Digital Commons Network^™

Pigeons And People Select Efficient Routes When Solving A One-Way “Traveling Salesperson” Task, Brett M. Gibson, Edward A. Wasserman, Alan C. Kamil

Papers in Behavior in Biological Sciences

The authors presented people (Experiment 1) and pigeons (Experiments 2 and 3) with a large number of 1-way traveling salesperson problems that consisted of 3, 4, and 5 identical stimuli (nodes) on a computer monitor. The sequence of nodes that each traveler selected was recorded, and the distance of the route was subsequently determined. The routes the pigeons and people selected were reliably more efficient than those used by a Monte Carlo model given the same problems. The pigeons’ routes were significantly less efficient than a nearest neighbor model of performance, however. In Experiment 3, pigeons were required to select …

Identification Of Functional Subclasses In The Dj-1 Superfamily Proteins, Ying Wei, Dagmar Ringe, Mark A. Wilson, Mary Jo Ondrechen

Department of Biochemistry: Faculty Publications

Genomics has posed the challenge of determination of protein function from sequence and/or 3-D structure. Functional assignment from sequence relationships can be misleading, and structural similarity does not necessarily imply functional similarity. Proteins in the DJ-1 family, many of which are of unknown function, are examples of proteins with both sequence and fold similarity that span multiple functional classes. THEMATICS (theoretical microscopic titration curves), an electrostatics-based computational approach to functional site prediction, is used to sort proteins in the DJ-1 family into different functional classes. Active site residues are predicted for the eight distinct DJ-1 proteins with available 3-D structures. …

Expression, Processing, And Glycosaminoglycan Binding Activity Of The Recombinant Human 315-Kda Hyaluronic Acid Receptor For Endocytosis (Hare), Ed Harris, Svetlana V. Kyosseva, Janet A. Weigel, Paul H. Weigel

Department of Biochemistry: Faculty Publications

The hyaluronic acid (HA) receptor for endocytosis (HARE; also designated stabilin-2 and FEEL-2) mediates systemic clearance of glycosaminoglycans from the circulatory and lymphatic systems via coated pit-mediated uptake. HARE is primarily found as two isoforms (315- and 190-kDa) in sinusoidal endothelial cells of the liver, lymph node, and spleen. Here we characterize the ligand specificity and function of the large stably expressed 315-HARE isoform in Flp-In 293 cell lines. Like human spleen sinusoidal endothelial cells, Flp-In 293 cell lines transfected with a single cDNA encoding the full-length 315-HARE express both the 315-kDa and the proteolytically truncated 190-kDa isoforms in a …

Arabidopsis Thaliana Gh3.9 Influences Primary Root Growth, Sadaf Khan, Julie M. Stone

Department of Biochemistry: Faculty Publications

Auxins regulate a complex signal transduction network to direct plant development. Auxin-responsive genes fit into three major classes: the so-called auxin/indole- 3-acetic acid (Aux/IAA), the GH3, and the small auxin-up RNA (SAUR) gene families. The 20-member Arabidopsis thaliana GH3 gene family has been subdivided into three groups. In vitro studies have shown that most Group II members function as IAA–amido synthetases to conjugate amino acids to the plant hormone auxin. Here we report the role of a previously uncharacterized GH3 gene family member, GH3.9, in root growth. Unlike most other Group II family members, …

A New Strategy For Assessing Selenoprotein Function: Sirna Knockdown/Knock-In Targeting The 3'-Utr, Min-Hyuk Yoo, Xue-Ming Xu, Anton A. Turanov, Bradley A. Carlson, Vadim N. Gladyshev, Dolph L. Hatfield

Department of Biochemistry: Faculty Publications

Selenocysteine insertion into protein in mammalian cells requires RNA elements in the 3'-untranslated regions (3'-UTRs) of selenoprotein genes. The occurrence of these conserved sequences should make selenoproteins particularly amenable for knockdown/knock-in strategies to examine selenoprotein functions. Herein, we utilized the 3'-UTR of various selenoproteins to knock down their expression using siRNAs and then knock in expression using constructs containing mutations within the target region. Thioredoxin reductase 1 (TR1) knockdown in a mouse kidney cell line resulted in the cells growing about 10% more slowly, being more sensitive to UV radiation, and having increased apoptosis in response to UV than control …

Mechanistic Studies Of The Long Chain Acyl-Coa Synthetase Faa1p From Saccharomyces Cerevisiae, Hong Li, Elaina M. Melton, Steven Quackenbush, Concetta C. Dirusso, Paul N. Black

Department of Biochemistry: Faculty Publications

Long chain acyl-CoA synthetase (ACSL; fatty acid CoA ligase: AMP forming; EC 6.2.1.3) catalyzes the formation of acyl-CoA through a process, which requires fatty acid, ATP and coenzymeA as substrates. In the yeast Saccharomyces cerevisiae the principal ACSL is Faa1p (encoded by the FAA1 gene). The preferred substrates for this enzyme are cis-monounsaturated long chain fatty acids. Our previous work has shown Faa1p is a principal component of a fatty acid transport/activation complex that also includes the fatty acid transport protein Fat1p. In the present work hexameric histidine tagged Faa1p was purified to homogeneity through a two-step process in the …

Evidence For A Pro-Oxidant Intermediate In The Assembly Of Cytochrome Oxidase, Oleh Khalimonchuk, Amanda Bird, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The hydrogen peroxide sensitivity of cells lacking two proteins,

Sco1 and Cox11, important in the assembly of cytochrome

c oxidase (CcO), is shown to arise from the transient accumulation

of a pro-oxidant heme A-Cox1 stalled intermediate. The

peroxide sensitivity of these cells is abrogated by a reduction in

either Cox1 expression or hemeAformation but exacerbated by

either enhanced Cox1 expression or heme A production arising

from overexpression of COX15. Sco1 and Cox11 are implicated

in the formation of the Cu_A and Cu_B sites of CcO, respectively.

The respective wild-type genes suppress the peroxide sensitivities

of sco1∆ …

Coa1 Links The Mss51 Post-Translational Function To Cox1 Cofactor Insertion In Cytochrome C Oxidase Assembly, Fabien Pierrel, Megan L. Bestwick, Paul A. Cobine, Oleh Khalimonchuk, Julia A. Cricco, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The assembly of cytochrome c oxidase (CcO) in yeast mitochondria is shown to be dependent on a new assembly factor designated Coa1 that associates with the mitochondrial inner membrane. Translation of the mitochondrial-encoded subunits of CcO occurs normally in coa1Δ cells, but these subunits fail to accumulate. The respiratory defect in coa1Δ cells is suppressed by high-copy MSS51, MDJ1 and COX10. Mss51 functions in Cox1 translation and elongation, whereas Cox10 participates in the biosynthesis of heme a, a key cofactor of CcO. Respiration in coa1Δ and shy1Δ cells is enhanced when Mss51 and …

Nonylphenol Stimulates Fecundity But Not Population Growth Rate (Λ) Of Folsomia Candida, T. H. Widarto, P. H. Krogh, Valery E. Forbes

Valery Forbes Publications

The toxicity of nonylphenol (NP) to springtails was pronounced at 40 mg/kg dry weight soil, at which no animals survived. Body length and fecundity were the individual life-history traits significantly stimulated by sublethal concentrations of NP during a 64-day experiment. However, the effects of NP on these traits did not result in a statistically significant increase in population growth rate (λ). Decomposition analysis indicated that fecundity was the main contributor to the (non-significant) changes observed in λ. However, since the elasticity of fecundity was very low, large changes in fecundity resulted in a minimal effect on λ. Juvenile survival had …

Does Bisphenol A Induce Superfeminization In Marisa Cornuarietis? Part I: Intra- And Inter-Laboratory Variability In Test Endpoints, Valery E. Forbes, Henriette Selck, Annemette Palmqvist, John Aufderheide, Ryan Warbritton, Nadine Pounds, Roy Thompson, Norbert Caspers

Valery Forbes Publications

It has been claimed that bisphenol A (BPA) induces superfeminization in the freshwater gastropod, Marisa cornuarietis. To explore the reproducibility of prior work, here we present results from a three-laboratory study, the objectives of which were to determine the mean and variability in test endpoints (i.e., adult fecundity, egg hatchability, and juvenile growth) under baseline conditions and to identify the sources of variability. A major source of variability for all of the measured endpoints was due to differences within and among individuals. With few exceptions, variability among laboratories and among replicate tanks within laboratories contributed little to the observed variability …

Does Bisphenol A Induce Superfeminization In Marisa Cornuarietis? Part Ii: Toxicity Test Results And Requirements For Statistical Power Analyses, Valery E. Forbes, John Aufderheide, Ryan Warbritton, Nelly Van Der Hoeven, Norbert Caspers

Valery Forbes Publications

This study presents results of the effects of bisphenol A (BPA) on adult egg production, egg hatchability, egg development rates and juvenile growth rates in the freshwater gastropod, Marisa cornuarietis. We observed no adult mortality, substantial inter-snail variability in reproductive output, and no effects of BPA on reproduction during 12 weeks of exposure to 0, 0.1, 1.0, 16, 160 or 640 μg/L BPA. We observed no effects of BPA on egg hatchability or timing of egg hatching. Juveniles showed good growth in the control and all treatments, and there were no significant effects of BPA on this endpoint. Our …

A Practical Approach To Phylogenomics: The Phylogeny Of Ray-Finned Fish (Actinopterygii) As A Case Study, Chenhong Li, Guillermo Ortí, Gong Zhang, Guoqing Lu

School of Biological Sciences: Faculty Publications

Background: Molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. Surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently developing new phylogenetic makers. We report here a genome-comparison strategy to identifying nuclear gene markers for phylogenetic inference and apply it to the …

Genetic Microheterogeneity And Phenotypic Variation Of Helicobacter Pylori Arginase In Clinical Isolates, Justin Hovey, Emily Watson, Melanie Langford, Ellen Hildebrandt, Sangeetha Bathala, Jeffrey Bolland, Domenico Spadafora, George Mendz, David Mcgee

School of Biological Sciences: Faculty Publications

Background: Clinical isolates of the gastric pathogen Helicobacter pylori display a high level of genetic macro- and microheterogeneity, featuring a panmictic, rather than clonal structure. The ability of H. pylori to survive the stomach acid is due, in part, to the arginase-urease enzyme system. Arginase (RocF) hydrolyzes L-arginine to L-ornithine and urea, and urease hydrolyzes urea to carbon dioxide and ammonium, which can neutralize acid.

Results: The degree of variation in arginase was explored at the DNA sequence, enzyme activity and protein expression levels. To this end, arginase activity was measured from 73 minimally-passaged clinical isolates and six laboratory-adapted strains …

Habitat Area Affects Arthropd Communities Directly And Indirectly Through Top Predators, Örjan Östman, Nicholas W. Griffin, Jared L. Strasburg, Jennifer A. Brisson, Alan R. Templeton, Tiffany M. Knight, Jonathan M. Chase

School of Biological Sciences: Faculty Publications

Both habitat area and predators are known to affect the diversity and composition of species that live in a locality. In addition, habitat area can influence the presence of predators, indirectly affecting the diversity of prey. Thus, habitat area may influence species diversity directly and indirectly through the presence of top predators. Here we examine the effects of habitat area and predators on the species richness and composition of a foliage living arthropod community in a fragmented complex of glades (small grassland patches within a forested matrix) in the Ozark Plateau, Missouri. We find that a top predator, the eastern …

Molecular Phylogenetics Of The Phyllostomid Bat Genus Micronycteris With Descriptions Of Two New Subgenera, Calvin A. Porter, Steven R. Hoofer, Chrissy A. Cline, Federico G. Hoffmann, Robert J. Baker

School of Biological Sciences: Faculty Publications

We analyzed DNA sequence variation in the cytochrome-b gene and intron 7 of the nuclear fibrinogen, B beta polypeptide gene for 45 specimens of the bat genus Micronycteris, including all currently recognized species except M. sanborni. Phylogenetic analyses of both data sets supported 4 primary lineages within Micronycteris, which we recognize as subgenera: Leuconycteris new subgenus (M. brosseti), Micronycteris Gray (M. megalotis, M. microtis, M. matses, and M. giovanniae), Schizonycteris new subgenus (M. minuta, M. schimdtorum, and M. sanborni), and Xenoctenes Miller (M. hirsuta). …

Robust Population Management Under Uncertainty For Structured Population Models, A. Deines, E. Peterson, Derek Boeckner, J. Boyle, A. Keighley, J. Kogut, J. Lubben, Richard Rebarber, R. Ryan, Brigitte Tenhumberg, S. Townley, Andrew J. Tyre

School of Biological Sciences: Faculty Publications

Structured population models are increasingly used in decision making, but typically have many entries that are unknown or highly uncertain. We present an approach for the systematic analysis of the effect of uncertainties on long-term population growth or decay. Many decisions for threatened and endangered species are made with poor or no information. We can still make decisions under these circumstances in a manner that is highly defensible, even without making assumptions about the distribution of uncertainty, or limiting ourselves to discussions of single, infinitesimally small changes in the parameters. Suppose that the model (determined by the data) for the …

Systematics Of Iochrominae (Solanaceae): Patterns In Floral Diversity And Interspecific Crossability, Stacey Dewitt Smith, David A. Baum

School of Biological Sciences: Faculty Publications

Iochrominae is a florally diverse clade of 34 Andean species and six traditionally recognized genera within Physaleae. Recent phylogenetic estimates suggest that four of the six traditional genera of Iochrominae are not monophyletic. Using this phylogenetic framework, we examine the evolution of floral morphology and interspecific crossability in Iochrominae. Iochrominae is inferred to have had ancestrally a purple corolla, but now manifests a wide range of colors (red/orange, yellow, green, purple or white), several of which appear to have arisen multiple times. Other floral traits traditionally employed in taxonomy, including corolla shape, corolla length, and stapet form, are similarly evolutionarily …

Negative Correlation Does Not Imply A Tradeoff Between Growth And Reproduction In California Oaks, Johannes M. H. Knops, Walter D. Koenig, William J. Carmen

School of Biological Sciences: Faculty Publications

A tradeoff between growth and reproduction, often inferred from an inverse correlation between these two variables, is a fundamental paradigm of life-history evolution. Oak species provide a unique test of this relationship because different species mature acorns either in the year of pollination or in the year after pollination. This difference allows for an interspecific comparison testing whether the apparent tradeoff is causal or the result of confounding factors influencing growth and reproduction independently. Based on 13 years of data on five California oak species, we found significant negative correlations between radial growth and seed production in the three species …

Germ-Line Chimerism And Paternal Care In Marmosets (Callithrix Kuhlii), C. N. Ross, J. A. French, Guillermo Ortí

School of Biological Sciences: Faculty Publications

The formation of viable genetic chimeras in mammals through the transfer of cells between siblings in utero is rare. Using microsatellite DNA markers, we show here that chimerism in marmoset (Callithrix kuhlii) twins is not limited to blood-derived hematopoietic tissues as was previously described. All somatic tissue types sampled were found to be chimeric. Notably, chimerism was demonstrated to be present in germ-line tissues, an event never before documented as naturally occurring in a primate. In fact, we found that chimeric marmosets often transmit sibling alleles acquired in utero to their own offspring. Thus, an individual that contributes …

Bayesian Estimation Of Concordance Among Gene Trees, Cécile Ané, Bret Larget, David A. Baum, Stacey Dewitt Smith, Antonis Rokas

School of Biological Sciences: Faculty Publications

Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach …

Electrochemical Stimulation Of Microbial Perchlorate Reduction, J. Cameron Thrash, J. Ian Van Trump, Karrie A. Weber, Elisabeth Miller, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

As part of our studies into the diversity of dissimilatory perchlorate reducing bacteria (DPRB) we investigated the reduction of perchlorate in the cathodic chamber of a bioelectrical reactor (BER). Our results demonstrated that washed cells of Dechloromonas and Azospira species readily reduced 90 mg L^-1 perchlorate in the BER with 2,6- anthraquinone disulfonate (AQDS) as a mediator. No perchlorate was reduced in the absence of cells or AQDS, or in an open-circuit control. Similar results were observed when a natural microbial community was inoculated into a fed-batch BER. After 70 days of operation, a novel DPRB, strain VDY, was …

Alkaline Iron(Iii) Reduction By A Novel Alkaliphilic, Halotolerant, Bacillus Sp. Isolated From Salt Flat Sediments Of Soap Lake, Jarrod Pollock, Karrie A. Weber, Joe Lack, Laurie A. Achenbach, Melanie R. Mormile, John D. Coates

School of Biological Sciences: Faculty Publications

A halotolerant, alkaliphilic dissimilatory Fe(III)-reducing bacterium, strain SFB, was isolated from salt flat sediments collected from Soap Lake, WA. 16S ribosomal ribonucleic acid gene sequence analysis identified strain SFB as a novel Bacillus sp. most similar to Bacillus agaradhaerens (96.7% similarity). Strain SFB, a fermentative, facultative anaerobe, fermented various hexoses including glucose and fructose. The fructose fermentation products were lactate, acetate, and formate. Under fructose-fermenting conditions in a medium amended with Fe(III), Fe(II) accumulated concomitant with a stoichiometric decrease in lactate and an increase in acetate and CO₂. Strain SFB was also capable of respiratory Fe(III) reduction with …

Growth-Size Scaling Relationships Of Woody Plant Species Differ From Predictions Of The Metabolic Ecology Model, Sabrina E. Russo, Susan K. Wiser, David A. Coomes

School of Biological Sciences: Faculty Publications

The Metabolic Ecology Model predicts that tree diameter (D) growth (dD/dt) scales with D1/3. Using data on diameter growth and height–diameter relationships for 56 and 40 woody species, respectively, from forests throughout New Zealand, we tested one prediction and two assumptions of this model: (i) the exponent of the growth–diameter scaling relationship equals 1/3 and is invariant among species and growth forms, (ii) small and large individuals are invariant in their exponents and (iii) tree height scales with D2/3. We found virtually no support for any prediction or assumption: growth–diameter scaling exponents varied substantially among species and growth forms, correlated …

Origin Of The Bacterial Set Domain Genes: Vertical Or Horizontal?, Raul Alvarez-Venegas, Monther Sadder, Alexander Tikhonov, Zoya Avramova

School of Biological Sciences: Faculty Publications

The presence of Supressor of variegation-Enhanser of zeste-Trithorax (SET) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. Consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was taken as evidence that bacteria have obtained the SET domain genes from their hosts. Furthermore, it was proposed that the products of the genes would, most likely, …

The Arabidopsis Homologs Of Trithorax (Atx1) And Enhancer Of Zeste (Clf) Establish ‘Bivalent Chromatin Marks’ At The Silent Agamous Locus, Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, Zoya Avramova

School of Biological Sciences: Faculty Publications

Tightly balanced antagonism between the Polycomb group (PcG) and the Trithorax group (TrxG) complexes maintain Hox expression patterns in Drosophila and murine model systems. Factors belonging to the PcG/TrxG complexes control various processes in plants as well but whether they participate in mechanisms that antagonize, balance or maintain each other’s effects at a particular gene locus is unknown. CURLY LEAF (CLF), an Arabidopsis homolog of enhancer of zeste (EZ) and the ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) control the expression of the flower homeotic gene AGAMOUS (AG). Disrupted ATX1 or CLF function results in misexpression of AG, recognizable …

Virgin Birth In A Hammerhead Shark, Demian D. Chapman, Mahmood S. Shivji, Ed Louis, Julie Sommer, Hugh Fletcher, Paulo A. Prodöhl

School of Biological Sciences: Faculty Publications

Parthenogenesis has been documented in all major jawed vertebrate lineages except mammals and cartilaginous fishes (class Chondrichthyes: sharks, batoids and chimeras). Reports of captive female sharks giving birth despite being held in the extended absence of males have generally been ascribed to prior matings coupled with long-term sperm storage by the females. Here, we provide the first genetic evidence for chondrichthyan parthenogenesis, involving a hammerhead shark (Sphyrna tiburo). This finding also broadens the known occurrence of a specific type of asexual development (automictic parthenogenesis) among vertebrates, extending recently raised concerns about the potential negative effect of this type …

Flagellar Motility And Structure In The Hyperthermoacidophilic Archaeon Sulfolobus Solfataricus, Zalán Szabó, Musa Sani, Maarten Groeneveld, Benham Zolghadr, James Schelert, Sonja-Verena Albers, Paul H. Blum, Egbert J. Boekema, Arnold J.M. Driessen

School of Biological Sciences: Faculty Publications

Flagellation in archaea is widespread and is involved in swimming motility. Here, we demonstrate that the

structural flagellin gene from the crenarchaeaon Sulfolobus solfataricus is highly expressed in stationary-phasegrown

cells and under unfavorable nutritional conditions. A mutant in a flagellar auxiliary gene, flaJ, was

found to be nonmotile. Electron microscopic imaging of the flagellum indicates that the filaments are composed

of right-handed helices.

Geographic Distribution: Ramphotyphlops Braminus (Brahminy Blindsnake). Usa: Florida: Volusia Co, Louis A. Somma, Paul E. Skelley

Papers in Herpetology

RAMPHOTYPHLOPS BRAMINUS (Brahminy Blindsnake). USA: FLORIDA: VOLUSIA Co.: New Smyrna Beach. 23Septernber 2006. Collected by Stacy Simmons. Verified by Kenneth L. Krysko, Florida Museum ofN atural History, University of Florida. One individual found on floor of residence. UF 151313. First county record. Originally turned in to Division of Plant Industry (DPI) , Florida Department of Agriculture and Consumer Services, Gainesville, Florida, as a "worm for ID" on 27 September 2006; Entomology Log No. 6879. It is not clear if this single specimen indicates an established breeding colony in this county. However, this invasive, parthenogenic exotic is established in other Florida …

Genome-Enabled Hitchhiking Mapping Identifies Qtls For Stress Resistance In Natural Drosophila, Sergey V. Nuzhdin, Lawrence G. Harshman, M. Zhou, K. Harmon

Lawrence G. Harshman Publications

Identification of genes underlying complex traits is an important problem. Quantitative trait loci (QTL) are mapped using marker-trait co-segregation in large panels of recombinant genotypes. Most frequently, recombinant inbred lines derived from two isogenic parents are used. Segregation pat-terns are also studied in pedigrees from multiple families. Great advances have been made through creative use of these techniques, but narrow sampling and inadequate power represent strong limi-tations. Here, we propose an approach combining the strengths of both techniques. We established a mapping population from a sample of natural genotypes and applied artificial selection for a com-plex character. Selection changed the …

Evaluation Of Metals In A Defined Medium For Pichia Pastoris Expressing Recombinant Β-Galactosidase, Bradley A. Plantz, Kenneth W. Nickerson, Stephen D. Kachman, Vicki L. Schlegel

School of Biological Sciences: Faculty Publications

Culture growth and recombinant protein yield of the Pichia pastoris GS115 methanol utilization positive system were studied in response to the types and levels of metals present in the growth medium and the supplemental salts typically used for these fermentations. Magnesium and zinc were both required to support cell growth but at significantly reduced levels compared to the control. However, supplementation with calcium, cobalt, iron, manganese, iodine, boron, and molybdenum were not required to sustain cell mass. When the medium was reformulated with only zinc and magnesium, the cells grew to 12–15 generations, which are expected for high cell density …