Life Sciences Commons^™

Molecular Phylogenetics Of Alternanthera (Gomphrenoideae, Amaranthaceae): Resolving A Complex Taxonomic History Caused By Different Interpretations Of Morphological Characters In A Lineage With C4 And C3-C4 Intermediate Species, Ivonne Sánchez-Del Pino, Timothy J. Motley, Thomas Borsch

Biological Sciences Faculty Publications

Aternanthera (Amaranthaceae) is a diverse genus (80-200 species) largely restricted to the American Tropics. With Pedersenia and Tidestromia, it makes up the Alternantheroid clade in Gomphrenoideae. Parsimony and Bayesian analyses of nucleotide sequences of nuclear (ITS) and plastid (rpl16, trnL-F) and morphological characters identify that the capitate stigma of Alternanthera is a synapomorpy within the Alternantheroids. Within Alternanthera, two major clades were resolved, both of which were marked by otherwise homoplasious characters of the gynoecium: Clade A [99% jackknife (JK); 1.0 posterior probability (PP)] with nine species and Clade B (60% JK; 0.98 PP) with 22 …

Testing The Role Of Male-Male Competition In The Evolution Of Sexual Dimorphism: A Comparison Between Two Species Of Porcelain Crabs, J. Antonio Baeza, Cynthia M. Asorey

Biological Sciences Faculty Publications

Theory predicts marked sexual dimorphism in terms of body size and body structures used as weapons (e.g. chelipeds) in gonochoric species with intense male sexual competition for receptive females and reduced or no sexual dimorphism in species where competition among males is trivial. We tested this hypothesis using a pair of closely-related species of symbiotic porcelain crabs as a model. In one species that inhabits sea anemones solitarily, competition among males for receptive females is unimportant. In a second species that dwells as dense aggregations on sea urchins, malemale competition for sexual partners is recurrent. We expected considerable sexual dimorphism …

Mutation In The Plasmodium Falciparum Crt Protein Determines The Stereospecific Activity Of Antimalarial Cinchona Alkaloids, Carol E. Griffin, Jonathan M. Hoke, Upeka Samarakoon, Junhui Duan, Jianbing Mu, Michael T. Ferdig, David C. Warhurst, Roland A. Cooper

Biological Sciences Faculty Publications

The Cinchona alkaloids are quinoline aminoalcohols that occur as diastereomer pairs, typified by (-)-quinine and (+)-quinidine. The potency of (+)-isomers is greater than the (-)-isomers in vitro and in vivo against Plasmodium falciparum malaria parasites. They may act by the inhibition of heme crystallization within the parasite digestive vacuole in a manner similar to chloroquine. Earlier studies showed that a K76I mutation in the digestive vacuole-associated protein, PfCRT (P. falciparum chloroquine resistance transporter), reversed the normal potency order of quinine and quinidine toward P. falciparum. To further explore PfCRT-alkaloid interactions in the malaria parasite, we measured the in …

Extinction Risk And Bottlenecks In The Conservation Of Charismatic Marine Species, Loren Mcclenachan, Andrew B. Cooper, Kent E. Carpenter, Nicholas K. Dulvy

Biological Sciences Faculty Publications

The oceans face a biodiversity crisis, but the degree and scale of extinction risk remains poorly characterized. Charismatic species are most likely to gar- ner greatest support for conservation and thus provide a best-case scenario of the status of marine biodiversity. We summarize extinction risk and diagnose impediments to successful conservation for 1,568 species in 16 families of marine animals in the movie Finding Nemo. Sixteen percent (12–34%) of those that have been evaluated are threatened, ranging from 9% (7–28%) of bony fishes to 100% (83–100%) of marine turtles. A lack of scientific knowledge impedes analysis of threat status …

A Global Diatom Database- Abundance, Biovolume And Biomass In The World Ocean, K. Leblanc, J. Aristegui, L. Armand, P. Assmy, B. Becker, A. Bode, E. Breton, V. Cornet, J. Gibson, M. P. Gosselin, H. Marshall

Biological Sciences Faculty Publications

Phytoplankton identification and abundance data are now commonly feeding plankton distribution databases worldwide. This study is a first attempt to compile the largest possible body of data available from different databases as well as from individual published or unpublished datasets regarding diatom distribution in the world ocean. The data obtained originate from time series studies as well as spatial studies. This effort is supported by the Marine Ecosystem Model Inter-Comparison Project (MAREMIP), which aims at building consistent datasets for the main plankton functional types (PFTs) in order to help validate biogeochemical ocean models by using carbon (C) biomass derived from …

Toxin-Antitoxic Loci Vapbc-1 And Vapxd Contribute To Survival And Virulence In Nontypeable Haemophilus Influenzae, Dabin Ren, Anna N. Walker, Dayle A. Daines

Biological Sciences Faculty Publications

Background: Nontypeable Haemophilus influenzae (NTHi) is a significant human pathogen responsible for respiratory tract infections and the most common cause of recurrent otitis media. Type II toxin-antitoxin (TA) systems are genetic elements that code for a stable protein toxin and a labile antitoxin that are thought to be involved in metabolic regulation of bacteria by enabling a switch to a dormant state under stress conditions. The contribution to infection persistence of the NTHi TA loci vapBC-1 and vapXD was examined in this study.

Results: Deletions in vapBC-1, vapXD and vapBC-1 vapXD significantly decreased the survival of NTHi co-cultured with …

Genotypic And Phenotypic Variation In Pseudomonas Aeruginosa Reveals Signatures Of Secondary Infection And Mutator Activity In Certain Cystic Fibrosis Patients With Chronic Lung Infections, Ashley E. Warren, Carla M. Boulianne-Larsen, Christine B. Chandler, Kami Chiotti, Evgueny Kroll, Scott R. Miller, Francois Taddei, Isabelle Sermet-Gaudelus, Agnes Ferroni, Kathleen Mcinnerney, Michael J. Franklin, Frank Rosenzweig

Biological Sciences Faculty Publications

Evolutionary adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung is limited by genetic variation, which depends on rates of horizontal gene transfer and mutation supply. Because each may increase following secondary infection or mutator emergence, we sought to ascertain the incidence of secondary infection and genetic variability in populations containing or lacking mutators. Forty-nine strains collected over 3 years from 16 patients were phenotyped for antibiotic resistance and mutator status and were genotyped by repetitive-sequence PCR (rep-PCR), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Though phenotypic and genetic polymorphisms were widespread and clustered more strongly within than …

Lack Of Fire Has Limited Physiological Impact On Old-Growth Ponderosa Pine In Dry Montane Forests Of North-Central Idaho, Eric Keeling, Anna Sala, Thomas H. Deluca

Biological Sciences Faculty Publications

Reduced frequency of fire in historically fire-adapted ecosystems may have adverse effects on ecosystem structure, function, and resilience. Lack of fire increases stand density and promotes successional replacement of seral dominant trees by late-successional, more shade-tolerant species. These changes are thought to increase competition for limited resources among trees and to increase physiological stress of dominant, fire-adapted species. However, there has been little effort to directly investigate effects of lack of fire on the physiological status of old trees, especially in unlogged, protected forests. At four remote sites in the Selway-Bitterroot region of Idaho, we tested whether the physiological status …

Evolution Of Coordinated Mutagenesis And Somatic Hypermutation In Vh5, Barbara E. Wright, Karen H. Schmidt, Aaron T. Hunt, Dennis K. Reschke, Michael F. Minnick

Biological Sciences Faculty Publications

The VH5 human antibody gene was analyzed using a computer program (mfg) which simulates transcription, to better understand transcription-driven mutagenesis events that occur during "phase 1" of somatic hypermutation. Results show that the great majority of mutations in the non-transcribed strand occur within loops of two predicted high-stability stem-loop structures, termed SLSs 14.9 and 13.9. In fact, 89% of the 2505 mutations reported are within the encoded complementarity-determining region (CDR) and occur in loops of these high-stability structures. In vitro studies were also done and verified the existence of SLS 14.9. Following the formation of SLSs 14.9 and 13.9, a …

Escape From Competition: Neighbors Reduce Centaurea Stoebe Performance At Home But Not Away, Ragan M. Callaway, Lauren P. Waller, Alecu Diaconu, Robert Pal, Alexandra R. Collins, Heingz Mueller-Schaerer, John L. Maron

Biological Sciences Faculty Publications

The greater abundance of some exotic plants in their nonnative ranges might be explained in part by biogeographic differences in the strength of competition, but these competitive effects have not been experimentally examined in the field. We compared the effects of neighbors on the growth and reproduction of spotted knapweed (Centaurea stoebe) in Europe, where it is native, and in Montana, where it is invasive. There were strong negative competitive effects of neighboring vegetation on C. stoebe growth and reproduction in Europe. In contrast, identical experiments in Montana resulted in insignificant impacts on C. stoebe. Although the …

Shifting Species Interactions In Terrestrial Dryland Ecosystems Under Altered Water Availability And Climate Change, Kevin E. Mccluney, Jayne Belnap, Scott L. Collins, Angélica L. González, Elizabeth M. Hagen, J. Nathaniel Holland, Burt P. Kotler, Fernando T. Maestre, Stanley D. Smith, Blair O. Wolf

Biological Sciences Faculty Publications

No abstract provided.

Genetics Of Coxiella Burnetii: On The Path Of Specialization, Michael F. Minnick, Rahul Raghavan

Biological Sciences Faculty Publications

Coxiella burnetii is an extremely infectious, zoonotic agent that causes Q fever in humans. With the exception of New Zealand, the bacterium is distributed worldwide. Coxiella is classified as a select agent based on its past and potential use as a bioweapon and its threat to public health. Despite decades of research, we know relatively little regarding Coxiella?s molecular pathogenesis, and a vaccine is not widely available. This article briefly reviews the unusual genetics of C. burnetii; a pathogen that retains telltale genetic mementos collected over the course of its evolutionary path from a free-living bacterium to an obligate intracellular …

River Drying Lowers The Diversity And Alters The Composition Of An Assemblage Of Desert Riparian Arthropods, Kevin E. Mccluney, John L. Sabo

Biological Sciences Faculty Publications

Summary 1. Many studies have shown negative effects of river drying on in‐stream animals. However, the influence of river drying on riparian animals remains poorly studied. We examined ground‐dwelling riparian arthropod assemblages along a drying section of the semi‐arid San Pedro River in southeastern Arizona, U.S.A.

2. We found strong differences in assemblage composition, taxon diversity and the abundance of key taxa between dry and flowing sites, with higher diversity and abundance of most taxa at flowing sites.

3. Changes in assemblage composition, taxon diversity and abundance of representative taxa were associated with a combined measure of water availability that …

Ribozyme Stability, Exon Skipping, And A Potential Role For Rna Helicase In Group I Intron Splicing By Coxiella Burnetii, Linda D. Hicks, Indu Warrier, Rahul Raghavan, Michael F. Minnick

Biological Sciences Faculty Publications

The 23S rRNA gene of Coxiella burnetii, the agent of Q fever in humans, contains an unusually high number of conserved, selfish genetic elements, including two group I introns, termed Cbu.L1917 (L1917) and Cbu.L1951 (L1951). To better understand the role that introns play in Coxiella's biology, we determined the intrinsic stability time periods (in vitro half-lives) of the encoded ribozymes to be similar to 15 days for L1917 and similar to 5 days for L1951, possibly due to differences in their sizes (551 and 1,559 bases, respectively), relative degrees of compactness of the respective RNA structures, and amounts of single-stranded …

The Roles Of Transcription And Genotoxins Underlying P53 Mutagenesis In Vivo, Barbara E. Wright, Karen H. Schmidt, Aaron T. Hunt, J Stephen Lodmell, Michael F. Minnick, Dennis K. Reschke

Biological Sciences Faculty Publications

Transcription drives supercoiling which forms and stabilizes single-stranded (ss) DNA secondary structures with loops exposing G and C bases that are intrinsically mutable and vulnerable to non-enzymatic hydrolytic reactions. Since many studies in prokaryotes have shown direct correlations between the frequencies of transcription and mutation, we conducted in silico analyses using the computer program, mfg, which simulates transcription and predicts the location of known mutable bases in loops of high-stability secondary structures. Mfg analyses of the p53 tumor suppressor gene predicted the location of mutable bases and mutation frequencies correlated with the extent to which these mutable bases were exposed …

Death Of The Tonb Shuttle Hypothesis, Ray A. Larsen, Michael G. Gresock, Marina I. Savenkova, Anne A. Ollis, Kathleen Postle

Biological Sciences Faculty Publications

A complex of ExbB, ExbD, andTonB couples cytoplasmic membrane (CM) proton motive force (pmf) to the active transport of large, scarce, or important nutrients across the outer membrane (OM). TonB interacts with OM transporters to enable ligand transport. Several mechanical models and a shuttle model explain how TonB might work. In the mechanical models, TonB remains attached to the CM during energy transduction, while in the shuttle model theTonB N terminus leaves the CM to deliver conformationally stored potential energy to OM transporters. Previous studies suggested thatTonB did not shuttle based on the activity of a GFP-TonB fusion that was …

Use Of Optimal Control Models To Predict Treatment Time For Managing Tick-Borne Disease, Holly D. Gaff, Elsa Schaefer, Suzanne Lenhart

Biological Sciences Faculty Publications

Tick-borne diseases have been on the rise recently, and correspondingly, there is an increased interest in implementing control measures to decrease the risk. Optimal control provides an ideal tool to identify the best method for reducing risk while accounting for the associated costs. Using a previously published model, a variety of frameworks are assessed to identify the key factors influencing mitigation strategies. The level and duration of tick-reducing efforts are key metrics for understanding the successful reduction in tick-borne disease incidence. The results show that the punctuated nature of the tick's life history plays a critical role in reducing risk …

Biotic Resistance Via Granivory: Establishment By Invasive, Naturalized, And Native Asters Reflects Generalist Preference, Dean E. Pearson, Ragan M. Callaway, John L. Maron

Biological Sciences Faculty Publications

Escape from specialist natural enemies is frequently invoked to explain exotic plant invasions, but little attention has been paid to how generalist consumers in the recipient range may influence invasion. We examined how seed preferences of the widespread generalist granivore Peromyscus maniculatus related to recruitment of the strongly invasive exotic Centaurea stoebe and several weakly invasive exotics and natives by conducting laboratory feeding trials and seed addition experiments in the field. Laboratory feeding trials showed that P. maniculatus avoided consuming seeds of C. stoebe relative to the 12 other species tested, even when seeds of alternative species were 53–94% smaller …

First Transcriptome Of The Testis-Vas Deferens-Male Accessory Gland And Proteome Of The Spermatophore From Dermacentor Variabilis (Acari: Ixodidae), Daniel E. Sonenshine, Brooke W. Bissinger, Noble Egekwu, Kevin V. Donohue, Sayed M. Khalil, R. Michael Roe

Biological Sciences Faculty Publications

Ticks are important vectors of numerous human diseases and animal diseases. Feeding stimulates spermatogenesis, mating and insemination of male factors that trigger female reproduction. The physiology of male reproduction and its regulation of female development are essentially a black box. Several transcriptomes have catalogued expression of tick genes in the salivary glands, synganglion and midgut but no comprehensive investigation has addressed male reproduction and mating. Consequently, a new global approach using transcriptomics, proteomics, and quantitative gene expression is needed to understand male reproduction and stimulation of female reproduction.This first transcriptome to the reproductive biology of fed male ticks, Dermacentor variabilis …

A New Species Of Diploid Quillwort (Isoetes, Isoetaceae, Lycophyta) From Lebanon, Jay F. Bolin, Rebecca D. Bray, Lytton John Musselman

Biological Sciences Faculty Publications

A new species, Isoetes libanotica Musselman, Bolin & B. D. Bray (Isoetaceae, Lycophyta), is described from Akkar District of northern Lebanon. It is a seasonal terrestrial species of basaltic soils, diploid (2n = 22), with complete velum coverage. Megaspore diameter ranges from 338 to 477 mu m with remote, low tuberculate ornamentation and a low to obsolete equatorial girdle; microspore length ranges from 25 to 30 mu m, with echinate ornamentation. At the type locality of I. libanotica, two other Isoetes L. species occur sympatrically. These superficially similar Isoetes species can be differentiated from I. libanotica using megaspore …

The Fecal Viral Flora Of Wild Rodents, Tung G. Phan, Beatrix Kapusinszky, Chunlin Wang, Robert K. Rose, Howard L. Lipton, Eric L. Delwart

Biological Sciences Faculty Publications

The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially …

Structure-Activity Relationships For The Interactions Of 2'- And 3'-(O)-(N-Methyl)Anthraniloyl-Substituted Purine And Pyrimidine Nucleotides With Mammalian Adenylyl Cyclases, Cibele Pinto, Gerald H. Lushington, Mark Richter, Andreas Gille, Jens Geduhn, Burkhard König, Tung-Chung Mou, Stephen R. Sprang, Roland Seifert

Biological Sciences Faculty Publications

Membranous adenylyl cyclases (ACs) play a key role in signal transduction and are promising drug targets. In previous studies we showed that 2',3'-(O)-(N-methylanthraniloyl) (MANT)-substituted nucleotides are potent AC inhibitors. The aim of this study was to provide systematic structure-activity relationships for 21 (M)ANT-substituted nucleotides at the purified catalytic AC subunit heterodimer VC1:IIC2, the VC1:VC1 homodimer and recombinant ACs 1, 2 and 5. (M)ANT-nucleotides inhibited fully activated VC1:IIC2 in the order of affinity for bases hypoxanthine>uracil>cytosine>adenine∼guanine≫xanthine. Omission of a hydroxyl group at the 2' or 3'-position reduced inhibitor potency as did introduction of a γ-thiophosphate group or omission …

Physiological Trade-Offs In Self-Maintenance: Plumage Molt And Stress Physiology In Birds, Jamie M. Cornelius, Nicole Perfito, Richard Zann, Creagh W. Breuner, Thomas P. Hahn

Biological Sciences Faculty Publications

Trade-offs between self-maintenance processes can affect life-history evolution. Integument replacement and the stress response both promote self-maintenance and affect survival in vertebrates. Relationships between the two processes have been studied most extensively in birds, where hormonal stress suppression is down regulated during molt in seasonal species, suggesting a resource-based trade-off between the two processes. The only species found to differ are the rock dove and Eurasian tree sparrow, at least one of which performs a very slow molt that may reduce resource demands during feather growth, permitting investment in the stress response. To test for the presence of a molt–stress …

A Reply To King Et Al., Mark E. Swanson, Jerry F. Franklin, Robert L. Beschta, Charles M. Crisafulli, Dominick A. Dellasala, Richard L. Hutto, David B. Lindenmayer, Frederick J. Swanson

Biological Sciences Faculty Publications

No abstract provided.

Hunger Artists: Yeast Adapted To Carbon Limitation Show Trade-Offs Under Carbon Sufficiency, Jared W. Wenger, Jeffrey Piotrowski, Saisubramanian Nagarajan, Kami Chiotti, Gavin Sherlock, Frank Rosenzweig

Biological Sciences Faculty Publications

As organisms adaptively evolve to a new environment, selection results in the improvement of certain traits, bringing about an increase in fitness. Trade-offs may result from this process if function in other traits is reduced in alternative environments either by the adaptive mutations themselves or by the accumulation of neutral mutations elsewhere in the genome. Though the cost of adaptation has long been a fundamental premise in evolutionary biology, the existence of and molecular basis for trade-offs in alternative environments are not well-established. Here, we show that yeast evolved under aerobic glucose limitation show surprisingly few trade-offs when cultured in …

Variable Helper Effects, Ecological Conditions, And The Evolution Of Cooperative Breeding In The Acorn Woodpecker, Walter D. Koenig, Eric L. Walters, Joseph Haydock

Biological Sciences Faculty Publications

The ecological conditions leading to delayed dispersal and helping behavior are generally thought to follow one of two contrasting scenarios: that conditions are stable and predictable, resulting in young being ecologically forced to remain as helpers (extrinsic constraints and the habitat saturation hypothesis), or that conditions are highly variable and unpredictable, leading to the need for helpers to raise young, at least when conditions are poor (intrinsic constraints and the hard life hypothesis). We investigated how variability in ecological conditions influences the degree to which helpers augment breeder fitness in the cooperatively breeding acorn woodpecker (Melanerpes formicivorus), a …

Caenorhabditis Briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility And The Evolution Of Recombination, Joseph A. Ross, Daniel C. Koboldt, Julia E. Staisch, Helen M. Chamberlin, Bhagwati P. Gupta, Raymond D. Miller, Scott Everet Baird, Eric S. Haag

Biological Sciences Faculty Publications

The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by …

Exome-Wide Dna Capture And Next Generation Sequencing In Domestic And Wild Species, Albano Beja-Pereira, Shanyuan Chen, Theodore F. Cosart, Gordon Luikart, Sarah B. Ng, Jay Shendure

Biological Sciences Faculty Publications

Our understanding of the molecular, genetic basis of adaptations and phenotypic differentiation among individuals will advance quickly thanks to new molecular techniques. This understanding is crucial given that accelerating environmental change and human population growth are increasingly threatening natural populations of fish and wildlife as well as increasing demands for agricultural production in domesticated species. This makes it urgent in many wild and domestic species to investigate the genetic basis of fitness, adaptation, and disease resistance [1], and to discover adaptive genes and speciation genes, i.e., the "loci of evolution" [2].

Viral Selex Reveals Individual And Cooperative Roles Of The C-Box And G-Box In Hiv-2 Replication, Christy L. Strong, Jean-Marc Lanchy, J. Stephen Lodmell

Biological Sciences Faculty Publications

The 5' UTR of HIV-2 genomic RNA contains signaling motifs that regulate specific steps of the replication cycle. Two motifs of interest are the C-box and the G-box. The C-box is found in the 5' untranslated region upstream of the primer binding site, while the G-box is found downstream from the major splice donor site, encompassing the gag start codon and flanking nucleotides. Together the C-box and the G-box form a long-range base-pairing interaction called the CGI. We and others have previously shown that formation of the CGI affects RNA dimerization in vitro and the positions of the C-box and …

Structural Basis For The High-Affinity Inhibition Of Mammalian Membranous Adenylyl Cyclase By 2',3'-O-(N-Methylanthraniloyl)-Inosine 5'-Triphosphate, Melanie Hübner, Anshuman Dixit, Tung-Chung Mou, Gerald H. Lushington, Cibele Pinto, Andreas Gille, Jens Geduhn, Burkhard König, Stephen Sprang, Roland Seifert

Biological Sciences Faculty Publications

2',3'-O-(N-Methylanthraniloyl)-ITP (MANT-ITP) is the most potent inhibitor of mammalian membranous adenylyl cyclase (mAC) 5 (AC5, K(i), 1 nM) yet discovered and surpasses the potency of MANT-GTP by 55-fold (J Pharmacol Exp Ther 329:1156-1165, 2009). AC5 inhibitors may be valuable drugs for treatment of heart failure. The aim of this study was to elucidate the structural basis for the high-affinity inhibition of mAC by MANT-ITP. MANT-ITP was a considerably more potent inhibitor of the purified catalytic domains VC1 and IIC2 of mAC than MANT-GTP (K(i), 0.7 versus 18 nM). Moreover, there was considerably more efficient fluorescence resonance energy transfer between Trp1020 …