Biology Commons^™

Subglacial Lake Vostok (Antarctica) Accretion Ice Contains A Diverse Set Of Sequences From Aquatic, Marine And Sediment-Inhabiting Bacteria And Eukarya, Scott O. Rogers, Yury M. Shtarkman, Zeynep A. Koçer, Robyn Edgar, Ram S. Veerapneni, Tom D'Elia, Paul F. Morris

Biological Sciences Faculty Publications

Lake Vostok, the 7th largest (by volume) and 4th deepest lake on Earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. The combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. Here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the Vostok 5G ice core. Two sections accreted in the vicinity of an embayment on the southwestern end of the lake, and the other two represented part of the southern main basin. We obtained 3,507 …

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 …

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 …

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, …

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 …

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 …

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 …

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. …

Reproductive Isolation In The Elegans-Group Of Caenorhabditis, Scott Everet Baird, Sara Rose Seibert

Biological Sciences Faculty Publications

Reproductive isolation is the basis of the Biological Species Definition and can be a driving force of speciation. Theoretical studies have provided models of how reproductive isolation can arise within individual species. Genetic tests of these models are limited to populations in which reproductive isolation is present but not complete. Here, reproductive isolation in the Elgans-Group of the nematode genus Caenorhabditis is reviewed. Pre-mating barriers, assortative fertilization and post-zygotic barriers all have been observed in this clade. In some combinations of species, fertile F1 hybrids can be obtained. Therefore, the Elegans-Group of Caenorhabditis is poised to become an important experimental …

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 …

Adenosine Triphosphate (Atp) Is A Candidate Signaling Molecule In The Mitochondria-To-Nucleus Retrograde Response Pathway, Feng Zhang, Tammy Pracheil, Janet Thornton, Zhengchang Liu

Biological Sciences Faculty Publications

Intracellular communication from the mitochondria to the nucleus is achieved via the retrograde response. In budding yeast, the retrograde response, also known as the RTG pathway, is regulated positively by Rtg1, Rtg2, Rtg3 and Grr1 and negatively by Mks1, Lst8 and two 14-3-3 proteins, Bmh1/2. Activation of retrograde signaling leads to activation of Rtg1/3, two basic helix-loop-helix leucine zipper transcription factors. Rtg1/3 activation requires Rtg2, a cytoplasmic protein with an N-terminal adenosine triphosphate (ATP) binding domain belonging to the actin/Hsp70/sugar kinase superfamily. The critical regulatory step of the retrograde response is the interaction between Rtg2 and Mks1. Rtg2 binds to …

Release Of Avian Neurotensin In Response To Intraluminal Contents In The Duodenum Of Chickens, Teresa F. Degolier, Robert E. Carraway

Biological Sciences Faculty Publications

Peripheral and hepatic-portal plasma levels of neurotensin (NT) in fed and fasted chickens were determined using RIA. Portal levels of NT1-13 (fed = 61.3 ± 3.9 fmol/mL; fasted = 44.5 ± 3.9 fmol/mL) were significantly higher than peripheral levels (fed = 8.2 ± 3.3 fmol/mL; fasted = 7.8 ± 3.0 fmol/mL) collected from the wing vein, indicating that some NT is metabolized in the liver. Portal plasma levels of NT collected from fed birds were also significantly higher than portal plasma levels of NT collected from fasted birds. Neurotensin, as identified by HPLC, exhibited a 2-fold increase in plasma extracts …

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 …

Phylogenetic Analyses Of Tolpis Adans. (Asteraceae) Reveal Patterns Of Adaptive Radiation, Multiple Colonization And Interspecific Hybridization, Michael Gruenstaeudl, Arnoldo Santos-Guerra, Robert K. Jansen

Biological Sciences Faculty Publications

The plant genus Tolpis (Asteraceae) has been the subject of several investigations on the evolution of oceanic island plants. Its insular species were utilized in studies of artificial hybrid fertility, testing the validity of Baker’s law, the application of DNA barcodes, and the phylogenetic utility of inter-simple sequence repeat markers. Despite this considerable interest in Tolpis, little is known about its phylogenetic history. Past investigations were unable to resolve most of the interspecific relationships, especially within the Canary Islands, where the genus is particularly diverse. Incomplete taxon sampling, the use of ambiguous outgroups and the limited utility of slowly evolving …

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 …

Prolonged Dormancy Interacts With Senescence For Two Perennial Herbs, Juha Tuomi, Elizabeth E. Crone, Jennifer R. Gremer, Anne Jakalaniemi, Peter Lesica, Bard Pedersen, Satu Ramula

Biological Sciences Faculty Publications

1. Senescence is characterized by a decline in survival, fecundity and reproductive value with age among adult individuals. Simple age-dependent life cycles progress forward through developmental stages, with each successive stage being characterized by age-specific vital rates. In contrast, size- or stage-based life cycles for perennial plants are more complex and often include stasis and retrogression to previous vegetative or reproductive life stages, indicating possible slowing or even reversing the developmental progress.

2. Many plants remain in nonemergent, below-ground stages during the growing season (prolonged dormancy), which may affect the process of senescence. Stasis in the dormant stage implies that …

Morphological And Ecological Segregation Of Two Sympatric Lomatium Triternatum (Apiaceae) Varities In Montana, Peter Lesica, Pamela Kittelson

Biological Sciences Faculty Publications

The Lomatium triternatum complex is widespread in the Columbia River Basin. Lomatium triternatum (Pursh) J. M. Coult. & Rose var. triternatum and L. triternatum (Pursh) J. M. Coult. & Rose var. anomalum (M. E. Jones ex J. M. Coult. & Rose) Mathias are sympatric throughout much of their range and are reported to have similar fruit but different leaves. Plants of the two varieties repeatedly occur within 5–30 m of each other at an unusual site in northwest Montana, USA. We collected data on leaf and fruit morphological characters and habitat associations at this site to help address whether the …

Progress Towards A Phylogeny Of World Tachinidae. Year 1, John O. Stireman Iii, James E. O'Hara, Michael C. Moulton, Pierfilippo Cerretti, Isaac S. Winkler

Biological Sciences Faculty Publications

D eveloping a structural phylogenetic framework for the family Tachinidae has been an interest of mine since I first started working on tachinids as a graduate student. It was then that I developed a new phylogenetic perspective with which to view the world, and many of the questions I wanted to ask of tachinids depended on some level of phylogenetic knowledge of them. I was surprised at the time that no one had attempted a broad quantitative phylogenetic analysis of the family, and a publication from my thesis work on the Exoristinae (Stireman 2002) became the first such study that …

Food Limitation As A Potentially Emerging Contributor To The Asian Vulture Crisis, Fakhar -I- Abbas, Thomas P. Rooney, Jibran Haider, Afsar Mian

Biological Sciences Faculty Publications

It was believed that the reason for decline in Asian vulture population is the drug, Diclofenac sodium (DFS), used in livestock. Even after declaring the DFS use banned by the government, apparent decrease in the population of vultures was reported. Alternate hypothesis was suggested that food limitation may be a cause of Asian vulture crisis in Pakistan. Very recent shifts in livestock utilization observed in Pakistan may present a significant barrier to vulture recovery. Increased livestock utilization is translated to fewer carcasses. Since 2005, no livestock carcasses were found in 1650 km transect in the habitat of vultures. Carcasses recorded …

Game-Based Curricula In Biology Classes: Multi-Level Assessment Of Science Learning, Troy D. Sadler, William L. Romine, Parker E. Stuart

Biological Sciences Faculty Publications

Video games played on computers, game consoles, tablets and smart phones have become a very popular medium in our society. A growing body of scholarship suggests that video games can support substantial learning (for reviews see Gee, 2007; Honey & Hilton, 2011; Squire, 2011). Research has documented ways in which games engage students deeply in thinking, learning, and collaboration (Gee, 2005). Evidence suggests that games can support development of critical thinking (Squire, 2006), creativity (Annetta, Cheng, & Holmes, 2010), and mastery and application of target concepts (Squire, 2011).

To 'Die Hel' And Back. Expeditions Of The Phylogeny Of World Tachinidae Project. Part I: Western Cape, South Africa, Pierfilippo Cerretti, James E. O'Hara, John O. Stireman Iii, Isaac S. Winkler, Ashley H. Kirk-Spriggs

Biological Sciences Faculty Publications

The “Phylogeny of World Tachinidae” project kicked off with an operational meeting in June 2012 at the Canadian National Collection of Insects (CNC) in Ottawa. Goals were discussed, work plans prepared, and of course the destinations and timing of major field expeditions were debated. During our three years of National Science Foundation funding we hope to gather fresh material for molecular analysis from all biogeographic regions of the world.

A New Method For Identifying Stem-Like Cells In Esophageal Cancer Cell Lines, Michael Eric Geusz, Taghreed N. Almanaa, Roudabeh J. Jamasbi

Biological Sciences Faculty Publications

Cancer stem cells (CSCs) appear to resist chemo-radiotherapy and initiate tumor recurrence in patients. Isolation and further characterization of this subpopulation is important for targeting CSCs. Flow cytometry using Aldefluor, a fluorescent substrate of aldehyde dehydrogenase, has been used to isolate CSCs from various cancer cell lines. However, newtechniques are needed to locate and identify CSCs in culture for live-cell analyses such as fluorescence microscopy without introducing artifacts during cell sorting and to observe CSC and non-CSC interactions. Previously, we characterized a distinct CSC subpopulation within human esophageal cancer cell lines (ESCC). In this study we introduce the attached-cell Aldefluor …

Mitochondrial Dna Instability In Cells Lacking Aconitase Correlates With Iron Citrate Toxicity, Zhengchang Liu, Fei Xiao, Zhejun Dong, Tammy Pracheil, Muhammad Farooq

Biological Sciences Faculty Publications

Aconitase, the second enzyme of the tricarboxylic acid cycle encoded by ACO1 in the budding yeast Saccharomyces cerevisiae, catalyzes the conversion of citrate to isocitrate. aco1Δ results in mitochondrial DNA (mtDNA) instability. It has been proposed that Aco1 binds to mtDNA and mediates its maintenance. Here we propose an alternative mechanism to account for mtDNA loss in aco1Δ mutant cells. We found that aco1Δ activated the RTG pathway, resulting in increased expression of genes encoding citrate synthase. By deleting RTG1, RTG3, or genes encoding citrate synthase, mtDNA instability was prevented in aco1Δ mutant cells. Increased activity of citrate synthase leads …

Pronounced Genetic Structure In A Highly Mobile Coral Reef Fish, Caesio Cuning, In The Coral Triangle, Amanda S. Ackiss, Shinta Pardede, Eric D. Crandall, Ma Carmen A. Ablan-Lagman, Ambariyanto, November Romena, Paul H. Barber, Kent E. Carpenter

Biological Sciences Faculty Publications

The redbelly yellowtail fusilier Caesio cuning has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of multiple limits to connectivity. However, these studies have focused almost exclusively on benthic, reef-dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no indepth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We …

Identifying Requirements For The Invasion Of A Tick Species And Tick-Borne Pathogen Through Ticksim, Holly Gaff, Robyn Nadolny

Biological Sciences Faculty Publications

Ticks and tick-borne diseases have been on the move throughout the United State over the past twenty years. We use an agent-based model, TICKSIM, to identify the key parameters that determine the success of invasion of the tick and if that is successful, the success of the tick-borne pathogen. We find that if an area has competent hosts, an initial population of ten ticks is predicted to always establish a new population. The establishment of the tick-borne pathogen depends on three parameters: the initial prevalence in the ten founding ticks, the probability that a tick infects the longer-lived hosts and …