Life Sciences Commons^™

Population Genetic Structure In A Social Landscape: Barley In A Traditional Ethiopian Agricultural System, Leah H. Samberg, Lila Fishman, Fred W. Allendorf

Biological Sciences Faculty Publications

Conservation strategies are increasingly driven by our understanding of the processes and patterns of gene flow across complex landscapes. The expansion of population genetic approaches into traditional agricultural systems requires understanding how social factors contribute to that landscape, and thus to gene flow. This study incorporates extensive farmer interviews and population genetic analysis of barley landraces (Hordeum vulgare) to build a holistic picture of farmer-mediated geneflow in an ancient, traditional agricultural system in the highlands of Ethiopia. We analyze barley samples at 14 microsatellite loci across sites at varying elevations and locations across a contiguous mountain range, and across farmer-identified …

Experimental Evolution Of An Alternating Uni- And Multicellular Life Cycle In Chlamydomonas Reinhardtii, William C. Ratcliff, Matthew D. Herron, Kathryn Howell, Jennifer T. Pentz, Frank Rosenzweig, Michael Travisano

Biological Sciences Faculty Publications

The transition to multicellularity enabled the evolution of large, complex organisms, but early steps in this transition remain poorly understood. Here we show that multicellular complexity, including development from a single cell, can evolve rapidly in a unicellular organism that has never had a multicellular ancestor. We subject the alga Chlamydomonas reinhardtii to conditions that favour multicellularity, resulting in the evolution of a multicellular life cycle in which clusters reproduce via motile unicellular propagules. While a single-cell genetic bottleneck during ontogeny is widely regarded as an adaptation to limit among-cell conflict, its appearance very early in this transition suggests that …

Sequestration And Scavenging Of Iron In Infection, Nermi Lee Parrow, Robert E. Fleming, Michael F. Minnick

Biological Sciences Faculty Publications

The proliferative capability of many invasive pathogens is limited by the bioavailability of iron. Pathogens have thus developed strategies to obtain iron from their host organisms. In turn, host defense strategies have evolved to sequester iron from invasive pathogens. This review explores the mechanisms employed by bacterial pathogens to gain access to host iron sources, the role of iron in bacterial virulence, and iron-related genes required for the establishment or maintenance of infection. Host defenses to limit iron availability for bacterial growth during the acute-phase response and the consequences of iron overload conditions on susceptibility to bacterial infection are also …

Bacterial Endophytes Enhance Competition By Invasive Plants, Marnie E. Rout, Thomas H. Chrzanowski, Tara K. Westlie, Thomas H. Deluca, Ragan M. Callaway, William E. Holben

Biological Sciences Faculty Publications

• Premise of the study: Invasive plants can alter soil microbial communities and profoundly alter ecosystem processes. In the invasive grass Sorghum halepense, these disruptions are consequences of rhizome-associated bacterial endophytes. We describe the effects of N₂-fixing bacterial strains from S. halepense (Rout and Chrzanowski, 2009) on plant growth and show that bacteria interact with the plant to alter soil nutrient cycles, enabling persistence of the invasive.
• Methods: We assessed fluxes in soil nutrients for ~4 yr across a site invaded by S. halepense. We assayed the N₂-fixing bacteria in vitro for phosphate solubilization, …

An Acid Test For G Proteins, Stephen R. Sprang

Biological Sciences Faculty Publications

Heterotrimeric G proteins are cytoplasmic transducers of signals generated by ligandactivated 7-transmembrane receptors (G protein-coupled receptors, or GPCRs) embedded in the plasma membranes of cells. GPCRs activate G proteins by catalyzing exchange of GDP for GTP at the alpha subunit (Gα) with the concomitant release of the Gβγ heterodimer. Separately or together Gα•GTP and Gβγ stimulate enzymes that produce second messengers (e.g. cyclic AMP), control ion channels, Ras-family G proteins and regulate transcription (Cabrera-Vera et al., 2003). In yeast, GPCRs intercept mating pheromones and monitor extracellular glucose concentration, and so generate intracellular signals either to arrest growth or to proliferate. …

Rcytoscape: Tools For Exploratory Network Analysis, Paul Shannon, Mark L. Grimes, Burak Kutlu, Jan J. Bit, David J. Galas

Biological Sciences Faculty Publications

Background: Biomolecular pathways and networks are dynamic and complex, and the perturbations to them which cause disease are often multiple, heterogeneous and contingent. Pathway and network visualizations, rendered on a computer or published on paper, however, tend to be static, lacking in detail, and ill-equipped to explore the variety and quantities of data available today, and the complex causes we seek to understand.

Results: RCytoscape integrates R (an open-ended programming environment rich in statistical power and datahandling facilities) and Cytoscape (powerful network visualization and analysis software). RCytoscape extends Cytoscape's functionality beyond what is possible with the Cytoscape graphical user interface. …

An Inverted Repeat In The Ospc Operator Is Required For Induction In Borrelia Burgdorferi, Dan Drecktrah, Laura S. Hall, Laura L. Hoon-Hanks, D. Scott Samuels

Biological Sciences Faculty Publications

Borrelia burgdorferi, the spirochete that causes Lyme disease, differentially regulates synthesis of the outer membrane lipoprotein OspC to infect its host. OspC is required to establish infection but then repressed in the mammal to avoid clearance by the adaptive immune response. Inverted repeats (IR) upstream of the promoter have been implicated as an operator to regulate ospC expression. We molecularly dissected the distal inverted repeat (dIR) of the ospC operator by site-directed mutagenesis at its endogenous location on the circular plasmid cp26. We found that disrupting the dIR but maintaining the proximal IR prevented induction of OspC synthesis by …

Starvation-Associated Genome Restructuring Can Lead To Reproductive Isolation In Yeast, Evgueny Kroll, Scott Coyle, Barbara Dunn, Gregory Koniges, Anthony Aragon, Jeremy Edwards, Frank Rosenzweig

Biological Sciences Faculty Publications

Knowledge of the mechanisms that lead to reproductive isolation is essential for understanding population structure and speciation. While several models have been advanced to explain post-mating reproductive isolation, experimental data supporting most are indirect. Laboratory investigations of this phenomenon are typically carried out under benign conditions, which result in low rates of genetic change unlikely to initiate reproductive isolation. Previously, we described an experimental system using the yeast Saccharomyces cerevisiae where starvation served as a proxy to any stress that decreases reproduction and/or survivorship. We showed that novel lineages with restructured genomes quickly emerged in starved populations, and that these …

Breed Locally, Disperse Globally: Fine-Scale Genetic Structure Despite Landscape-Scale Panmixia In A Fire-Specialist, Jennifer C. Pierson, Fred W. Allendorf, Pierre Drapeau, Michael K. Schwartz

Biological Sciences Faculty Publications

An exciting advance in the understanding of metapopulation dynamics has been the investigation of how populations respond to ephemeral patches that go 'extinct' during the lifetime of an individual. Previous research has shown that this scenario leads to genetic homogenization across large spatial scales. However, little is known about fine-scale genetic structuring or how this changes over time in ephemeral patches. We predicted that species that specialize on ephemeral habitats will delay dispersal to exploit natal habitat patches while resources are plentiful and thus display fine-scale structure. To investigate this idea, we evaluated the effect of frequent colonization of ephemeral …

Native Congeners Provide Biotic Resistance To Invasive Potentilla Through Soil Biota, Ragan M. Callaway, Daniel Montesinos, Kimberlyn Williams, John L. Maron

Biological Sciences Faculty Publications

Soil biota can facilitate exotic plant invasions and these effects can be influenced by specific phylogenetic relationships among plant taxa. We measured the effects of sterilizing soils from different native plant monocultures on the growth of Potentilla recta, an exotic invasive forb in North America, and conducted plant–soil feedback experiments with P. recta, two native congeners, a close confamilial, and Festuca idahoensis, a native grass species. We also reanalyzed data comparing the ability of P. recta to invade experimentally constructed congeneric monocultures vs. monocultures of a broad suite of non-congeners. We found that monocultures as a group, …

Environment, Behavior And Physiology: Do Birds Use Barometric Pressure To Predict Storms?, Creagh W. Breuner, Rachel Seabury Sprague, Stephen Harold Patterson, H. Arthur Woods

Biological Sciences Faculty Publications

Severe storms can pose a grave challenge to the temperature and energy homeostasis of small endothermic vertebrates. Storms are accompanied by lower temperatures and wind, increasing metabolic expenditure, and can inhibit foraging, thereby limiting energy intake. To avoid these potential problems, most endotherms have mechanisms for offsetting the energetic risks posed by storms. One possibility is to use cues to predict oncoming storms and to alter physiology and behavior in ways that make survival more likely. Barometric pressure declines predictably before inclement weather, and several lines of evidence indicate that animals alter behavior based on changes in ambient pressure. Here …

Effects Of Experimentally Elevated Traffic Noise On Nestling White-Crowned Sparrow Stress Physiology, Immune Function And Life History, Ondi L. Crino, Erin E. Johnson, Jessica L. Blickley, Gail L. Patricelli, Creagh W. Breuner

Biological Sciences Faculty Publications

Roads have been associated with behavioral and physiological changes in wildlife. In birds, roads decrease reproductive success and biodiversity and increase physiological stress. Although the consequences of roads on individuals and communities have been well described, the mechanisms through which roads affect birds remain largely unexplored. Here, we examine one mechanism through which roads could affect birds: traffic noise. We exposed nestling mountain white-crowned sparrows (Zonotrichia leucophrys oriantha) to experimentally elevated traffic noise for 5 days during the nestling period. Following exposure to traffic noise we measured nestling stress physiology, immune function, body size, condition and survival. Based …

Three-Dimensional, High-Resolution Skeletal Kinematics Of The Avian Wing And Shoulder During Ascending Flapping Flight And Uphill Flap-Running, David B. Baier, Stephen M. Gatesy, Kenneth P. Dial

Biological Sciences Faculty Publications

Past studies have shown that birds use their wings not only for flight, but also when ascending steep inclines. Uphill flap-running or wing-assisted incline running (WAIR) is used by both flight-incapable fledglings and flight-capable adults to retreat to an elevated refuge. Despite the broadly varying direction of travel during WAIR, level, and descending flight, recent studies have found that the basic wing path remains relatively invariant with reference to gravity. If so, joints undergo disparate motions to maintain a consistent wing path during those specific flapping modes. The underlying skeletal motions, however, are masked by feathers and skin. To improve …

A Field Experiment Demonstrating Plant Life-History Evolution And Its Eco-Evolutionary Feedback To Seed Predator Populations, Anurag A. Agrawal, Marc T. J. Johnson, Amy P. Hastings, John L. Maron

Biological Sciences Faculty Publications

The extent to which evolutionary change occurs in a predictable manner under field conditions and how evolutionary changes feed back to influence ecological dynamics are fundamental, yet unresolved, questions. To address these issues, we established eight replicate populations of native common evening primrose (Oenothera biennis). Each population was planted with 18 genotypes in identical frequency. By tracking genotype frequencies with microsatellite DNA markers over the subsequent three years (up to three generations, approximate to 5,000 genotyped plants), we show rapid and consistent evolution of two heritable plant life-history traits (shorter life span and later flowering time). This rapid evolution was …

The Early Dissemination Defect Attributed To Disruption Of Decorin-Binding Proteins Is Abolished In Chronic Murine Lyme Borreliosis, Denise M. Imai, D. Scott Samuels, Sunlian Feng, Emir Hodzic, Kim Olsen, Stephen W. Barthold

Biological Sciences Faculty Publications

The laboratory mouse model of Lyme disease has revealed that Borrelia burgdorferi differentially expresses numerous outer surface proteins that influence different stages of infection (tick-borne transmission, tissue colonization, dissemination, persistence, and tick acquisition). Deletion of two such outer surface proteins, decorin-binding proteins A and B (DbpA/B), has been documented to decrease infectivity, impede early dissemination, and, possibly, prevent persistence. In this study, DbpA/B-deficient spirochetes were confirmed to exhibit an early dissemination defect in immunocompetent, but not immunodeficient, mice, and the defect was found to resolve with chronicity. Development of disease (arthritis and carditis) was attenuated only in the early stage …

Sh3 Interactome Conserves General Function Over Specific Form, Xiaofeng Xin, David Gfeller, Jackie Cheng, Raffi Tonikian, Lin Sun, Ailan Guo, Lianet Lopez, Alevtina Pavlenco, Adenrele Akintobi, Yingnan Zhang, Jean-Francois Rual, Bridget Currell, Somasekar Seshagiri, Tong Hao, Xinping Yang, Yun A. Shen, Kourosh Salehi-Ashtiani, Jingjing Li, Aaron T. Cheng, Dryden Bouamalay, Adrien Lugari, David E. Hill, Mark L. Grimes, David. G. Drubin, Barth D. Grant, Marc Vidal, Charles Boone, Sachdev S. Sidhu, Gary D. Bader

Biological Sciences Faculty Publications

Src homology 3 (SH3) domains bind peptides to mediate protein–protein interactions that assemble and regulate dynamic biological processes. We surveyed the repertoire of SH3 binding specificity using peptide phage display in a metazoan, the worm Caenorhabditis elegans, and discovered that it structurally mirrors that of the budding yeast Saccharomyces cerevisiae.We then mapped the worm SH3 interactome using stringent yeast two-hybrid and compared it with the equivalent map for yeast.We found that the wormSH3 interactome resembles the analogous yeast network because it is significantly enriched for proteins with roles in endocytosis. Nevertheless, orthologous SH3 domain mediated interactions are highly …

Abundance As A Conservation Value, Kent H. Redford, Joel Berger, Steve Zack

Biological Sciences Faculty Publications

No abstract provided.

Robust Detection Of Rare Species Using Environmental Dna: The Importance Of Primer Specificity, Taylor M. Wilcox, Kevin S. Mckelvey, Michael K. Young, Stephen F. Jane, Winsor H. Lowe, Andrew R. Whiteley, Michael K. Schwartz

Biological Sciences Faculty Publications

Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method's sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. …

Molecular Chaperoning Function Of Ric-8 Is To Fold Nascent Heterotrimeric G Protein Α Subunits, Puiyee Chan, Celestine J. Thomas, Stephen R. Sprang, Gregory G. Tall

Biological Sciences Faculty Publications

We have shown that resistance to inhibitors of cholinesterase 8 (Ric-8) proteins regulate an early step of heterotrimeric G protein α (Gα) subunit biosynthesis. Here, mammalian and plant cell-free translation systems were used to study Ric-8A action during Gα subunit translation and protein folding. Gα translation rates and overall produced protein amounts were equivalent in mock and Ric-8A-immunodepleted rabbit reticulocyte lysate (RRL). GDP-AlF4(-)-bound Gαi, Gαq, Gα13, and Gαs produced in mock-depleted RRL had characteristic resistance to limited trypsinolysis, showing that these G proteins were folded properly. Gαi, Gαq, and Gα13, but not Gαs produced from Ric-8A-depleted RRL were not protected …

Recurrent Rearrangement During Adaptive Evolution In An Interspecific Yeast Hybrid Suggests A Model For Rapid Introgression, Barbara Dunn, Terry Paulish, Alison Stanbery, Jeff Piotrowski, Gregory Koniges, Evgueny Kroll, Edward J. Louis, Gianni Liti, Gavin Sherlock, Frank Rosenzweig

Biological Sciences Faculty Publications

Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow similar to 1-kb region of chromosome 14, and all producing an …

Ecological Divergence Of A Novel Group Of Chloroflexus Strains Along A Geothermal Gradient, Michael L. Weltzer, Scott R. Miller

Biological Sciences Faculty Publications

Environmental gradients are expected to promote the diversification and coexistence of ecological specialists adapted to local conditions. Consistent with this view, genera of phototrophic microorganisms in alkaline geothermal systems generally appear to consist of anciently divergent populations which have specialized on different temperature habitats. At White Creek (Lower Geyser Basin, Yellowstone National Park), however, a novel, 16S rRNA-defined lineage of the filamentous anoxygenic phototroph Chloroflexus (OTU 10, phylum Chloroflexi) occupies a much wider thermal niche than other 16S rRNA-defined groups of phototrophic bacteria. This suggests that Chloroflexus OTU 10 is either an ecological generalist or, alternatively, a group of cryptic …

Wrangling Phosphoproteomic Data To Elucidate Cancer Signaling Pathways, Mark L. Grimes, Wan-Jui Lee, Laurens Van Der Maaten, Paul Shannon

Biological Sciences Faculty Publications

The interpretation of biological data sets is essential for generating hypotheses that guide research, yet modern methods of global analysis challenge our ability to discern meaningful patterns and then convey results in a way that can be easily appreciated. Proteomic data is especially challenging because mass spectrometry detectors often miss peptides in complex samples, resulting in sparsely populated data sets. Using the R programming language and techniques from the field of pattern recognition, we have devised methods to resolve and evaluate clusters of proteins related by their pattern of expression in different samples in proteomic data sets. We examined tyrosine …

Kinetic Models Reveal The In Vivo Mechanisms Of Mutagenesis In Microbes And Man, Barbara E. Wright, Karen H. Schmidt, Michael F. Minnick

Biological Sciences Faculty Publications

This review summarizes the evidence indicating that mutagenic mechanisms in vivo are essentially the same in all living cells. Unique metabolic reactions to a particular environmental stress apparently target specific genes for increased rates of transcription and mutation, resulting in higher mutation rates for those genes most likely to solve the problem. Kinetic models which have demonstrated predictive value are described and are shown to simulate mutagenesis in vivo in Escherichia coli, the p53 tumor suppressor gene, and somatic hypermutation. In all three models, direct correlations are seen between mutation frequencies and transcription rates. G and C nucleosides in single-stranded …