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Near-Infrared Fluorescent Nanogumbos For Biomedical Imaging, David K. Bwambok, Bilal El-Zahab, Santhosh K. Challa, Min Li, Lin Chandler, Gary A. Baker, Isiah M. Warner Dec 2009

Near-Infrared Fluorescent Nanogumbos For Biomedical Imaging, David K. Bwambok, Bilal El-Zahab, Santhosh K. Challa, Min Li, Lin Chandler, Gary A. Baker, Isiah M. Warner

Faculty Publications

Herein, we report on near-infrared (NIR) fluorescent nanoparticles generated from an emergent class of materials we refer to as a Group of Uniform Materials Based on Organic Salts (GUMBOS). GUMBOS are largely frozen ionic liquids, although the concept is more general and is also easily applied to solid ionic materials with melting points in excess of 100 °C. Nanoparticles based on GUMBOS (nanoGUMBOS) derived from a NIR fluorophore are prepared using a reprecipitation method and evaluated for in vivo fluorescence imaging. Due to their uniformity, single-step preparation, and composite nature, nanoGUMBOS help to resolve issues with dye leakage problems innate …

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Phylogeny Of The Macaques (Cercopithecidae: Macaca) Based On Alu Elements, Jing Li, Kyudong Han, Jinchuan Xing, Heui Soo Kim, Jeffrey Rogers, Oliver A. Ryder, Todd Disotell, Bisong Yue, Mark A. Batzer Dec 2009

Phylogeny Of The Macaques (Cercopithecidae: Macaca) Based On Alu Elements, Jing Li, Kyudong Han, Jinchuan Xing, Heui Soo Kim, Jeffrey Rogers, Oliver A. Ryder, Todd Disotell, Bisong Yue, Mark A. Batzer

Faculty Publications

Genus Macaca (Cercopithecidae: Papionini) is one of the most successful primate radiations. Despite previous studies on morphology and mitochondrial DNA analysis, a number of issues regarding the details of macaque evolution remain unsolved. Alu elements are a class of non-autonomous retroposons belonging to short interspersed elements that are specific to the primate lineage. Because retroposon insertions show very little homoplasy, and because the ancestral state (absence of the SINE) is known, Alu elements are useful genetic markers and have been utilized for analyzing primate phylogenentic relationships and human population genetic relationships. Using PCR display methodology, 298 new Alu insertions have …

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Internal Priming: An Opportunistic Pathway For L1 And Alu Retrotransposition In Hominins, Deepa Srikanta, Shurjo K. Sen, Erin M. Conlin, Mark A. Batzer Dec 2009

Internal Priming: An Opportunistic Pathway For L1 And Alu Retrotransposition In Hominins, Deepa Srikanta, Shurjo K. Sen, Erin M. Conlin, Mark A. Batzer

Faculty Publications

Retrotransposons, specifically Alu and L1 elements, have been especially successful in their expansion throughout primate genomes. While most of these elements integrate through an endonuclease-mediated process termed target primed reverse transcription, a minority integrate using alternative methods. Here we present evidence for one such mechanism, which we term internal priming and demonstrate that loci integrating through this mechanism are qualitatively different from "classical" insertions. Previous examples of this mechanism are limited to cell culture assays, which show that reverse transcription can initiate upstream of the 3′ poly-A tail during retrotransposon integration. To detect whether this mechanism occurs in vivo as …

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A Tale Of Two Functions: Enzymatic Activity And Translational Repression By Carboxyltransferase, Glen Meades, Brian K. Benson, Anne Grove, Grover L. Waldrop Dec 2009

A Tale Of Two Functions: Enzymatic Activity And Translational Repression By Carboxyltransferase, Glen Meades, Brian K. Benson, Anne Grove, Grover L. Waldrop

Faculty Publications

Acetyl-CoA Carboxylase catalyzes the first committed step in fatty acid synthesis. Escherichia coli acetyl-CoA carboxylase is composed of biotin carboxylase, carboxyltransferase and biotin carboxyl carrier protein functions. The accA and accD genes that code for the α- and β-subunits, respectively, are not in an operon, yet yield an α2β2 carboxyltransferase. Here, we report that carboxyltransferase regulates its own translation by binding the mRNA encoding its subunits. This interaction is mediated by a zinc finger on the β-subunit; mutation of the four cysteines to alanine diminished nucleic acid binding and catalytic activity. Carboxyltransferase binds the coding regions of both subunit mRNAs …

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Yy1'S Dna-Binding Motifs In Mammalian Olfactory Receptor Genes, Christopher D. Faulk, Joomyeong Kim Dec 2009

Yy1'S Dna-Binding Motifs In Mammalian Olfactory Receptor Genes, Christopher D. Faulk, Joomyeong Kim

Faculty Publications

Background: YY1 is an epigenetic regulator for a large number of mammalian genes. While performing genome-wide YY1 binding motif searches, we discovered that the olfactory receptor (OLFR) genes have an unusual cluster of YY1 binding sites within their coding regions. The statistical significance of this observation was further analyzed. Results: About 45% of the olfactory genes in the mouse have a range of 4-8 YY1 binding sites within their respective 1 kb coding regions. Statistical analyses indicate that this enrichment of YY1 motifs has likely been driven by unknown selection pressures at the DNA level, but not serendipitously by some …

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Sphingosine-1-Phosphate Elicits Receptor-Dependent Calcium Signaling In Retinal Amacrine Cells, Scott Crousillac, Jeremy Colonna, Emily Mcmains, Jill Sayes Dewey, Evanna Gleason Dec 2009

Sphingosine-1-Phosphate Elicits Receptor-Dependent Calcium Signaling In Retinal Amacrine Cells, Scott Crousillac, Jeremy Colonna, Emily Mcmains, Jill Sayes Dewey, Evanna Gleason

Faculty Publications

Evidence is emerging indicating that sphingosine-1-phosphate (S1P) participates in signaling in the retina. To determine whether S1P might be involved in signaling in the inner retina specifically, we examine the effects of this sphingolipid on cultured retinal amacrine cells. Whole cell voltage-clamp recordings reveal that S1P activates a cation current that is dependent on signaling through Gi and phospholipase C. These observations are consistent with the involvement of members of the S1P receptor family of G-protein-coupled receptors in the production of the current. Immunocytochemistry and PCR amplification provide evidence for the expression of S1P1R and S1P3R in amacrine cells. The …

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Water Stress Impacts On Bacterial Carbon Monoxide Oxidation On Recent Volcanic Deposits, Carolyn F. Weber, Gary M. King Dec 2009

Water Stress Impacts On Bacterial Carbon Monoxide Oxidation On Recent Volcanic Deposits, Carolyn F. Weber, Gary M. King

Faculty Publications

Water availability oscillates dramatically on young volcanic deposits, and may control the distribution and activity of microbes during early stages of biological succession. Carbon monoxide (CO)-oxidizing bacteria are among the pioneering colonists on volcanic deposits and are subjected to these water stresses. We report here the effects of water potential on CO-oxidizing bacteria in unvegetated (bare) and vegetated (canopy) sites on a 1959 volcanic deposit on Kilauea Volcano (Hawai'i). Time course measurements of water potential showed that average water potentials in the surface layer (0-1 cm) of canopy soil remained between 0.1 and 0 MPa, whereas dramatic diurnal oscillations (for …

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The Amino Terminus Of Herpes Simplex Virus Type 1 Glycoprotein K (Gk) Modulates Gb-Mediated Virus-Induced Cell Fusion And Virion Egress, Vladimir N. Chouljenko, Arun V. Iyer, Sona Chowdhury, Dmitry V. Chouljenko, Konstantin G. Kousoulas Dec 2009

The Amino Terminus Of Herpes Simplex Virus Type 1 Glycoprotein K (Gk) Modulates Gb-Mediated Virus-Induced Cell Fusion And Virion Egress, Vladimir N. Chouljenko, Arun V. Iyer, Sona Chowdhury, Dmitry V. Chouljenko, Konstantin G. Kousoulas

Faculty Publications

Herpes simplex virus type 1 (HSV-1)-induced cell fusion is mediated by viral glycoproteins and other membrane proteins expressed on infected cell surfaces. Certain mutations in the carboxyl terminus of HSV-1 glycoprotein B (gB) and in the amino terminus of gK cause extensive virus-induced cell fusion. Although gB is known to be a fusogenic glycoprotein, the mechanism by which gK is involved in virus-induced cell fusion remains elusive. To delineate the amino-terminal domains of gK involved in virus-induced cell fusion, the recombinant viruses gKΔ31-47, gKΔ31-68, and gKΔ31-117, expressing gK carrying in-frame deletions spanning the amino terminus of gK immediately after the …

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Sex Ratio Of Bovine Embryos And Calves Originating From The Left And Right Ovaries, Darin Hylan, Angelica M. Giraldo, Joel A. Carter, Glen T. Gentry, Kenneth R. Bondioli, Robert A. Godke Dec 2009

Sex Ratio Of Bovine Embryos And Calves Originating From The Left And Right Ovaries, Darin Hylan, Angelica M. Giraldo, Joel A. Carter, Glen T. Gentry, Kenneth R. Bondioli, Robert A. Godke

Faculty Publications

An asymmetric distribution of the sexes within the left and right uterine horns has been described in multiple species. A series of experiments were conducted to evaluate the sex ratio (% male) of calves gestated in the left and right uterine horns, as well as the sex ratio of embryos originating from the left and right ovaries of cattle. The sex ratio of calves gestated in the right uterine horn of naturally mated cows was significantly higher compared with the sex ratio of calves gestated in the left uterine horn. In addition, the sex ratio of the left and right …

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High Frequency Of The D Allele Of The Angiotensin-Converting Enzyme Gene In Arabic Populations, Abdel Halim Salem, Mark A. Batzer Dec 2009

High Frequency Of The D Allele Of The Angiotensin-Converting Enzyme Gene In Arabic Populations, Abdel Halim Salem, Mark A. Batzer

Faculty Publications

Background. The angiotensin-converting enzyme (ACE) gene in humans has an insertion-deletion (I/D) polymorphic state in intron 16 on chromosome 17q23. This polymorphism has been widely investigated in different populations due to its association with the renin-angiotensin system. However, similar studies for Arab populations are limited. This study addresses the distribution of the ACE gene polymorphism in three Arab populations (Egyptians, Jordanians and Syrians). Findings. The polymorphisms of ACE gene were investigated using polymerase chain reaction for detection of an I/D mutation. The results showed a high frequency of the ACE D allele among the three Arab populations, Egyptians (0.67), Jordanians …

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Temperature-Dependent Development Of The Cycad Aulacaspis Scale, Aulacaspis Yasumatsui (Hemiptera: Diaspididae), Ronald D. Cave, Cora Sciacchetano, Rodrigo Diaz Dec 2009

Temperature-Dependent Development Of The Cycad Aulacaspis Scale, Aulacaspis Yasumatsui (Hemiptera: Diaspididae), Ronald D. Cave, Cora Sciacchetano, Rodrigo Diaz

Faculty Publications

Egg duration period, immature development time, and pre-oviposition period of the cycad aulacaspis scale, Aulacaspis yasumatsui Takagi, were measured at 9 constant temperatures in the laboratory. Egg duration period ranged from 15 d at 20°C to 7 d at 30°C. First instar development time was 30 d at 18°C but only 4 d at 35°C. No first instars completed development below 18°C or above 35°C. Development time of second instar females ranged from 19 d at 18 and 20°C to 9 d at 30°C. Development time of male second instar + pupa ranged from 15 d at 20°C to 910 …

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The Structure And Peroxidase Activity Of A 33-Kda Catalase-Related Protein From Mycobacterium Avium Ssp. Paratuberculosis, Svetlana Pakhomova, Benlian Gao, William E. Boeglin, Alan R. Brash, Marcia E. Newcomer Dec 2009

The Structure And Peroxidase Activity Of A 33-Kda Catalase-Related Protein From Mycobacterium Avium Ssp. Paratuberculosis, Svetlana Pakhomova, Benlian Gao, William E. Boeglin, Alan R. Brash, Marcia E. Newcomer

Faculty Publications

True catalases are tyrosine-liganded, usually tetrameric, hemoproteins with subunit sizes of ∼55-84 kDa. Recently characterized hemoproteins with a catalase-related structure, yet lacking in catalatic activity, include the 40-43 kDa allene oxide synthases of marine invertebrates and cyanobacteria. Herein, we describe the 1.8 Å X-ray crystal structure of a 33 kDa subunit hemoprotein from Mycobacterium avium ssp. paratuberculosis (annotated as MAP-2744c), that retains the core elements of the catalase fold and exhibits an organic peroxide-dependent peroxidase activity. MAP-2744c exhibits negligible catalatic activity, weak peroxidatic activity using hydrogen peroxide (20/s) and strong peroxidase activity (∼300/s) using organic hydroperoxides as co-substrate. Key amino …

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How Do Animal Mitochondria Tolerate Water Stress?, Michael A. Menze, Steven C. Hand Dec 2009

How Do Animal Mitochondria Tolerate Water Stress?, Michael A. Menze, Steven C. Hand

Faculty Publications

The vast majority of animal species do not tolerate severe water stress, but the encysted embryo of the brine shrimp Artemia franciscana is an exceptionally useful organism to investigate physiological mechanisms for enduring extreme environmental insults. Any substantial reduction in cellular water poses a threat to survival. Nevertheless anhydrobiotic animals survive virtually complete loss of cellular water. The mechanisms that govern " life without water" (anhydrobiosis) are still not well understood. With certain exceptions, it seems that a recurring strategy for tolerating severe water loss involves the accumulation of both low molecular weight solutes (e.g., trehalose or other polyol) and …

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Allele Frequencies Of The Human Platelet Antigen-1 In The Egyptian Population, Abdel Halim Salem, Kyudong Han, Mark A. Batzer Dec 2009

Allele Frequencies Of The Human Platelet Antigen-1 In The Egyptian Population, Abdel Halim Salem, Kyudong Han, Mark A. Batzer

Faculty Publications

Background. The human platelet alloantigen system HPA-1 in the Egyptian population was examined by polymerase chain reaction using sequence-specific primers (PCR-SSP). The objectives of this study were to evaluate the allele frequency of HPA-1a and -1b in healthy Egyptian individuals and compare these with the international literature. Human platelet antigen (HPA) systems are associated with alloimmunization and organ transplantation rejection as well as the development of cardiovascular disease. Of the various HPA systems, HPA-1 specifically has been considered to be the most important antigenic system implicated in the Caucasian population. No study has yet examined this system in the Egyptian …

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Impact Of Reproductive Effort On Survival Of Rio Grande Wild Turkey Meleagris Gallop Intermedia Hens In Texas, Bret A. Collier, Kyle B. Melton, Jason B. Hardin, Nova J. Silvy, Markus J. Peterson Dec 2009

Impact Of Reproductive Effort On Survival Of Rio Grande Wild Turkey Meleagris Gallop Intermedia Hens In Texas, Bret A. Collier, Kyle B. Melton, Jason B. Hardin, Nova J. Silvy, Markus J. Peterson

Faculty Publications

The southeastern portion of the Edwards Plateau of Texas, historically a stronghold of Rio Grande wild turkeys Meleagris gallopavo intermedia, has seen the numbers of turkeys declining since the 1970s. Because hen survival is a key parameter affecting turkey population dynamics, we monitored radio-tagged Rio Grande wild turkey hens on the Edwards Plateau during 2001-2007 to compare survival during the breeding season in areas where turkey abundance has declined vs areas with stable populations. Breeding season survival was best predicted by a model that allowed variation during different periods of the reproductive season (initial nesting during 25 March 21 April, …

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Existing Biomass Infrastructure And Theoretical Potential Biomass Production In The U.S, Jeremy R. Porter, Frank M. Howell, Philip B. Mason, Troy C. Blanchard Dec 2009

Existing Biomass Infrastructure And Theoretical Potential Biomass Production In The U.S, Jeremy R. Porter, Frank M. Howell, Philip B. Mason, Troy C. Blanchard

Faculty Publications

The recent and projected status of energy production and consumption in the U.S., resulting in substantial dependencies upon foreign oil, has continued to provide pressure on domestic energy security. All told, bio-energy systems, and biomass crop production in particular, will be important elements of national security, economic vitality, and public policy. Using biomass crop estimates based upon models developed at the Oak Ridge National Laboratory, we identify potential biomass crop production zones within the contiguous 48 states of the United States using spatially centered analytic methods. The Midwest and the South regions of the United States are, by far, the …

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Cellular Biophysics During Freezing Of Rat And Mouse Sperm Predicts Post-Thaw Motility, Mie Hagiwara, Jeung Hwan Choi, Ramachandra V. Devireddy, Kenneth P. Roberts, Willem F. Wolkers, Antoine Makhlouf, John C. Bischof Dec 2009

Cellular Biophysics During Freezing Of Rat And Mouse Sperm Predicts Post-Thaw Motility, Mie Hagiwara, Jeung Hwan Choi, Ramachandra V. Devireddy, Kenneth P. Roberts, Willem F. Wolkers, Antoine Makhlouf, John C. Bischof

Faculty Publications

Though cryopreservation of mouse sperm yields good survival and motility after thawing, cryopreservation of rat sperm remains a challenge. This study was designed to evaluate the biophysics (membrane permeability) of rat in comparison to mouse to better understand the cooling rate response that contributes to cryopreservation success or failure in these two sperm types. In order to extract subzero membrane hydraulic permeability in the presence of ice, a differential scanning calorimeter (DSC) method was used. By analyzing rat and mouse sperm frozen at 5°C/min and 20°C/min, heat release signatures characteristic of each sperm type were obtained and correlated to cellular …

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Space-Efficient Framework For Top-K String Retrieval Problems, Wing Kai Hon, Rahul Shah, Jeffrey Scott Vitter Dec 2009

Space-Efficient Framework For Top-K String Retrieval Problems, Wing Kai Hon, Rahul Shah, Jeffrey Scott Vitter

Faculty Publications

Given a set D = {d1,d2, ⋯, dD} of D strings of total length n, our task is to report the "most relevant" strings for a given query pattern P. This involves somewhat more advanced query functionality than the usual pattern matching, as some notion of "most relevant" is involved. In information retrieval literature, this task is best achieved by using inverted indexes. However, inverted indexes work only for some predefined set of patterns. In the pattern matching community, the most popular pattern-matching data structures are suffix trees and suffix arrays. However, a typical suffix tree search involves going through …

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Nanophotothermolysis Of Multiple Scattered Cancer Cells With Carbon Nanotubes Guided By Time-Resolved Infrared Thermal Imaging, Alexandru S. Biris, Dorin Boldor, Jason Palmer, William T. Monroe, Meena Mahmood, Enkeleda Dervishi, Yang Xu, Zhongrui Li, Ekaterina I. Galanzha, Vladimir P. Zharov Dec 2009

Nanophotothermolysis Of Multiple Scattered Cancer Cells With Carbon Nanotubes Guided By Time-Resolved Infrared Thermal Imaging, Alexandru S. Biris, Dorin Boldor, Jason Palmer, William T. Monroe, Meena Mahmood, Enkeleda Dervishi, Yang Xu, Zhongrui Li, Ekaterina I. Galanzha, Vladimir P. Zharov

Faculty Publications

Nanophotothermolysis with long laser pulses for treatment of scattered cancer cells and their clusters is introduced with the main focus on real-time monitoring of temperature dynamics inside and around individual cancer cells labeled with carbon nanotubes. This technique utilizes advanced time- and spatially-resolved thermal radiometry imaging for the visualization of laser-induced temperature distribution in multiple-point absorbing targets. The capability of this approach was demonstrated for monitoring of thermal effects under long laser exposure (from millisecond to seconds, wavelength 1064nm, maximum power 1W) of cervical cancer HeLa cells labeled with carbon nanotubes in vitro. The applications are discussed with a focus …

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Alternative Mrna Splicing Produces A Novel Biologically Active Short Isoform Of Pgc-1Α, Yubin Zhang, Peter Huypens, Aaron W. Adamson, Ji Suk Chang, Tara M. Henagan, Anik Boudreau, Natalie R. Lenard, David Burk, Johannes Klein, Nina Perwitz, Jeho Shin, Mathias Fasshauer, Anastasia Kralli, Thomas W. Gettys Nov 2009

Alternative Mrna Splicing Produces A Novel Biologically Active Short Isoform Of Pgc-1Α, Yubin Zhang, Peter Huypens, Aaron W. Adamson, Ji Suk Chang, Tara M. Henagan, Anik Boudreau, Natalie R. Lenard, David Burk, Johannes Klein, Nina Perwitz, Jeho Shin, Mathias Fasshauer, Anastasia Kralli, Thomas W. Gettys

Faculty Publications

The transcriptional co-activator PGC-1α regulates functional plasticity in adipose tissue by linking sympathetic input to the transcriptional program of adaptive thermogenesis. We report here a novel truncated form of PGC-1α(NT-PGC-1α) produced by alternative 3′ splicing that introduces an in-frame stop codon into PGC-1α mRNA. The expressed protein includes the first 267 amino acids of PGC-1α and 3 additional amino acids from the splicing insert. NT-PGC-1α contains the transactivation and nuclear receptor interaction domains but is missing key domains involved in nuclear localization, interaction with other transcription factors, and protein degradation. Expression and subcellular localization of NT-PGC-1α are dynamically regulated in …

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Ultrafast Vibrational Spectroscopy Of A Degenerate Mode Of Guanidinium Chloride, Dmitriy Yu Vorobyev, Chun Hung Kuo, Jian Xin Chen, Daniel G. Kuroda, J. Nathan Scott, Jane M. Vanderkooi, Robin M. Hochstrasser Nov 2009

Ultrafast Vibrational Spectroscopy Of A Degenerate Mode Of Guanidinium Chloride, Dmitriy Yu Vorobyev, Chun Hung Kuo, Jian Xin Chen, Daniel G. Kuroda, J. Nathan Scott, Jane M. Vanderkooi, Robin M. Hochstrasser

Faculty Publications

Nearly degenerate asymmetric stretches with perpendicular transition dipóle moments of the deuterated guanidinium cation (DGdm-) in D2O and D-glycerol/D2O mixtures at 1600 cm-1 were investigated by linear FTIR spectroscopy and polarization dependent femtosecond pump-probe spectroscopy. The vibrational coupling of the asymmetric stretches of guanidinium occurs within 0.5 ps and leads to fast decay of the anisotropy to a level of 0.1. A systematic study of the influence of the coherence transfer on pump-probe signals is given. Following this decay, the anisotropy decays with a time constant of 4.1 ps in D2O by rotational diffusion about an axis perpendicular to the …

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The Yeast High Mobility Group Protein Hmo2, A Subunit Of The Chromatin-Remodeling Complex Ino80, Binds Dna Ends, Sreerupa Ray, Anne Grove Nov 2009

The Yeast High Mobility Group Protein Hmo2, A Subunit Of The Chromatin-Remodeling Complex Ino80, Binds Dna Ends, Sreerupa Ray, Anne Grove

Faculty Publications

DNA damage is a common hazard that all cells have to combat. Saccharomyces cerevisiae HMO2 is a high mobility group protein (HMGB) that is a component of the chromatin-remodeling complex INO80, which is involved in double strand break (DSB) repair. We show here using DNA end-joining and exonuclease protection assays that HMO2 binds preferentially to DNA ends. While HMO2 binds DNA with both blunt and cohesive ends, the sequence of a single stranded overhang significantly affects binding, supporting the conclusion that HMO2 recognizes features at DNA ends. Analysis of the effect of duplex length on the ability of HMO2 to …

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Alu Repeats Increase Local Recombination Rates, David J. Witherspoon, W. Scott Watkins, Yuhua Zhang, Jinchuan Xing, Whitney L. Tolpinrud, Dale J. Hedges, Mark A. Batzer, Lynn B. Jorde Nov 2009

Alu Repeats Increase Local Recombination Rates, David J. Witherspoon, W. Scott Watkins, Yuhua Zhang, Jinchuan Xing, Whitney L. Tolpinrud, Dale J. Hedges, Mark A. Batzer, Lynn B. Jorde

Faculty Publications

Background: Recombination rates vary widely across the human genome, but little of that variation is correlated with known DNA sequence features. The genome contains more than one million Alu mobile element insertions, and these insertions have been implicated in non-homologous recombination, modulation of DNA methylation, and transcriptional regulation. If individual Alu insertions have even modest effects on local recombination rates, they could collectively have a significant impact on the pattern of linkage disequilibrium in the human genome and on the evolution of the Alu family itself. Results: We carried out sequencing, SNP identification, and SNP genotyping around 19 AluY insertion …

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3d-Surfer: Software For High-Throughput Protein Surface Comparison And Analysis, David La, Juan Esquivel-Rodríguez, Vishwesh Venkatraman, Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt, Daisuke Kihara Nov 2009

3d-Surfer: Software For High-Throughput Protein Surface Comparison And Analysis, David La, Juan Esquivel-Rodríguez, Vishwesh Venkatraman, Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt, Daisuke Kihara

Faculty Publications

Summary: We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by a vector of 3D Zernike descriptors, comparison times for a query protein against the entire PDB take, on an average, only a couple of seconds. The web interface has been designed to be as interactive as possible with displays showing animated protein rotations, CATH codes and structural alignments using the CE program. In addition, geometrically interesting local features of the protein surface, such as pockets that often correspond to ligand binding sites …

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A Novel Plant Virus With Unique Properties Infecting Japanese Holly Fern, Rodrigo A. Valverde, Sead Sabanadzovic Nov 2009

A Novel Plant Virus With Unique Properties Infecting Japanese Holly Fern, Rodrigo A. Valverde, Sead Sabanadzovic

Faculty Publications

A novel RNA virus with a bipartite genome has been found associated with an emerging disease affecting Japanese holly fern (Cyrtomium falcatum). Diseased Japanese holly fern plants showed a variety of foliar symptoms and reduction in size. The virus was transmitted by grafting, as well as through spores from an infected plant. Partially purified preparations of the virus from infected ferns contained quasi-spherical particles that ranged from 30 to 40 nm in diameter. Doublestranded RNA (dsRNA) analyses from diseased plants yielded two major molecules of approximately 6.2 and 3.0 kbp in size, together with three other dsRNAs ascertained to be …

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Novel Begomovirus Species Of Recombinant Nature In Sweet Potato (Ipomoea Batatas) And Ipomoea Indica: Taxonomic And Phylogenetic Implications, Gloria Lozano, Helena P. Trenado, Rodrigo A. Valverde, Jesús Navas-Castillo Nov 2009

Novel Begomovirus Species Of Recombinant Nature In Sweet Potato (Ipomoea Batatas) And Ipomoea Indica: Taxonomic And Phylogenetic Implications, Gloria Lozano, Helena P. Trenado, Rodrigo A. Valverde, Jesús Navas-Castillo

Faculty Publications

Viral diseases occur wherever sweet potato (Ipomoea batatas) is cultivated and because this crop is vegetatively propagated, accumulation and perpetuation of viruses can become a major constraint for production. Up to 90% reductions in yield have been reported in association with viral infections. About 20 officially accepted or tentative virus species have been found in sweet potato and other Ipomoea species. They include three species of begomoviruses (genus Begomovirus, family Geminiviridae) whose genomes have been fully sequenced. In this investigation, we conducted a search for begomoviruses infecting sweet potato and Ipomoea indica in Spain and characterized the complete genome of …

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Morphological Evolution: By Any Means Necessary?, John C. Larkin Nov 2009

Morphological Evolution: By Any Means Necessary?, John C. Larkin

Faculty Publications

Recent debate has focused on the role of cis-regulatory mutations in the evolution of genes controlling morphology. Identification of the molecular basis of naturally occurring variation in leaf hair (trichome) density in Arabidopsis, combined with earlier work in the same system, sheds light on this debate. © 2009 Elsevier Ltd. All rights reserved.

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6-Azahemiporphycene: A New Member Of The Porphyrinoid Family, Federica Mandoj, Sara Nardis, Giuseppe Pomarico, Manuela Stefanelli, Luca Schiaffino, Gianfranco Ercolani, Luca Prodi, Damiano Genovese, Nelsi Zaccheroni, Frank R. Fronczek, Kevin M. Smith, Xiao Xiao, Jing Shen, Karl M. Kadish, Roberto Paolesse Nov 2009

6-Azahemiporphycene: A New Member Of The Porphyrinoid Family, Federica Mandoj, Sara Nardis, Giuseppe Pomarico, Manuela Stefanelli, Luca Schiaffino, Gianfranco Ercolani, Luca Prodi, Damiano Genovese, Nelsi Zaccheroni, Frank R. Fronczek, Kevin M. Smith, Xiao Xiao, Jing Shen, Karl M. Kadish, Roberto Paolesse

Faculty Publications

The reaction of 5,10,15-triarylcorrole with 4-amino-4H-1,2,4-triazole provides another example of corroie ring expansion to give the corresponding 6-azahemiporphycene, a novel porphyrin analogue. The facile oxidation of the corroie ring is a required step for the ring expansion and for this reason the reaction fails in the case of corroles bearing meso-phenyl groups carrying electron-withdrawing substituents. Sterlc requirements also limited the scope of the reaction, which is not successful In the case of 2,6-disubstituted meso-aryl corroles. The occurrence of an initial oxidation is further supported by formation of the 6-azahemiporphycene derivative when the reaction is carried out under the same conditions, …

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Comparative Acute Toxicity Of Neonicotinoid And Pyrethroid Insecticides To Non-Target Crayfish (Procambarus Clarkii) Associated With Rice-Crayfish Crop Rotations, Gary C. Barbee, Michael J. Stout Nov 2009

Comparative Acute Toxicity Of Neonicotinoid And Pyrethroid Insecticides To Non-Target Crayfish (Procambarus Clarkii) Associated With Rice-Crayfish Crop Rotations, Gary C. Barbee, Michael J. Stout

Faculty Publications

Background: Most insecticides used to control rice water weevil (Lissorhoptrus oryzophilus Kuscel) infestations are pyrethroids. However, pyrethroids are highly toxic to non-target crayfish associated with rice-crayfish crop rotations. One solution to the near-exclusive reliance on pyrethroids in a rice-crayfish pest management program is to incorporate neonicotinoid insecticides, which are insect specific and effective against weevils but not extremely toxic to crayfish. This study aimed to take the first step to assess neonicotinoids as alternatives to pyrethroids in rice-crayfish crop rotations by measuring the acute toxicities of three candidate neonicotinoid insecticides, clothianidin, dinotefuran and thiamethoxam, to juvenile Procambarus clarkii (Girard) crayfish …

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Edwardsiella Ictaluri Encodes An Acid-Activated Urease That Is Required For Intracellular Replication In Channel Catfish (Ictalurus Punctatus) Macrophages, Natha J. Booth, Judith B. Beekman, Ronald L. Thune Nov 2009

Edwardsiella Ictaluri Encodes An Acid-Activated Urease That Is Required For Intracellular Replication In Channel Catfish (Ictalurus Punctatus) Macrophages, Natha J. Booth, Judith B. Beekman, Ronald L. Thune

Faculty Publications

Genomic analysis indicated that Edwardsiella ictaluri encodes a putative urease pathogenicity island containing the products of nine open reading frames, including urea and ammonium transporters. In vitro studies with wild-type E. ictaluri and a ureG::kan urease mutant strain indicated that E. ictaluri is significantly tolerant of acid conditions (pH 3.0) but that urease activity is not required for acid tolerance. Growth studies demonstrated that E. ictaluri is unable to grow at pH 5 in the absence of urea but is able to elevate the environmental pH from pH 5 to pH 7 and grow when exogenous urea is available. Substantial …

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