chou, Shun Jun Xu, Dong Liu, Yee Koh Gar, Jian Zhang, Zhijun Liu

Faculty Publications

The quality of botanical food is increasingly assessed by the content of multiple bioactive compounds. This study reports, for the first time, an HPLC fingerprinting method for the quality evaluation of Rubus suavissimus leaves possessing multiple bioactivities. Five constituents, gallic acid, rutin, ellagic acid, rubusoside, and steviol monoside, were quantified and used in developing qualitative chromatographic fingerprints. The limits of detection and quantification ranged from 0.29 to 37.86 μg/mL. The relative standard deviations (RSDs) of intra- and interday precisions were no more than 3.14 and 3.01%, respectively. The average recoveries were between 93.1 and 97.5%. The developed method was validated …

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Biosynthesis Of The Caenorhabditis Elegans Dauer Pheromone, Rebecca A. Butcher, Justin R. Ragains, Weiqing Li, Gary Ruvkun, Jon Clardy, Yi Mak Ho Feb 2009

Biosynthesis Of The Caenorhabditis Elegans Dauer Pheromone, Rebecca A. Butcher, Justin R. Ragains, Weiqing Li, Gary Ruvkun, Jon Clardy, Yi Mak Ho

Faculty Publications

To sense its population density and to trigger entry into the stress-resistant dauer larval stage, Caenorhabditis elegans uses the dauer pheromone, which consists of ascaroside derivatives with short, fatty acid-like side chains. Although the dauer pheromone has been studied for 25 years, its biosynthesis is completely uncharacterized. The daf-22 mutant is the only known mutant defective in dauer pheromone production. Here, we show that daf-22 encodes a homolog of human sterol carrier protein SCPx, which catalyzes the final step in peroxisomal fatty acid β-oxidation. We also show that dhs-28, which encodes a homolog of the human D-bifunctional protein that acts …

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Rationally Designed Integrin Β3 Mutants Stabilized In The High Affinity Conformation, Bing Hao Luo, John Karanicolas, Laura D. Harmacek, David Baker, Timothy A. Springer Feb 2009

Rationally Designed Integrin Β3 Mutants Stabilized In The High Affinity Conformation, Bing Hao Luo, John Karanicolas, Laura D. Harmacek, David Baker, Timothy A. Springer

Faculty Publications

Integrins are important cell surface receptors that transmit bidirectional signals across the membrane. It has been shown that a conformational change of the integrin β-subunit headpiece (i.e. the β I domain and the hybrid domain) plays a critical role in regulating integrin ligand binding affinity and function. Previous studies have used coarse methods (a glycan wedge, mutations in transmembrane contacts) to force the β-subunit into either the open or closed conformation. Here, we demonstrate a detailed understanding of this conformational change by applying computational design techniques to select five amino acid side chains that play an important role in the …

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Mycobacterium Smegmatis Histone-Like Protein Hlp Is Nucleoid Associated: Research Letter, Anirban Mukherjee, Patrick J. Dimario, Anne Grove Feb 2009

Mycobacterium Smegmatis Histone-Like Protein Hlp Is Nucleoid Associated: Research Letter, Anirban Mukherjee, Patrick J. Dimario, Anne Grove

Faculty Publications

Eubacteria encode proteins that are required for nucleoid organization and for regulation of DNA-dependent processes. Of these histone-like proteins (Hlps), Escherichia coli HU has been shown to associate with the nucleoid and to regulate processes such as DNA repair and recombination. In contrast, the divergent HU homologs encoded by mycobacteria have been variously identified as involved in the physiology of dormancy, in the response to cold shock, or as laminin-binding proteins associated with the cell envelope. We show here, contrary to previous reports that the HU-related Hlp from Mycobacterium smegmatis associates with the nucleoid in vivo. Using indirect fluorescent antibody …

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Reactivity Of Nitric Oxide With The [4fe-4s] Cluster Of Dihydroxyacid Dehydratase From Escherichia Coli, Xuewu Duan, Juanjuan Yang, Binbin Ren, Guoqiang Tan, Huangen Ding Feb 2009

Reactivity Of Nitric Oxide With The [4fe-4s] Cluster Of Dihydroxyacid Dehydratase From Escherichia Coli, Xuewu Duan, Juanjuan Yang, Binbin Ren, Guoqiang Tan, Huangen Ding

Faculty Publications

Although the NO (nitric oxide)-mediated modification of iron-sulfur proteins has been well-documented in bacteria and mammalian cells, specific reactivity of NO with iron-sulfur proteins still remains elusive. In the present study, we report the first kinetic characterization of the reaction between NO and iron-sulfur clusters in protein using the Escherichia coli IlvD (dihydroxyacid dehydratase) [4Fe-4S] cluster as an example. Combining a sensitive NO electrode with EPR (electron paramagnetic resonance) spectroscopy and an enzyme activity assay, we demonstrate that NO is rapidly consumed by the IlvD [4Fe-4S] cluster with the concomitant formation of the IlvD-bound DNIC (dinitrosyl-iron complex) and inactivation of …

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Yy1'S Longer Dna-Binding Motifs, Jeong Do Kim, Joomyeong Kim Feb 2009

Yy1'S Longer Dna-Binding Motifs, Jeong Do Kim, Joomyeong Kim

Faculty Publications

The DNA-binding sites of YY1 located within two newly identified downstream genes of YY1, Peg3 (GGCGCCATnTT) and Xist (CCGCCATnTT), are longer than the known motif of YY1 (CGCCATnTT). Gel shift assays indicated that these DNA-binding sites are previously unnoticed, longer motifs of YY1. Independent DNA-binding motif studies further confirmed that YY1 recognizes a longer sequence (GCCGCCATTTTG) as its consensus motif. This longer motif exhibited higher affinity to the YY1 protein than the known motif. Another DNA-binding motif study was also performed using a protein containing three amino acid substitutions in the first zinc finger unit of YY1, mimicking the zinc …

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Puma: Bayesian Analysis Of Partitioned (And Unpartitioned) Model Adequacy, Jeremy M. Brown, Robert Eldabaje Feb 2009

Puma: Bayesian Analysis Of Partitioned (And Unpartitioned) Model Adequacy, Jeremy M. Brown, Robert Eldabaje

Faculty Publications

The accuracy of Bayesian phylogenetic inference using molecular data depends on the use of proper models of sequence evolution. Although choosing the best model available from a pool of alternatives has become standard practice in statistical phylogenetics, assessment of the chosen model's adequacy is rare. Programs for Bayesian phylogenetic inference have recently begun to implement models of sequence evolution that account for heterogeneity across sites beyond variation in rates of evolution, yet no program exists to assess the adequacy of these models. PuMA implements a posterior predictive simulation approach to assessing the adequacy of partitioned, unpartitioned and mixture models of …

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An Rig-I-Like Rna Helicase Mediates Antiviral Rnai Downstream Of Viral Sirna Biogenesis In Caenorhabditis Elegans, Rui Lu, Erbay Yigit, Wan Xiang Li, Shou Wei Ding Feb 2009

An Rig-I-Like Rna Helicase Mediates Antiviral Rnai Downstream Of Viral Sirna Biogenesis In Caenorhabditis Elegans, Rui Lu, Erbay Yigit, Wan Xiang Li, Shou Wei Ding

Faculty Publications

Dicer ribonucleases of plants and invertebrate animals including Caenorhabditis elegans recognize and process a viral RNA trigger into virus-derived small interfering RNAs (siRNAs) to guide specific viral immunity by Argonaute-dependent RNA interference (RNAi). C. elegans also encodes three Dicer-related helicase (drh) genes closely related to the RIG-I-like RNA helicase receptors which initiate broad-spectrum innate immunity against RNA viruses in mammals. Here we developed a transgenic C. elegans strain that expressed intense green fluorescence from a chromosomally integrated flock house virus replicon only after knockdown or knockout of a gene required for antiviral RNAi. Use of the reporter nematode strain in …

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Association Of Regions On Chromosomes 6 And 7 With Blood Pressure In Nigerian Families, Bamidele O. Tayo, Amy Luke, Xiaofeng Zhu, Adebowale Adeyemo, Richard S. Cooper Feb 2009

Association Of Regions On Chromosomes 6 And 7 With Blood Pressure In Nigerian Families, Bamidele O. Tayo, Amy Luke, Xiaofeng Zhu, Adebowale Adeyemo, Richard S. Cooper

Faculty Publications

Background: Elevated blood pressure (BP) shares a level of heritability similar to many other traits related to cardiovascular risk; however, specific susceptibility loci have been difficult to localize. We conducted a multistage study of BP as a continuous trait in a low-risk West African population in which it was anticipated that environmental exposures would be reduced in complexity and intensity. In our earlier genome-wide linkage study for BP in this population, strong linkage evidence was noted on chromosomes 6 and 7. Methods and Results: We subsequently genotyped a total of 3431 tag single-nucleotide polymorphisms (SNPs) in 3 regions (viz, 152.68 …

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Response Of Melittia Oedipus (Lepidoptera: Sesiidae) To Visual Cues Is Increased By The Presence Of Food Source, G. V.P. Reddy, Z. T. Cruz, N. Braganza, R. Muniappan Feb 2009

Response Of Melittia Oedipus (Lepidoptera: Sesiidae) To Visual Cues Is Increased By The Presence Of Food Source, G. V.P. Reddy, Z. T. Cruz, N. Braganza, R. Muniappan

Faculty Publications

Visual and olfactory cues were shown to mediate short-distance orientation to different colors in the presence and in the absence of food in Melittia oedipus Oberthür (Lepidoptera: Sesiidae), a biological control agent of Coccinia grandis (L.) Voigt (Violales: Cucurbitaceae). Yellow was the color most preferred by M. oedipus, and adults landed significantly more on yellow paper moistened with honey-water. The next preferred colors were gray and white with the identical food source. Colors such as red, blue, green, brown, and black were least preferred by M. oedipus and attracted the adults on par with each other. The M. oedipus landings …

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Biophysics Of Zebrafish (Danio Rerio) Sperm, M. Hagedorn, J. Ricker, M. Mccarthy, S. A. Meyers, T. R. Tiersch, Z. M. Varga, F. W. Kleinhans Feb 2009

Biophysics Of Zebrafish (Danio Rerio) Sperm, M. Hagedorn, J. Ricker, M. Mccarthy, S. A. Meyers, T. R. Tiersch, Z. M. Varga, F. W. Kleinhans

Faculty Publications

In the past two decades, laboratories around the world have produced thousands of mutant, transgenic, and wild-type zebrafish lines for biomedical research. Although slow-freezing cryopreservation of zebrafish sperm has been available for 30 years, current protocols lack standardization and yield inconsistent post-thaw fertilization rates. Cell cryopreservation cannot be improved without basic physiological knowledge, which was lacking for zebrafish sperm. The first goal was to define basic cryobiological values for wild-type zebrafish sperm and to evaluate how modern physiological methods could aid in developing improved cryopreservation protocols. Coulter counting methods measured an osmotically inactive water fraction (Vb) of 0.37 ± 0.02 …

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Line Edge Detection And Characterization In Sem Images Using Wavelets, Wei Sun, Jose A. Romagnoli, Joseph W. Tringe, Sonia E. Létant, Pieter Stroeve, Ahmet Palazoglu Feb 2009

Line Edge Detection And Characterization In Sem Images Using Wavelets, Wei Sun, Jose A. Romagnoli, Joseph W. Tringe, Sonia E. Létant, Pieter Stroeve, Ahmet Palazoglu

Faculty Publications

Edge characterization has become increasingly important in nanotechnology due to the growing demand for precise nanoscale structure fabrication and assembly. Edge detection is often performed by thresholding the spatial information of a top-down image obtained by scanning electron microscopy or other surface characterization techniques. Results are highly dependent on an arbitrary threshold value, which makes it difficult to reveal the nature of the real surface and to compare results among images. In this paper, we present an alternative edge boundary detection technique based on the wavelet framework. Our results indicate that the method facilitates nanoscale edge detection and characterization by …

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Dietary Resistant Starch Increases Hypothalamic Pomc Expression In Rats, Li Shen, Michael J. Keenan, Roy J. Martin, Richard T. Tulley, Anne M. Raggio, Kathleen L. Mccutcheon, Jun Zhou Jan 2009

Dietary Resistant Starch Increases Hypothalamic Pomc Expression In Rats, Li Shen, Michael J. Keenan, Roy J. Martin, Richard T. Tulley, Anne M. Raggio, Kathleen L. Mccutcheon, Jun Zhou

Faculty Publications

Resistant starch (RS) is fermentable dietary fiber. Inclusion of RS in the diet causes decreased body fat accumulation and altered gut hormone profile. This study investigates the effect of feeding RS on the neuropeptide messenger RNA (mRNA) expressions in the arcuate nucleus (ARC) of the hypothalamus and whether vagal afferent nerves are involved. The rats were injected intraperitoneally with capsaicin to destroy unmyelinated small vagal afferent nerve fibers. The cholecystokinin (CCK) food suppression test was performed to validate the effectiveness of the capsaicin treatment. Then, capsaicin-treated rats and vehicle-treated rats were subdivided into a control diet or a RS diet …

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Race And Ancestry In Biomedical Research: Exploring The Challenges, Timothy Caulfield, Stephanie M. Fullerton, Sarah E. Ali-Khan, Laura Arbour, Esteban G. Burchard, Richard S. Cooper, Billie Jo Hardy, Simrat Harry, Robyn Hyde-Lay, Jonathan Kahn, Rick Kittles, Barbara A. Koenig, Sandra S.J. Lee, Michael Malinowski, Vardit Ravitsky, Pamela Sankar, Stephen W. Scherer, Béatrice Séguin, Darren Shickle, Guilherme Suarez-Kurtz, Abdallah S. Daar Jan 2009

Race And Ancestry In Biomedical Research: Exploring The Challenges, Timothy Caulfield, Stephanie M. Fullerton, Sarah E. Ali-Khan, Laura Arbour, Esteban G. Burchard, Richard S. Cooper, Billie Jo Hardy, Simrat Harry, Robyn Hyde-Lay, Jonathan Kahn, Rick Kittles, Barbara A. Koenig, Sandra S.J. Lee, Michael Malinowski, Vardit Ravitsky, Pamela Sankar, Stephen W. Scherer, Béatrice Séguin, Darren Shickle, Guilherme Suarez-Kurtz, Abdallah S. Daar

Faculty Publications

The use of race in biomedical research has, for decades, been a source of social controversy. However, recent events, such as the adoption of racially targeted pharmaceuticals, have raised the profile of the race issue. In addition, we are entering an era in which genomic research is increasingly focused on the nature and extent of human genetic variation, often examined by population, which leads to heightened potential for misunderstandings or misuse of terms concerning genetic variation and race. Here, we draw together the perspectives of participants in a recent interdisciplinary workshop on ancestry and health in medicine in order to …

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Structural Characterization Of The Hemophore Hasap From Pseudomonas Aeruginosa: Nmr Spectroscopy Reveals Protein-Protein Interactions Between Holo-Hasap And Hemoglobin, Aileen Y. Alontaga, Juan Carlos Rodriguez, Ernst Schönbrunn, Andreas Becker, Todd Funke, Erik T. Yukl, Takahiro Hayashi, Jordan Stobaugh, Pierre Moënne-Loccoz, Mario Rivera Jan 2009

Structural Characterization Of The Hemophore Hasap From Pseudomonas Aeruginosa: Nmr Spectroscopy Reveals Protein-Protein Interactions Between Holo-Hasap And Hemoglobin, Aileen Y. Alontaga, Juan Carlos Rodriguez, Ernst Schönbrunn, Andreas Becker, Todd Funke, Erik T. Yukl, Takahiro Hayashi, Jordan Stobaugh, Pierre Moënne-Loccoz, Mario Rivera

Faculty Publications

Pseudomonas aeruginosa secretes a 205 residue long hemophore (full-length HasAp) that is subsequently cleaved at the C'-terminal domain to produce mainly a 184 residue long truncated HasAp that scavenges heme [Letoffé, S., Redeker, V., and Wandersman, C. (1998) Mol. Microbiol. 28, 1223-1234]. HasAp has been characterized by X-ray crystallography and in solution by NMR spectroscopy. The X-ray crystal structure of truncated HasAp revealed a polypeptide αβ fold and a ferriheme coordinated axially by His32 and Tyr75, with the side chain of His83 poised to accept a hydrogen bond from the Tyr75 phenolic acid group. NMR investigations conducted with full-length HasAp …

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Monte Carlo Fast Dose Calculator For Proton Radiotherapy: Application To A Voxelized Geometry Representing A Patient With Prostate Cancer, Pablo Yepes, Sharmalee Randeniya, Phillip J. Taddei, Wayne D. Newhauser Jan 2009

Monte Carlo Fast Dose Calculator For Proton Radiotherapy: Application To A Voxelized Geometry Representing A Patient With Prostate Cancer, Pablo Yepes, Sharmalee Randeniya, Phillip J. Taddei, Wayne D. Newhauser

Faculty Publications

The Monte Carlo method is used to provide accurate dose estimates in proton radiation therapy research. While it is more accurate than commonly used analytical dose calculations, it is computationally intense. The aim of this work was to characterize for a clinical setup the fast dose calculator (FDC), a Monte Carlo track-repeating algorithm based on GEANT4. FDC was developed to increase computation speed without diminishing dosimetric accuracy. The algorithm used a database of proton trajectories in water to calculate the dose of protons in heterogeneous media. The extrapolation from water to 41 materials was achieved by scaling the proton range …

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Stretching The Envelope Of Past Surface Environments: Neoproterozoic Glacial Lakes From Svalbard, Huiming Bao, Ian J. Fairchild, Peter M. Wynn, Christoph Spötl Jan 2009

Stretching The Envelope Of Past Surface Environments: Neoproterozoic Glacial Lakes From Svalbard, Huiming Bao, Ian J. Fairchild, Peter M. Wynn, Christoph Spötl

Faculty Publications

The oxygen isotope composition of terrestrial sulfate is affected measurably by many Earth-surface processes. During the Neoproterozoic, severe "snowball" glaciations would have had an extreme impact on the biosphere and the atmosphere. Here, we report that sulfate extracted from carbonate lenses within a Neoproterozoic glacial diamictite suite from Svalbard, with an age of ∼635 million years ago, falls well outside the currently known natural range of triple oxygen isotope compositions and indicates that the atmosphere had either an exceptionally high atmospheric carbon dioxide concentration or an utterly unfamiliar oxygen cycle during deposition of the diamictites.

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