Biology Commons^™

Evidence For Microbial Fe(Iii) Reduction In Anoxic, Mining-Impacted Lake Sediments (Lake Coeur D’Alene, Idaho), David E. Cummings, Anthony W. March, Benjamin Bostick, Stefan Spring, Frank Caccavo Jr., Scott Fendorf, Frank Rosenzweig

Biological Sciences Faculty Publications

Mining-impacted sediments of Lake Coeur d'Alene, Idaho, contain more than 10% metals on a dry weight basis, approximately 80% of which is iron. Since iron (hydr)oxides adsorb toxic, ore-associated elements, such as arsenic, iron (hydr)oxide reduction may in part control the mobility and bioavailability of these elements. Geochemical and microbiological data were collected to examine the ecological role of dissimilatory Fe(III)-reducing bacteria in this habitat. The concentration of mild-acid-extractable Fe(II) increased with sediment depth up to 50 g kg⁻¹, suggesting that iron reduction has occurred recently. The maximum concentrations of dissolved Fe(II) in interstitial water (41 mg liter …

Molecular Evidence For A New Bacteriophage Of Borrelia Burgdorferi, Christian H. Eggers, D. Scott Samuels

Biological Sciences Faculty Publications

We have recovered a DNase-protected, chloroform-resistant molecule of DNA from the cell-free supernatant of a Borrelia burgdorferi culture. The DNA is a 32-kb double-stranded linear molecule that is derived from the 32-kb circular plasmids (cp32s) of the B. burgdorferi genome. Electron microscopy of samples from which the 32-kb DNA molecule was purified revealed bacteriophage particles. The bacteriophage has a polyhedral head with a diameter of 55 nm and appears to have a simple 100-nm-long tail. The phage is produced constitutively at low levels from growing cultures of some B. burgdorferi strains and is inducible to higher levels with 10 mu …

Three-Dimensional Structure Of A Complex Between The Death Domains Of Pelle And Tube, Tsan Xiao, Par Towb, Steven A. Wasserman, Stephen R. Sprang

Biological Sciences Faculty Publications

The interaction of the serine/threonine kinase Pelle and adaptor protein Tube through their N-terminal death domains leads to the nuclear translocation of the transcription factor Dorsal and activation of zygotic patterning genes during Drosophila embryogenesis. Crystal structure of the Pelle and Tube death domain heterodimer reveals that the two death domains adopt a six-helix bundle fold and are arranged in an open-ended linear array with plastic interfaces mediating their interactions. The Tube death domain has an insertion between helices 2 and 3, and a C-terminal tail making significant and indispensable contacts in the heterodimer. In vivo assays of Pelle and …

Systematic Changes In Gene Expression Patterns Following Adaptive Evolution In Yeast, Tracy L. Ferea, David Botstein, Patrick O. Brown, R. Frank Rosenzweig

Biological Sciences Faculty Publications

Culturing a population of Saccharomyces cerevisiae for many generations under conditions to which it is not optimally adapted selects for fitter genetic variants. This simple experimental design provides a tractable model of adaptive evolution under natural selection. Beginning with a clonal, founding population, independently evolved strains were obtained from three independent cultures after continuous aerobic growth in glucose-limited chemostats for more than 250 generations. DNA microarrays were used to compare genome-wide patterns of gene expression in the evolved strains and the parental strain. Several hundred genes were found to have significantly altered expression in the evolved strains. Many of these …

Development Of A System For Genetic Manipulation Of Bartonella Bacilliformis, James M. Battisti, Michael F. Minnick

Biological Sciences Faculty Publications

Lack of a system for site specific genetic manipulation has severely hindered studies on the molecular biology of all Bartonella species. We report the first site-specific mutagenesis and complementation for a Bartonella species. A highly transformable strain of B. bacilliformis, termed JB584, was isolated and found to exhibit a significant increase in transformation efficiency with the broad-host-range plasmid pBBR1MCS-2, relative to wild-type strains. Restriction analyses of genomic preparations with the methylation-sensitive restriction enzymes ClaI and StuI suggest that strain JB584 possesses a dcm methylase mutation that contributes to its enhanced transformability. A suicide plasmid, pUB1, which contains a polylinker, a …

Using Atlas Data To Model The Distribution Of Woodpecker Species In The Jura, France, Claudine Tobalske, Bret W. Tobalske

Biological Sciences Faculty Publications

Breeding bird atlases providing distribution data at a regional scale are becoming increasingly common. To assess the ability of such data to develop bread-scale bird-habitat models, we used data from a breeding bird atlas and landscape variables obtained From a geographic information system (GIS) to study the distribution of seven woodpecker species in the Jura, France: the Black (Dryocopus martins), Green (Picus viridis). Grey-headed (P. canus), Great Spotted (Dendrocopos major), Middle Spotted (D. medius), and Lesser Spotted (D. minor) Woodpeckers, and the Wryneck (Jynx torquilla). We used logistic regression to develop predictive models from variables that described each 575-ha atlas …

Two-Metal-Ion Catalysis In Adenylyl Cyclase, John J.G. Tesmer, Roger K. Sunahara, Roger A. Johnson, Gilles Gosselin, Alfred G. Gilman, Stephen R. Sprang

Biological Sciences Faculty Publications

Adenylyl cyclase (AC) converts adenosine triphosphate (ATP) to cyclic adenosine monophosphate, a ubiquitous second messenger that regulates many cellular functions. Recent structural studies have revealed much about the structure and function of mammalian AC but have not fully defined its active site or catalytic mechanism. Four crystal structures were determined of the catalytic domains of AC in complex with two different ATP analogs and various divalent metal ions. These structures provide a model for the enzyme- substrate complex and conclusively demonstrate that two metal ions bind in the active site. The similarity of the active site of AC to those …

Positions In The 30s Ribosomal Subunit Proximal To The 790 Loop As Determined By Phenanthroline Cleavage, Gregory W. Muth, Scott P. Hennelly, Walter E. Hill

Biological Sciences Faculty Publications

Positioning rRNA within the ribosome remains a challenging problem. Such positioning is critical to understanding ribosome function, as various rRNA regions interact to form suitable binding sites for ligands, such as tRNA and mRNA. We have used phenanthroline, a chemical nuclease, as a proximity probe, to help elucidate the regions of rRNA that are near neighbors of the stem-loop structure centering at nt 790 in the 16S rRNA of the Escherichia coli 30S ribosomal subunit. Using phenanthroline covalently attached to a DNA oligomer complementary to nt 787-795, we found that nt 582-584, 693-694, 787-790, and 795-797 were cleaved robustly and …

Effects Of Fire On The Demography Of The Endangered, Geophytic Herb Silene Spaldingii (Caryophyllaceae), Peter Lesica

Biological Sciences Faculty Publications

Understanding the effects of disturbances such as fire on plant demography helps elucidate the mechanisms that cause changes in community composition. I studied the effects of spring and fall fires on Silene spaldingii, an endangered perennial herb of grasslands in northwest Montana. Individual S. spaldingii plants were mapped, and size and flowering were recorded for 1 yr prior and 5 yr subsequent to the burn treatments. Enhanced seedling recruitment (70–410%) and a 22% increase in population size were the principal effects of fire on S. spaldingii, and fall burn plots had lower recruitment than spring burn plots. These effects were …

Structure Of G(Iα1)·Gppnhp, Autoinhibition In A Gα Protein-Substrate Complex, David E. Coleman, Stephen R. Sprang

Biological Sciences Faculty Publications

The structure of the G protein G(i 1/4 ) complexed with the nonhydrolyzable GTP analog guanosine-5'-(βγ-imino)triphosphate (GppNHp) has been determined at a resolution of 1.5 Å. In the active site of G(i 1/4 )·GppNHp, a water molecule is hydrogen bonded to the side chain of Glu⁴³ and to an oxygen atom of the γ-phosphate group. The side chain of the essential catalytic residue Gln²⁰⁴ assumes a conformation which is distinctly different from that observed in complexes with either guanosine 5'-O-3-thiotriphosphate or the transition state analog GDP·A1F₄^-. Hydrogen bonding and steric interactions position Gln²⁰⁴ such …

Mycorrhizae Indirectly Enhance Competitive Effects Of An Invasive Forb On A Native Bunchgrass, Marilyn J. Marler, Catherine A. Zabinski, Ragan M. Callaway

Biological Sciences Faculty Publications

Mycorrhizae are important mediators of plant competition, but little is known about the role of mycorrhizae in the intense competitive effects that exotic plants can have on native species. In the greenhouse, we tested the effect of arbuscular mycorrhizal (AM) fungi on interspecific competition between Centaurea maculosa and Festuca idahoensis, on intraspecific competition between individuals of both species, and the growth of C. maculosa with either inorganic or organic phosphorus. Mycorrhizae had no direct effect on either species, but mycorrhizae increased C. maculosa's negative effect on F. idahoensis. When competing with C. maculosa, nonmycorrhizal F. idahoensis were 171% larger than …

Biological-Control Herbivores May Increase Competitive Ability Of The Noxious Weed Centaurea Maculosa, Ragan M. Callaway, Thomas H. Deluca, Wendy M. Belliveau

Biological Sciences Faculty Publications

Biocontrol organisms are generally applied in an attempt to reduce the vigor of target species and provide native species with an competitive advantage. We tested the effectiveness of a widely used biocontrol moth, Agapeta zoegana (knapweed root moth) for two years in the field and found that it had no significant direct effect on the biomass of Centaurea maculosa (spotted knapweed), one of the most destructive invasive plants in North America. Instead of releasing a native grass from competition, the reproductive output of Festuca idahoensis planted with Centaurea was significantly lower when neighboring Centaurea had been attacked by Agapeta. In …

Cleavage Of A 23s Rrna Pseudoknot By Phenanthroline-Cu(Ii), G. W. Muth, Charles M. Thompson, Walter E. Hill

Biological Sciences Faculty Publications

Studying the intricate folding of rRNA within the ribosome remains a complex problem. Phenanthroline-Cu(II) complexes cleave phosphodiester bonds in rRNA in specific regions, apparently especially where the rRNA structure is constrained in some fashion. We have introduced phenanthroline-copper complexes into 50S Escherichia coli ribosomal subunits and shown specific cleavages in the regions containing nucleotides 60-66 and 87-100. This specificity of cleavage is reduced when the ribosome is heated to 80 degrees C and reduced to background when the ribosomal proteins are extracted and the cleavage repeated on protein-free 23S rRNA, It has been suggested that nucleotides 60-66 and 87-95 in …

Toward An Evolutionary Understanding Of Song Diversity In Oscines, Erick Greene

Biological Sciences Faculty Publications

No abstract provided.

Bush Lupine Mortality, Altered Resource Availability, And Alternative Vegetaion States, John L. Maron, Robert L. Jefferies

Biological Sciences Faculty Publications

Nitrogen-fixing plants, by altering the availability of soil N, potentially facilitate plant invasion. Here we describe how herbivore-driven mortality of a native N-fixing shrub, bush lupine (Lupinus arboreus), increases soil N and light availability, which promotes invasion by introduced grasses to the detriment of a native plant community.

Soils under live and dead lupine stands contained large amounts of total N, averaging 3.14 mg N/g dry mass of soil (398 g/m²) and 3.45 mg N/g dry mass of soil (438 g/m²), respectively, over four years. In contrast, similar lupine-free soil was low in N …

Habitat Relationships Of Landbirds In The Northern Region, Usda Forest Service, Richard L. Hutto, Jock S. Young

Biological Sciences Faculty Publications

A series of first-generation habitat-relationships models for 83 bird species were detected in a 3-year study on point counts conducted in association with the USDA Forest Service's Northern Region Landbird Monitoring Program. The models depict probabilities of detection for each of the bird species on 100-m-radius, 10-minute point counts conducted across a series of major vegetation cover types. Based on these models, some bird species appear to be restricted in their habitat distribution to: (1) postfire, standing-dead forests, (2) relatively uncut, older forests, (3) harvested forest types, (4) marshes, (5) riparian environments, and (6) grasslands and sagebrush. Such restricted distributions …

Structure Of The Protein Kinase Cβ Phospholipid-Binding C2 Domain Complexed With Ca2+, R. Bryan Sutton, Stephen R. Sprang

Biological Sciences Faculty Publications

Background: Conventional isoforms (α, β and γ) of protein kinase C (PKC) are synergistically activated by phosphatidylserine and Ca²⁺; both bind to C2 domains located within the PKC amino-terminal regulatory regions. C2 domains contain a bipartite or tripartite Ca²⁺-binding site formed by opposing loops at one end of the protein. Neither the structural basis for cooperativity between phosphatidylserine and Ca²⁺, nor the binding site for phosphatidylserine are known. Results: The structure of the C2 domain from PKCβ complexed with Ca²⁺ and o-phospho-L-serine has been determined to 2.7 Å resolution using X-ray crystallography. The …

Mutations In Bartonella Bacilliformis Gyrb Confer Resistance To Coumermycin A(1), James M. Battisti, Laura A. Smitherman, D. Scott Samuels, Michael F. Minnick

Biological Sciences Faculty Publications

This study describes the first isolation and characterization of spontaneous mutants conferring natural resistance to an antibiotic for any Bartonella species. The Bartonella bacilliformis gyrB gene, which encodes the B subunit of DNA gyrase, was cloned and sequenced. The gyrB open reading frame (ORF) is 2,079 bp and encodes a deduced amino acid sequence of 692 residues, corresponding to a predicted protein of similar to 77.5 kDa. Sequence alignment indicates that B. bacilliformis GyrB is most similar to the GyrB protein from Bacillus subtilis (40.1% amino acid sequence identity) and that it contains the longest N-terminal tail (52 residues) of …

Invasion Of The Nucleotide Snatchers, Stephen R. Sprang, David E. Coleman

Biological Sciences Faculty Publications

Although the mechanics differ, GEFs appear to deform their substrates in similar ways. In all cases, switch I is pulled away from switch II and the P loop, exposing the active site; dislocation of switch I also displaces a Mg²⁺-binding residue, but this in itself should have little affect on GDP affinity. GEFs also restructure and displace the amino terminus of switch II and consequently dismantle the χ-phosphate-binding site, at the same time moving a conserved aspartate residue that serves as a water-mediated Mg²⁺ ligand. Residues, either from the GEF or the G protein, are positioned to …

Identification Of A G(Iα) Binding Site On Type V Adenylyl Cyclase, Carmen W. Dessauer, John J.G. Tesmer, Stephen R. Sprang, Alfred G. Gilman

Biological Sciences Faculty Publications

The stimulatory G protein α subunit G(sα) binds within a cleft in adenylyl cyclase formed by the α1-α2 and α3-β4 loops of the C₂ domain. The pseudosymmetry of the C₁ and C₂ domains of adenylyl cyclase suggests that the homologous inhibitory α subunit G(iα) could bind to the analogous cleft within C₁. We demonstrate that myristoylated guanosine 5'-3-O- (thio)triphosphate-G(iα1) forms a stable complex with the C₁ (but not the C₂) domain of type V adenylyl cyclase. Mutagenesis of the membrane-bound enzyme identified residues whose alteration either increased or substantially decreased the IC …

Grizzly Bear Digging: Effects On Subalpine Meadow Plants In Relation To Mineral Nitrogen Availability, Sandra E. Tardiff, Jack Arthur Stanford

Biological Sciences Faculty Publications

Grizzly bears (Ursus arctos horribilis) affect plant distributions and mineral nitrogen availability when they forage by digging for the bulbs of glacier lilies (Erythronium grandiflorum) growing in subalpine meadows of Glacier National Park, Montana, United States. Our working hypothesis is that grizzly bears structure plant communities and influence nitrogen availability when they selectively dig for preferred plants. In this paper, we report on differences found in recently disturbed digs (<5 yr old) when compared to adjacent, undisturbed meadow.

We used ion exchange resin bags to determine the availability of mineral nitrogen in grizzly bear digs compared to undisturbed meadow. Soil in digs contained significantly …

Effective Recovery Of Bacterial Dna And Percent-Guanine-Plus-Cytosine-Based Analysis Of Community Structure In The Gastrointestinal Tract Of Broiler Chickens, Juha H. A. Apajalahti, Laura K. Särkilahti, Brita R. E. Mäki, J. Pekka Heikkinen, Päivi H. Nurminen, William E. Holben

Biological Sciences Faculty Publications

A DNA-based, direct method for initial characterization of the total bacterial community in ileum and cecum of the chicken gastrointestinal (GI) tract was developed. The efficiencies of bacterial extraction and lysis were >95 and >99%, respectively, and therefore the DNA recovered should accurately reflect the bacterial communities of the ileal and cecal digesta. Total bacterial DNA samples were fractionated according to their percent G+C content. The profiles reflecting the composition of the bacterial community were reproducible within each compartment, but different between the compartments of the GI tract. This approach is independent of the culturability of the bacteria in the …

Asymmetrical Force Production In The Maneuvering Flight Of Pigeons, Douglas R. Warrick, Kenneth P. Dial, Andrew A. Biewener

Biological Sciences Faculty Publications

Downstroke force produced by Rock Doves (Columba livia) as they negotiated an obstacle course was measured using in vivo recordings of delto-pectoral crest strain. During this slow $(<6\ {\rm m}\ {\rm s}^{-1})$ , maneuvering flight, pigeons produced a series of four to six successive wingbeats in which the wing on the outside of the turn produced greater peak force than the wing on the inside of the turn, suggesting that the birds maneuvered in a saltatory manner during slow flight. This asymmetrical downstroke force may be used to increase or reestablish bank lost during upstroke, or it may be directed as thrust to compensate for adverse yaw or create excess yaw to alter the bird's direction of flight. Continuous production of asymmetrical downstroke force through a turn differs from the traditional model of maneuvering flight, in which asymmetrical force is used only to initiate a bank, the forces are briefly reversed to arrest the momentum of the roll and then equalized to maintain the established bank, and the redirected lift of the wings then effects a turn. Although this traditional model probably describes most turns initiated during fast and gliding flight in birds, it underestimates the complexity of maneuvering during slow, flapping flight, where sophisticated kinematics and neuromuscular control are needed to change direction effectively.

On The Importance Of Stopover Sites To Migrating Birds, Richard L. Hutto

Biological Sciences Faculty Publications

No abstract provided.

Increased Photosynthesis Offsets Costs Of Allocation To Sapwood In An Arid Environment, Eileen V. Carey, Ragan M. Callaway, Evan H. Delucia

Biological Sciences Faculty Publications

We assessed the effect that varying patterns of biomass allocation had on growth of ponderosa pine (Pinus ponderosa) growing in the desert climate of the Great Basin and the montane climate of the eastern Sierra Nevada. Prior work established that desert trees have lower leaf:sapwood area ratios than montane trees (0.104 and 0.201 m²/cm², respectively) and proportionally greater stem respiration. Sapwood:leaf mass ratios are also greater and increase more as a function stem diameter in desert than in montane trees. We hypothesized that this increased allocation of carbon to stem sapwood and stem respiration …

Structural Basis Of Activity And Subunit Recognition In G Protein Heterotrimers, Mark A. Wall, Bruce A. Posner, Stephen R. Sprang

Biological Sciences Faculty Publications

Background: Inactive heterotrimeric G proteins are composed of a GDP-bound α subunit (G(α)) and a stable heterodimer of G(β) and G(γ) subunits. Upon stimulation by a receptor, G(α) subunits exchange GDP for GTP and dissociate from G(βγ) both G(α) and G(βγ) then interact with downstream effectors. Isoforms of G(α), G(β) and G(γ) potentially give rise to many heterotrimeric combinations, limited in part by amino acid sequence differences that lead to selective interactions. The mechanism by which GTP promotes G(βγ) dissociation is incompletely understood. The Gly203→Ala mutant of G(iα1) binds and hydrolyzes GTP normally but does not dissociate from G(βγ) demonstrating …

Continued Utilization Of Ccr5 Coreceptor By A Newly Derived T-Cell Line-Adapted Isolate Of Human Immunodeficiency Virus Type 1, Kathryn E. Follis, Meg Trahey, Rachel A. Lacasse, Jack H. Nunberg

Biological Sciences Faculty Publications

The differential use of CC chemokine receptor 5 (CCR5) and CXC chemokine receptor 4 (CXCR4) may be intimately involved in the transmission and progression of human immunodeficiency virus infection. Changes in coreceptor utilization have also been noted upon adaptation of primary isolates (PI) to growth in established T-cell lines. All of the T-cell line-adapted (TCLA) viruses studied to date utilize CXCR4 but not CCR5. This observation had been suggested as an explanation for the sensitivity of TCLA, but not PI, viruses to neutralization by recombinant gp120 antisera and V3-directed monoclonal antibodies, but recent studies have shown coreceptor utilization to be …

Bowen Ratio Estimates Of Evapotranspiration For Tamarix Ramosissima Stands On The Virgin River In Southern Nevada, D. A. Devitt, Anna Sala, S. D. Smith, J. Cleverly, L. K. Shaulis, R. Hammett

Biological Sciences Faculty Publications

A Bowen ratio energy balance was conducted over a Tamarix ramosissima (saltcedar) stand growing in a riparian corridor along the Virgin River in southern Nevada, Measurements in two separate years were compared and contrasted on the basis of changes in growing conditions. In 1994, a drought year, record high temperatures, dry winds, and a falling water table caused partial wilt of outer smaller twigs in the canopy of many trees in the stand around the Bowen tower. Subsequently, evapotranspiration (ET) estimates declined dramatically over a 60-day period (11 mm d(-1) to <1 mm d(-1)). In 1995, the Virgin River at the Bowen tower area changed its course, hydrologically isolating the Tamarix stand in the vicinity of the tower. In 1996, a 25% canopy loss was visually estimated for the Tamarix growing in the area of the tower. Higher soil temperatures relative to air temperatures were recorded in 1996 in response to this loss in canopy, With a more open canopy, thermally induced turbulence was observed in 1996, On day 160 of 1996, a 28 degrees C rise over a 9-hour period was correlated with increased wind speeds of greater than 4 m s(-1). Subsequently, higher ET estimates were made in 1996 compared to 1994 (145 cm versus 75 cm), However, the energy balance was dominated by advection in 1996, with latent energy flux exceeding net radiation 65% of the measurement days compared to only 11% in 1994, We believe this advection was on a scale of the floodplain (hundreds of meters) as opposed to regional advection, since the majority of wind (90%) was in a N-S direction along the course of the river, and that a more open canopy allowed the horizontal transfer of energy into the Tamarix stand at the Bowen tower. Our results suggest that Tamarix has the potential to be both a low water user and a high water user, depending on moisture availability, canopy development, and atmospheric demand, and that advection can dominate energy balances and ET in aridland riparian zones such as the Virgin River.

The A326s Mutant Of G(Iα1) As An Approximation Of The Receptor-Bound State, Bruce A. Posner, Mark B. Mixon, Mark A. Wall, Stephen R. Sprang, Alfred G. Gilman

Biological Sciences Faculty Publications

Agonist-bound heptahelical receptors activate heterotrimeric G proteins by catalyzing exchange of GDP for GTP on their α subunits. In search of an approximation of the receptor-α subunit complex, we have considered the properties of A326S G(iα1), a mutation discovered originally in G(sα) (Iiri, T., Herzmark, P., Nakamoto, J. M., Van Dop, C., and Bourne, H. R. (1994) Nature 371, 164-168) that mimics the effect of receptor on nucleotide exchange. The mutation accelerates dissociation of GDP from the α(i1)β₁γ₂ heterotrimer by 250-fold. Nevertheless, affinity of mutant G(iα1) for GTPγS is high in the presence of Mg²⁺, …

Multiple Duplications Of Yeast Hexose Transport Genes In Response To Selection In A Glucose-Limited Environment, Celeste J. Brown, Kristy M. Todd, R. Frank Rosenzweig

Biological Sciences Faculty Publications

When microbes evolve in a nutrient-limited environment, natural selection can be predicted to favor genetic changes that give cells greater access to limiting substrate. We analyzed a population of baker's yeast that underwent 450 generations of glucose-limited growth. Relative to the strain used as the inoculum, the predominant cell type at the end of this experiment sustains growth at significantly lower steady-state glucose concentrations and demonstrates markedly enhanced cell yield per mole glucose, significantly enhanced high-affinity glucose transport, and greater relative fitness in pairwise competition. These changes are correlated with increased levels of mRNA hybridizing to probe generated from the …