Life Sciences Commons^™

Don't Diss Integration: A Comment On Ricklefs's Disintegrating Communities, Rob W. Booker, Ragan M. Callaway, Lohengrin A. Cavieres, Zaal Kikvidze, Christopher J. Lortie, Richard Michalet, Francisco I. Pugnaire, Alfonso Valiente-Banuet, Thomas G. Whitham

Biological Sciences Faculty Publications

No abstract provided.

E Unibus Plurum: Genomic Analysis Of An Experimentally Evolved Polymorphism In Escherichia Coli, Margie A. Kinnersley, William E. Holben, Frank Rosenzweig

Biological Sciences Faculty Publications

Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones. Apart from a 29 kb deletion in the dominant clone, no large-scale genomic changes distinguished evolved clones from their common ancestor. Using transcriptional profiling on co-evolved clones cultured separately under glucose-limitation we identified 180 genes significantly altered in expression relative to the common ancestor grown under similar conditions. Ninety of these were similarly expressed in all clones, and many of …

Group I Introns And Inteins: Disparate Origins But Convergent Parasitic Strategies, Rahul Raghavan, Michael F. Minnick

Biological Sciences Faculty Publications

No abstract provided.

Geographical Patterning Of Sixteen Goat Breeds From Italy, Albania And Greece Assessed By Single Nucleotide Polymorphisms, Lorraine Pariset, Antonella Cuteri, Christina Ligda, Alessio Valentini, Econogene Consortium

Biological Sciences Faculty Publications

Background: SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters.

Results: A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, …

Differential Inhibition Of Various Adenylyl Cyclase Isoforms And Soluble Guanylyl Cyclase By 2',3'-O-(2,4,6-Trinitrophenyl)-Substituted Nucleoside 5'-Triphosphates, Srividya Suryanarayana, Martin Göttle, Melanie Hübner, Andreas Gille, Tung-Chung Mou, Stephen R. Sprang, Mark Richter, Roland Seifert

Biological Sciences Faculty Publications

Adenylyl cyclases (ACs) catalyze the conversion of ATP into the second messenger cAMP and play a key role in signal transduction. In a recent study (Mol Pharmacol 70: 878-886, 2006), we reported that 2',3'-O-(2,4,6-trinitrophenyl)-substituted nucleoside 5'-triphosphates (TNP-NTPs) are potent inhibitors (K(i) values in the 10 nM range) of the purified catalytic subunits VC1 and IIC2 of membranous AC (mAC). The crystal structure of VC1: IIC2 in complex with TNP-ATP revealed that the nucleotide binds to the catalytic site with the TNP-group projecting into a hydrophobic pocket. The aims of this study were to analyze the interaction of TNP-nucleotides with VC1: …

Desulfovibrio Idahonensis Sp. Nov., Sulfatereducing Bacteria Isolated From A Metal(Loid)-Contaminated Freshwater Sediment, H. Sass, S. Ramamoorthy, C. Yarwood, H. Langner, P. Schumann, R. M. Kroppenstedt, S. Spring, R. Frank Rosenzweig

Biological Sciences Faculty Publications

Two novel sulfate-reducing bacteria, strains CY1 and CY2, were isolated from heavy-metal-contaminated sediments of Lake Coeur d'Alene, Idaho, USA. Strains CY1 and CY2 were found to contain c-type cytochromes and to reduce sulfate, sulfite, thiosulfate, elemental sulfur, DMSO, anthraquinone disulfonate and fumarate using lactate as an electron donor. In a comparison of 16S rRNA gene sequences, CY1 and CY2 were found to be 100% identical, but only 97 and 92.4% similar, respectively, to the type strains of Desulfovibrio mexicanus and Desulfovibrio aminophilus. Unlike these species, however, CY1 was neither able to disproportionate thiosulfate nor able to use yeast extract or …

Plasma Testosterone Correlates With Morph Type Across Breeding Substages In Male White-Throated Sparrows, M. B. Swett, Creagh W. Breuner

Biological Sciences Faculty Publications

White-throated sparrows (Zonotrichia albicollis) exhibit a genetic polymorphism that affects plumage and behavior in both sexes. White-striped morphs are more territorially aggressive, whereas tan-striped morphs provision nestlings at a higher rate. We investigated testosterone physiology in this species in an effort to understand hormonal mechanisms for the observed differences in aggression and parental care between the morphs. We found a small but significant difference in plasma testosterone between free-living white-striped and tan-striped males over the course of the breeding season. This difference correlates with previously observed differences in aggressive behavior and suggests that testosterone may mediate these differences. Testosterone remained …

Pestilence, Persistence And Pathogenicity: Infection Strategies Of Bartonella, Michael F. Minnick, James M. Battisti

Biological Sciences Faculty Publications

It has been nearly two decades since the discovery of Bartonella as an agent of bacillary angiomatosis in AIDS patients and persistent bacteremia and 'nonculturable' endocarditis in homeless people. Since that time, the number of Bartonella species identified has increased from one to 24, and 10 of these bacteria are associated with human disease. Although Bartonella is the only genus that infects human erythrocytes and triggers pathological angiogenesis in the vascular bed, the group remains understudied compared with most other bacterial pathogens. Numerous questions regarding Bartonella's molecular pathogenesis and epidemiology remain unanswered. Virtually every mammal harbors one or more Bartonella …

Tri-Trophic Linkages In Disease: Pathogen Transmission To Rainbow Trout Through Stonefly Prey, Sandra M. Adams, Aaron S. Adams, William E. Holben

Biological Sciences Faculty Publications

ABSTRACT Relationships between macroinvertebrates and microorganisms in aquatic environments are only poorly understood despite the fact that many aquatic macroinvertebrates feed on microbial biofilms during some life stage. Better understanding of trophic interactions between microbial biofims, macroinvertebrates, and fish may also help control fish diseases and loss of natural resources. It has also been suggested that pollution, habitat fragmentation, and poor water quality may contribute to increased pathogenesis and mortality in fish. Increased disease incidence is difficult to assess, however, in part because of the complexity of pathogen transmission dynamics. Several environmental pathogens exist whose reservoir(s) and means of transmission …

Ontogeny And Individual Variation In The Adrenocortical Response Of Zebra Finch (Taeniopygia Guttata) Nestlings, Haruka Wada, Katrina G. Salvante, Emily Wagner, Tony D. Williams, Creagh W. Breuner

Biological Sciences Faculty Publications

Numerous studies indicate interspecies variation in the ontogeny of the adrenocortical response in birds; however, little is known about the extent of interindividual variation in avian young. Toward this end, we examined the ontogeny and interindividual variation in the adrenocortical response in zebra finch (Taeniopygia guttata) nestlings. We measured baseline and stress-induced total (bound and free) corticosterone, corticosteroid binding globulin capacity, and resulting estimated free corticosterone levels in nestlings of four different ages ( days 5, 10, 16, and 21). In addition, we investigated the potential correlates of interindividual variation (brood size and mass). Nestlings at days 5 and 10 …

Differential Interactions Of The Catalytic Subunits Of Adenylyl Cyclase With Forskolin Analogs, Cibele Pinto, Melanie Hübner, Andreas Gille, Mark Richter, Tung-Chung Mou, Stephen R. Sprang, Roland Seifert

Biological Sciences Faculty Publications

The diterpene forskolin (FS) binds to, and activates, mammalian membranous adenylyl cyclase (AC) isoforms I-VIII. Diterpenes without C(1)-OH group do not activate ACs. The C(1)-OH group forms a hydrogen bond with the backbone oxygen of Val506 of the C1 catalytic subunit of AC (isoform V numbering). To better understand the mechanism of AC activation we examined the interactions of FS and eight FS analogs with purified catalytic AC subunits C1 (AC V) and C2 (AC II) by fluorescence spectroscopy, using 2',3'-O-(N-methylanthraniloyl)-guanosine 5'-triphosphate (MANT-GTP) as fluorescent reporter probe, and by enzymatic activity. FS analogs induced C1/C2 assembly as assessed by fluorescence …

A Continent-Wide Clone: Population Genetic Variation Of The Invasive Plant Hieracium Aurantiacum (Orange Hawkweed; Asteraceae) In North America, Eli S. Loomis, Lila Fishman

Biological Sciences Faculty Publications

We investigated the population genetic structure of the invasive plant Hieracium aurantiacum (Asteraceae), a facultative apomict. We generated amplified fragment length polymorphism fingerprints for H. aurantiacum samples from across its invasive range in North America (N = 226) and from six other North American native and invasive Hieracium species (N = 60). Almost no genetic variability was found in the North American H. aurantiacum across locations from Alaska and Oregon to Pennsylvania and Ontario (clonal diversity = 0.035). In contrast, other Hieracium species showed a range of clonal diversities (range = 0.154-1.0). The single H. aurantiacum genotype that dominated the …

Bar-Coded Pyrosequencing Reveals Shared Bacterial Community Properties Along The Temperature Gradients Of Two Alkaline Hot Springs In Yellowstone National Park, Scott R. Miller, Aaron L. Strong, Kenneter L. Jones, Mark C. Ungerer

Biological Sciences Faculty Publications

An understanding of how communities are organized is a fundamental goal of ecology but one which has historically been elusive for microbial systems. We used a bar-coded pyrosequencing approach targeting the V3 region of the bacterial small-subunit rRNA gene to address the factors that structure communities along the thermal gradients of two alkaline hot springs in the Lower Geyser Basin of Yellowstone National Park. The filtered data set included a total of nearly 34,000 sequences from 39 environmental samples. Each was assigned to one of 391 operational taxonomic units (OTUs) identified by their unique V3 sequence signatures. Although the two …

Bushmeat Poaching Reduces The Seed Dispersal And Population Growth Rate Of A Mammal-Dispersed Tree, Jedidiah F. Brodie, Olga E. Helmy, Warren Y. Brockelman, John L. Maron

Biological Sciences Faculty Publications

Myriad tropical vertebrates are threatened by overharvest. Whether this harvest has indirect effects on nonhunted organisms that interact with the game species is a critical question. Many tropical birds and mammals disperse seeds. Their overhunting in forests can cause zoochorous trees to suffer from reduced seed dispersal. Yet how these reductions in seed dispersal influence tree abundance and population dynamics remains unclear. Reproductive parameters in long-lived organisms often have very low elasticities; indeed the demographic importance of seed dispersal is an open question. We asked how variation in hunting pressure across four national parks with seasonal forest in northern Thailand …

A Unique Group I Intron In Coxiella Burnetii Is A Natural Splice Mutant, Rahul Raghavan, Linda D. Hicks, Michael F. Minnick

Biological Sciences Faculty Publications

Cbu.L1917, a group I intron present in the 23S rRNA gene of Coxiella burnetii, possesses a unique 3'-terminal adenine in place of a conserved guanine. Here, we show that, unlike all other group I introns, Cbu.L1917 utilizes a different cofactor for each splicing step and has a decreased self-splicing rate in vitro.

Transition State Structures And The Roles Of Catalytic Residues In Gap-Facilitated Gtpase Of Ras As Elucidated By (18)O Kinetic Isotope Effects, Xinlin Du, Stephen R. Sprang

Biological Sciences Faculty Publications

Ras-catalyzed guanosine 5' triphosphate (GTP) hydrolysis proceeds through a loose transition state as suggested in our previous study of (18)O kinetic isotope effects (KIE) [ Du , X. et al. ( 2004 ) Proc. Natl. Acad. Sci. U.S.A. 101 , 8858 - 8863 ]. To probe the mechanisms of GTPase activation protein (GAP)-facilitated GTP hydrolysis reactions, we measured the (18)O KIEs in GTP hydrolysis catalyzed by Ras in the presence of GAP(334) or NF1(333), the catalytic fragment of p120GAP or NF1. The KIEs in the leaving group oxygens (the beta nonbridge and the beta-gamma bridge oxygens) reveal that chemistry is …

What Drives Long-Distance Dispersal? A Test Of Theoretical Predictions, Winsor H. Lowe

Biological Sciences Faculty Publications

Long-distance dispersal (LDD) may contribute disproportionately to species persistence in fragmented landscapes, non-native invasions, and range shifts in response to climate change. However, direct data on LDD are extremely limited, leaving us with little understanding of why it occurs. I used six years of mark–recapture data on the stream salamander Gyrinophilus porphyriticus to test theoretical predictions of how variation in habitat quality affects LDD. Frequency of LDD was quantified using the kurtosis of yearly movement distributions from recaptured animals in a 1-km headwater stream. Temporal and spatial variation in habitat quality were quantified with spatially explicit data on the body …

Intersubunit Interactions Modulate Ph-Induced Activation Of Membrane Fusion By The Junín Virus Envelope Glycoprotein Gpc, Joanne York, Jack H. Nunberg

Biological Sciences Faculty Publications

The mature arenavirus envelope glycoprotein GPC is a tripartite complex comprising a stable signal peptide (SSP) in addition to the receptor-binding (G1) and transmembrane fusion (G2) subunits. We have shown previously that SSP is a key element in GPC-mediated membrane fusion, and that GPC sensitivity to acidic pH is modulated in part through the lysine residue at position 33 in the ectodomain loop of SSP (J. York and J. H. Nunberg, J. Virol. 80: 7775-7780, 2006). A glutamine substitution at this position stabilizes the native GPC complex and thereby prevents the induction of pH-dependent membrane fusion. In efforts to identify …

Common Garden Comparisons Of Native And Introduced Plant Populations: Latitudinal Clines Can Obscure Evolutionary Inferences, Robert I. Colautti, John L. Maron, Spencer C.H. Barrett

Biological Sciences Faculty Publications

Common garden studies are increasingly used to identify differences in phenotypic traits between native and introduced genotypes, often ignoring sources of among-population variation within each range. We re-analyzed data from 32 common garden studies of 28 plant species that tested for rapid evolution associated with biological invasion. Our goals were: (i) to identify patterns of phenotypic trait variation among populations within native and introduced ranges, and (ii) to explore the consequences of this variation for how differences between the ranges are interpreted. We combined life history and physiologic traits into a single principal component (PC_ALL) and also compared …

Ecological Facilitation May Drive Major Evolutionary Transitions, Zaal Kikvidze, Ragan M. Callaway

Biological Sciences Faculty Publications

There is a growing consensus among ecologists that ecological facilitation comprises a historically overlooked but crucial suite of biotic interactions. Awareness of such positive interactions has recently led to substantial modifications in ecological theory. In this article we suggest how facilitation may be included in evolutionary theory. Natural selection based on competition provides a conceptually complete paradigm for speciation, but not for major evolutionary transitions-the emergence of new and more complex biological structures such as cells, organisms, and eusocial populations. We find that the successful theories developed to solve these specific problematic transitions show a consistent pattern: they focus on …

Empirical Testing Of 16s Rrna Gene Pcr Primer Pairs Reveals Variance In Target Specificity And Efficacy Not Suggested By In Silico Analysis, Sergio E. Morales, William E. Holben

Biological Sciences Faculty Publications

Phylogenetic and "fingerprinting" analyses of the 16S rRNA genes of prokaryotes have been a mainstay of microbial ecology during the last two decades. However, many methods and results from studies that rely on the 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received only cursory or even no validation. To directly examine the efficacy and specificity of 16S rRNA gene-based primers for phylum-, class-, and operational taxonomic unit-specific target amplification in quantitative PCR, we created a collection of primers based solely on an extensive soil bacterial 16S rRNA gene clone library containing similar to 5,000 …

Structural Basis For Inhibition Of Mammalian Adenylyl Cyclase By Calcium, Tung-Chung Mou, Nanako Masada, Dermot M. Cooper, Stephen R. Sprang

Biological Sciences Faculty Publications

Type V and VI mammalian adenylyl cyclases (AC5, AC6) are inhibited by Ca(2+) at both sub- and supramicromolar concentration. This inhibition may provide feedback in situations where cAMP promotes opening of Ca(2+) channels, allowing fine control of cardiac contraction and rhythmicity in cardiac tissue where AC5 and AC6 predominate. Ca(2+) inhibits the soluble AC core composed of the C1 domain of AC5 (VC1) and the C2 domain of AC2 (IIC2). As observed for holo-AC5, inhibition is biphasic, showing "high-affinity" (K(i) = approximately 0.4 microM) and "low-affinity" (K(i) = approximately 100 microM) modes of inhibition. At micromolar concentration, Ca(2+) inhibition is …

Evidence For The Evolution Of Reduced Mycorrhizal Dependence During Plant Invasion, Elizabeth K. Seifert, James D. Bever, John L. Maron

Biological Sciences Faculty Publications

Introduced species inevitably experience novel selection pressures in their new environments as a result of changes in mutualist and antagonist relationships. While most previous work has examined how escape from specialist enemies has influenced herbivore or pathogen resistance of exotic species, post-introduction shifts in exotic dependence on mutualists have not been considered. In a common environment, we compared dependence on AM fungi of North American and European populations of Hypericum perforatum (St. John's Wort), a forb native to Europe. Introduced North American populations responded less to inoculation with AM fungi than did European populations. Root architecture was strongly correlated with …

Linking Wildlife Populations With Ecosystem Change: State-Of-The-Art Satellite Ecology For National-Park Science, Mark Hebblewhite

Biological Sciences Faculty Publications

As human impacts increase in national parks and the greater ecosystems surrounding them, the National Park Service faces the difficulty of monitoring ecosystem changes and responses of key wildlife indicator species within parks. Responses of bison to trail grooming in Yellowstone National Park (Wyoming, Montana, and Idaho) and control of the animals once they leave the park (Bruggeman et al. 2007), migration of wildlife across park boundaries (Griffith et al. 2002; Berger 2004), effects of restored wolves on vegetation communities through trophic cascades (Hebblewhite et al. 2005), and responses of wildlife to the use of prescribed fires all represent problems …

Functional Differences Within A Guild Of Tropical Mammalian Frugivores, Jedidiah F. Brodie, Olga E. Helmy, Warren Y. Brockelman, John L. Maron

Biological Sciences Faculty Publications

Many plants interact with groups of mutualist pollinators and seed dispersers. A key issue for both basic ecology and conservation is whether the different species within these guilds of mutualist animals are functionally equivalent. Comparing the relative effects of sympatric mutualists is important for understanding the evolution of multispecies mutualisms and for predicting mutualism stability in the face of anthropogenic change. However, empirical comparisons of the population-level impacts of mutualist animals on their host plant are rare, particularly for seed dispersal mutualisms in species-rich ecosystems. We compared the influence of three seed-dispersing tropical mammals, lar gibbons (Hylobates lar), …

Landscape Genomics And Biased Fst Approaches Reveal Single Nucleotide Polymorphisms Under Selection In Goat Breeds Of North-East Mediterranean, Lorraine Pariset, Stephane Joost, Paolo Ajmone Marsan, Alessio Valentini, Econogene Consortium

Biological Sciences Faculty Publications

Background: In this study we compare outlier loci detected using a F_st based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of goat breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring.

Results: The combined use of the two outlier detection approaches, never tested before using SNP polymorphisms, resulted in the …

Ecological Specialization In A Spatially Structured Population Of The Thermophilic Cyanobacterium Mastigocladus Laminosus, Scott R. Miller, Carin Williams, Aaron L. Strong, Darla Carvey

Biological Sciences Faculty Publications

Laboratory evolution experiments suggest the potential for microbial populations to contribute significant ecological variation to ecosystems, yet the functional importance of genetic diversity within natural populations of microorganisms is largely unknown. Here, we investigated the distribution of genetic and phenotypic variation for a population of the cyanobacterium Mastigocladus laminosus distributed along the temperature gradient of White Creek, Yellowstone NP. A total of 153 laboratory strains were directly isolated from five sites with mean annual temperatures ranging between 39 and 54 C. Genetic characterization at four nitrogen metabolism genes identified 15 closely related lineages in the population sample. These lineages were …

Randomization And In Vivo Selection Reveal A Ggrg Motif Essential For Packaging Human Immunodeficiency Virus Type 2 Rna, Tayyba T. Baig, Jean-Marc Lanchy, J. Stephen Lodmell

Biological Sciences Faculty Publications

The packaging signal (psi) of human immunodeficiency virus type 2 (HIV-2) is present in the 5' noncoding region of RNA and contains a 10-nucleotide palindrome (pal; 5'-392-GGAGUGCUCC) located upstream of the dimerization signal stem-loop 1 (SL1). pal has been shown to be functionally important in vitro and in vivo. We previously showed that the 3' side of pal (GCUCC-3') is involved in base-pairing interactions with a sequence downstream of SL1 to make an extended SL1, which is important for replication in vivo and the regulation of dimerization in vitro. However, the role of the 5' side of pal (5'-GGAGU) was …

Fluctuating Asymmetry In Elk Cervus Elaphus Antlers Is Unrelated To Environmental Conditions In The Greater Yellowstone Ecosystem, Scott L. Eggeman, Mark Hebblewhite, Julie Cunningham, Ken Hamlin

Biological Sciences Faculty Publications

Fluctuating asymmetry (FA) is a measure of the deviation from perfect bilateral symmetry, and has been used across mammals as a reliable indicator of environmental stress during growth and development. Antler size and symmetry can be an indicator of individual fitness and social rank among ungulates such as the North American elk Cervus elaphus. When environmental conditions are favourable, ungulates allocate additional resources to antler development to increase secondary sexual traits and enhance reproduction. We tested whether there was an appreciable change in antler length and the number of points as extreme climatic conditions (e.g. heavy snow and drought) …

Function, Regulation, And Transcriptional Organization Of The Hemin Utilization Locus Of Bartonella Quintana, Nermi L. Parrow, Jasmin Abbott, Amanda R. Lockwood, James M. Battisti, Michael F. Minnick

Biological Sciences Faculty Publications

Bartonella quintana is a gram-negative agent of trench fever, chronic bacteremia, endocarditis, and bacillary angiomatosis in humans. B. quintana has the highest known hemin requirement among bacteria, but the mechanisms of hemin acquisition are poorly defined. Genomic analyses revealed a potential locus dedicated to hemin utilization (hut) encoding a putative hemin receptor, HutA; a TonB-like energy transducer; an ABC transport system comprised of three proteins, HutB, HutC, and HmuV; and a hemin degradation/storage enzyme, HemS. Complementation analyses with Escherichia coli hemA show that HutA functions as a hemin receptor, and complementation analyses with E. coli hemA tonB indicate that HutA …