Biology Commons^™

Duplications In Corneous Beta Protein Genes And The Evolution Of Gecko Adhesion, Tony Gamble

Biological Sciences Faculty Research and Publications

Corneous proteins are an important component of the tetrapod integument. Duplication and diversification of keratins and associated proteins are linked with the origin of most novel integumentary structures like mammalian hair, avian feathers, and scutes covering turtle shells. Accordingly, the loss of integumentary structures often coincides with the loss of genes encoding keratin and associated proteins. For example, many hair keratins in dolphins and whales have become pseudogenes. The adhesive setae of geckos and anoles are composed of both intermediate filament keratins (IF-keratins, formerly known as alpha-keratins) and corneous beta‐proteins (CBPs, formerly known as beta-keratins) and recent whole genome assemblies …

Effects Of Dry‐Season Irrigation On Leaf Physiology And Biomass Allocation In Tropical Lianas And Trees, Chris M. Smith-Martin, Carolina L. Bastos

Biological Sciences Faculty Research and Publications

Lianas are more abundant in seasonal forests than in wetter forests and are thought to perform better than trees when light is abundant and water is limited. We tested the hypothesis that lianas perform better than trees during seasonal drought using a common garden experiment with 12 taxonomically diverse species (six liana and six tree species) in 12 replicated plots. We irrigated six of the plots during the dry season for four years, while the remaining six control plots received only ambient rainfall. In year 5, we measured stem diameters for all individuals and harvested above‐ and belowground biomass for …

Persistence Of A Geographically-Stable Hybrid Zone In Puerto Rican Dwarf Geckos, Brendan J. Pinto, James Titus-Mcquillan, Juan D. Daza, Tony Gamble

Biological Sciences Faculty Research and Publications

Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and Sphaerodactylus townsendi in Puerto Rico, …

Moving Beyond Noninformative Priors: Why And How To Choose Weakly Informative Priors In Bayesian Analyses, Nathan P. Lemoine

Biological Sciences Faculty Research and Publications

Throughout the last two decades, Bayesian statistical methods have proliferated throughout ecology and evolution. Numerous previous references established both philosophical and computational guidelines for implementing Bayesian methods. However, protocols for incorporating prior information, the defining characteristic of Bayesian philosophy, are nearly nonexistent in the ecological literature. Here, I hope to encourage the use of weakly informative priors in ecology and evolution by providing a ‘consumer's guide’ to weakly informative priors. The first section outlines three reasons why ecologists should abandon noninformative priors: 1) common flat priors are not always noninformative, 2) noninformative priors provide the same result as simpler frequentist …

Human Genotyping And An Experimental Model Reveal Npr-C As A Possible Contributor To Morbidity In Coarctation Of The Aorta, John F. Ladisa Jr., Aoy Tomita-Mitchell, Karl D. Stamm, Kathleen Bazan, Donna K. Mahnke, Mary A. Goetsch, Brandon Wegter, Jesse W. Gerringer, Kathryn Repp, Oleg Palygin, Adrian P. Zietara, Mary M. Krolikowski, Thomas J. Eddinger, Abdel A. Alli, Michael E. Mitchell

Biological Sciences Faculty Research and Publications

Coarctation of the aorta (CoA) is a common congenital cardiovascular (CV) defect characterized by a stenosis of the descending thoracic aorta. Treatment exists, but many patients develop hypertension (HTN). Identifying the cause of HTN is challenging because of patient variability (e.g., age, follow-up duration, severity) and concurrent CV abnormalities. Our objective was to conduct RNA sequencing of aortic tissue from humans with CoA to identify a candidate gene for mechanistic studies of arterial dysfunction in a rabbit model of CoA devoid of the variability seen with humans. We present the first known evidence of natriuretic peptide receptor C (NPR-C …

Repression Of Germline Genes In Caenorhabditis Elegans Somatic Tissues By H3k9 Dimethylation Of Their Promoters, Andreas Rechtsteiner, Meghan Elizabeth Costello, Thea A. Egelhofer, Jocob M. Garrigues, Susan Strome, Lisa N. Petrella

Biological Sciences Faculty Research and Publications

Repression of germline-promoting genes in somatic cells is critical for somatic development and function. To study how germline genes are repressed in somatic tissues, we analyzed key histone modifications in three Caenorhabditis elegans synMuv B mutants, lin-15B, lin-35, and lin-37—all of which display ectopic expression of germline genes in the soma. LIN-35 and LIN-37 are members of the conserved DREAM complex. LIN-15B has been proposed to work with the DREAM complex but has not been shown biochemically to be a member of the complex. We found that, in wild-type worms, synMuv B target genes and germline genes …

Lianas Have A Seasonal Growth Advantage Over Co‐Occurring Trees, Stefan A. Schnitzer, Geertje M. F. Van Der Heijden

Biological Sciences Faculty Research and Publications

The seasonal growth advantage hypothesis posits that plant species that grow well during seasonal drought will increase in abundance in forests with increasing seasonality of rainfall both in absolute numbers and also relative to co‐occurring plant species that grow poorly during seasonal drought. That is, seasonal drought will give some plant species a growth advantage that they lack in aseasonal forests, thus allowing them attain higher abundance. For tropical forest plants, the seasonal growth advantage hypothesis may explain the distribution of drought‐adapted species across large‐scale gradients of rainfall and seasonality. We tested the seasonal growth advantage hypothesis with lianas and …

The Hydraulic Efficiency–Safety Trade‐Off Differs Between Lianas And Trees, Masha T. Van Der Sande, Lourens Poorter, Stefan A. Schnitzer, Bettina M.J. Engelbrecht, Lars Markesteijn

Biological Sciences Faculty Research and Publications

Hydraulic traits are important for woody plant functioning and distribution. Associations among hydraulic traits, other leaf and stem traits, and species’ performance are relatively well understood for trees, but remain poorly studied for lianas. We evaluated the coordination among hydraulic efficiency (i.e., maximum hydraulic conductivity), hydraulic safety (i.e., cavitation resistance), a suite of eight morphological and physiological traits, and species’ abundances for saplings of 24 liana species and 27 tree species in wet tropical forests in Panama. Trees showed a strong trade‐off between hydraulic efficiency and hydraulic safety, whereas efficiency and safety were decoupled in lianas. Hydraulic efficiency was strongly …

Isolating And Quantifying The Role Of Developmental Noise In Generating Phenotypic Variation, Maria Kiskowski, Tilmann Glimm, Nickolas Moreno, Tony Gamble, Ylenia Chiari

Biological Sciences Faculty Research and Publications

Genotypic variation, environmental variation, and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals. Developmental noise, which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fixed, also contributes to phenotypic variation. While evolutionary biology has long focused on teasing apart the relative contribution of genes and environment to phenotypic variation, our understanding of the role of developmental noise has lagged due to technical difficulties in directly measuring the contribution of developmental noise. The influence of developmental noise is likely underestimated in studies of phenotypic variation due to …

Population Genetic Structure And Species Delimitation Of A Widespread, Neotropical Dwarf Gecko, Brendan J. Pinto, Guarino R. Colli, Timothy E. Higham, Anthony P. Russell, Daniel P. Scantlebury, Laurie J. Vitt, Tony Gamble

Biological Sciences Faculty Research and Publications

Amazonia harbors the greatest biological diversity on Earth. One trend that spans Amazonian taxa is that most taxonomic groups either exhibit broad geographic ranges or small restricted ranges. This is likely because many traits that determine a species range size, such as dispersal ability or body size, are autocorrelated. As such, it is rare to find groups that exhibit both large and small ranges. Once identified, however, these groups provide a powerful system for isolating specific traits that influence species distributions. One group of terrestrial vertebrates, gecko lizards, tends to exhibit small geographic ranges. Despite one exception, this applies to …

Blue Grama Grass Genotype Affects Palatability And Preference By Semi-Arid Steppe Grasshoppers, Ava M. Hoffman, Holly Perretta, Nathan P. Lemoine, Melinda D. Smith

Biological Sciences Faculty Research and Publications

The semi-arid shortgrass steppe ecosystem of North America is dominated by blue grama grass (Bouteloua gracilis), a species with substantial intraspecific variability, ecological significance, and economic value. Yet no studies have addressed within species differences in blue grama palatability or insect herbivore preference with respect to plant traits. We performed an experimental study to test the palatability and preference of two blue grama genotypes, wild type versus cultivar, by grasshopper herbivores in the Gomphocerinae subfamily. We found strong evidence that cultivar blue grama was more palatable than wild type and that grasshoppers preferred cultivar plants. Although we could …

Considering The Effects Of Temperature × Nutrient Interactions On The Thermal Response Curve Of Carrying Capacity, Nathan P. Lemoine

Biological Sciences Faculty Research and Publications

Climate warming will likely destabilize populations or drive consumers locally extinct. These predictions arise from consumer–resource models incorporating temperature‐dependent parameters, and the accuracy of these predictions hinges on the validity of temperature scalings for each parameter. Among all parameters, carrying capacity (K) is the most ill‐defined and the temperature scaling of this parameter has no empirically verified foundation. Most studies assume that K declines exponentially with warming, but others have assumed a positive or no relationship between K and temperature. Here, I developed a theoretical foundation for a temperature scaling of K based on physiological principles of temperature …

The Yeast Mitochondrial Proteins Rcf1 And Rcf2 Support The Enzymology Of The Cytochrome C Oxidase Complex And Generation Of The Proton Motive Force, Vera Strogolova, Ngoc H. Hoang, Jonathan Hosler, Rosemary A. Stuart

Biological Sciences Faculty Research and Publications

The yeast mitochondrial proteins Rcf1 and Rcf2 are associated with a subpopulation of the cytochrome bc₁–cytochrome c oxidase supercomplex and have been proposed to play a role in the assembly and/or modulation of the activity of the cytochrome c oxidase (complex IV, CIV). Yeast mutants deficient in either Rcf1 or Rcf2 proteins can use aerobic respiration–based metabolism for growth, but the absence of both proteins results in a strong growth defect. In this study, using assorted biochemical and biophysical analyses of Rcf1/Rcf2 single and double null-mutant yeast cells and mitochondria, we further explored how Rcf1 and Rcf2 support …

Connectivity Explains Local Ant Community Structure In A Neotropical Forest Canopy: A Large‐Scale Experimental Approach, Benjamin J. Adams, Stefan A. Schnitzer, Stephen P. Yanoviak

Biological Sciences Faculty Research and Publications

Understanding how habitat structure and resource availability affect local species distributions is a key goal of community ecology. Where habitats occur as a mosaic, variation in connectivity among patches influences both local species richness and composition, and connectivity is a key conservation concern in fragmented landscapes. Similarly, availability of limiting resources frequently determines species coexistence or exclusion. For primarily cursorial arthropods like ants, gaps between neighboring trees are a significant barrier to movement through the forest canopy. Competition for limited resources such as nest sites also promotes antagonistic interactions. Lianas (woody vines) connect normally isolated neighboring tree crowns and often …

Drought And Small-Bodied Herbivores Modify Nutrient Cycling In The Semi-Arid Shortgrass Steppe, Nathan P. Lemoine, Melinda D. Smith

Biological Sciences Faculty Research and Publications

Climate change will increase the frequency of droughts over the next century, with severe consequences for ecosystem function in semi-arid grasslands. The shortgrass steppe (SGS) experiences some of the largest interannual variation in precipitation among terrestrial biomes and exhibits extremely high sensitivity to drought. Yet despite decades of research describing the consequences of drought for ecosystem function in the SGS, we currently have little information regarding the impact of drought on bioavailability of important nutrients other than nitrogen, the contribution of herbivores to bioavailable concentrations of these nutrients, and whether drought alters herbivore-derived nutrient cycling. To quantify the impacts of …

Dynamics And Selective Remodeling Of The Dna-Binding Domains Of Rpa, Nilisha Pokhrel, Colleen C. Caldwell, Elliot I. Corless, Emma A. Tillison, Joseph Tibbs, Nina Jocic, S. M. Ali Tabei, Marc S. Wold, Maria Spies, Edwin Antony

Biological Sciences Faculty Research and Publications

Replication protein A (RPA) coordinates important DNA metabolic events by stabilizing single-stranded DNA (ssDNA) intermediates, activating the DNA-damage response and handing off ssDNA to the appropriate downstream players. Six DNA-binding domains (DBDs) in RPA promote high-affinity binding to ssDNA yet also allow RPA displacement by lower affinity proteins. We generated fluorescent versions of Saccharomyces cerevisiae RPA and visualized the conformational dynamics of individual DBDs in the context of the full-length protein. We show that both DBD-A and DBD-D rapidly bind to and dissociate from ssDNA while RPA remains bound to ssDNA. The recombination mediator protein Rad52 selectively modulates the dynamics …

Effect Of Lianas On Forest‐Level Tree Carbon Accumulation Does Not Differ Between Seasons: Results From A Liana Removal Experiment In Panama, Geertje M. F. Van Der Heijden, Jennifer S. Powers, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

1. Lianas are prevalent in Neotropical forests, where liana‐tree competition can be intense, resulting in reduced tree growth and survival. The ability of lianas to grow relative to trees during the dry season suggests that liana‐tree competition is also strongest in the dry season. If correct, the predicted intensification of the drying trend over large areas of the tropics in the future may therefore intensify liana‐tree competition resulting in a reduced carbon sink function of tropical forests. However, no study has established whether the liana effect on tree carbon accumulation is indeed stronger in the dry than in the wet season. …

Using Archival Dna To Elucidate Anole Phylogeny, Gregory C. Mayer, Tony Gamble

Biological Sciences Faculty Research and Publications

No abstract provided.

Vertical Sleeve Gastrectomy Improves Ventilatory Drive Through A Leptin-Dependent Mechanism, Deanna M. Arble, Alan R. Schwartz, Vsevolod Y. Polotsky, Darleen A. Sandoval, Randy J. Seeley

Biological Sciences Faculty Research and Publications

Obesity hypoventilation syndrome (OHS) is a serious disorder characterized by daytime hypercapnia, disordered breathing, and a reduction in chemosensitivity. Vertical sleeve gastrectomy (VSG), a bariatric surgical procedure resulting in weight loss and weight-independent improvements in glucose metabolism, has been observed to substantially improve sleep-disordered breathing. However, it is unclear if the ventilatory effects of VSG are secondary to weight loss or the marked change in metabolic physiology. Using preclinical mouse models, we found that VSG leads to an improvement in the hypercapnic ventilatory response (HCVR) and reductions in circulating leptin levels independent of reductions in body mass, fat mass, and …

Natural History Note: Anolis Sagrei Foraging On A Patch Of Obvious Prey, Stuart V. Nielsen, Aaron M. Bauer, Tony Gamble

Biological Sciences Faculty Research and Publications

No abstract provided.

A Multitrophic Perspective On Biodiversity–Ecosystem Functioning Research, Nico Eisenhauer, Holger Schielzeth, Andrew D. Barnes, Kathryn Barry, Aletta Bonn, Ulrich Brose, Helge Bruelheide, Nina Buchmann, Francois Buscott, Anne Ebeling, Olga Ferlian, Grégoire T. Freschet, Darren P. Giling, Stephan Hättenschwiler, Helmut Hillebrand, Jes Hines, Forest Isbell, Eva Koller-France, Birgitta König-Ries, Hans De Kroon, Sebastian T. Meyer, Alexandru Milcu, Jörg Müller, Charles A. Nock, Jana S. Petermann, Christiane Roscher, Christoph Scherber, Michael Scherer-Lorenzen, Bernhard Schmid, Andreas Schuldt, Teja Tscharntke, Manfred Türke, Nicole M. Van Dam, Fons Van Der Plas, Anja Vogel, Cameron Wagg, David A. Wardle, Alexandra Weigelt, Wolfgang W. Weisser, Christian Wirth, Malte Jochum

Biological Sciences Faculty Research and Publications

Concern about the functional consequences of unprecedented loss in biodiversity has prompted biodiversity–ecosystem functioning (BEF) research to become one of the most active fields of ecological research in the past 25 years. Hundreds of experiments have manipulated biodiversity as an independent variable and found compelling support that the functioning of ecosystems increases with the diversity of their ecological communities. This research has also identified some of the mechanisms underlying BEF relationships, some context-dependencies of the strength of relationships, as well as implications for various ecosystem services that mankind depends upon. In this paper, we argue that a multitrophic perspective of …

A Structural And Dynamic Model For The Assembly Of Replication Protein A On Single-Stranded Dna, Luke A. Yates, Ricardo J. Aramayo, Nilisha Pokhrel, Colleen C. Caldwell, Joshua A. Kaplan, Rajika L. Perera, Maria Spies, Edwin Antony, Xiaodong Zhang

Biological Sciences Faculty Research and Publications

Replication Protein A (RPA), the major eukaryotic single stranded DNA-binding protein, binds to exposed ssDNA to protect it from nucleases, participates in a myriad of nucleic acid transactions and coordinates the recruitment of other important players. RPA is a heterotrimer and coats long stretches of single-stranded DNA (ssDNA). The precise molecular architecture of the RPA subunits and its DNA binding domains (DBDs) during assembly is poorly understood. Using cryo electron microscopy we obtained a 3D reconstruction of the RPA trimerisation core bound with ssDNA (∼55 kDa) at ∼4.7 Å resolution and a dimeric RPA assembly on ssDNA. FRET-based solution studies …

A Force Sensor That Converts Fluorescence Signal Into Force Measurement Utilizing Short Looped Dna, Golam Mustafa, Cho-Ying Chuang, William A. Roy, Mohamed M. Farhath, Nilisha Pokhrel, Yue Ma, Kazuo Nagawawa, Edwin Antony, Matthew J. Comstock, Soumitra Basu, Hamza Balci

Biological Sciences Faculty Research and Publications

A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged …

Phosphate Removal And Recovery Using Immobilized Phosphatebinding Proteins, Kaushik Venkiteshwaran, Nilisha Pokhrel, Faten Hussein, Edwin Antony, Brooke K. Mayer

Biological Sciences Faculty Research and Publications

Progress towards a more circular phosphorus economy necessitates development of innovative water treatment systems which can reversibly remove inorganic phosphate (P_i) to ultra-low levels (<100 μg L⁻¹), and subsequently recover the P_i for reuse. In this study, a novel approach using the high-affinity E. coli phosphate binding protein (PBP) as a reusable P_i bio-adsorbent was investigated. PBP was expressed, extracted, purified and immobilized on NHS-activated Sepharose beads. The resultant PBP beads were saturated with P_i and exposed to varying pH (pH 4.7 to 12.5) and temperatures (25–45 °C) to induce P_i release. Increase in …

Distinct Proteostasis Circuits Cooperate In Nuclear And Cytoplasmic Protein Quality Control, Rahul S. Samant, Christine M. Livingston, Emily M. Sontag, Judith Frydman

Biological Sciences Faculty Research and Publications

Protein misfolding is linked to a wide array of human disorders, including Alzheimer’s disease, Parkinson’s disease and type II diabetes^1,2. Protective cellular protein quality control (PQC) mechanisms have evolved to selectively recognize misfolded proteins and limit their toxic effects^{3,4,5,6,7,8,9}, thus contributing to the maintenance of the proteome (proteostasis). Here we examine how molecular chaperones and the ubiquitin–proteasome system cooperate to recognize and promote the clearance of soluble misfolded proteins. Using a panel of PQC substrates with distinct characteristics and localizations, we define distinct chaperone and ubiquitination circuitries that execute quality control in the cytoplasm and nucleus. …

A Host–Parasite Model Explains Variation In Liana Infestation Among Co‐Occurring Tree Species, Marco D. Visser, Helene C. Muller-Laudau, Stefan A. Schnitzer, Hans De Kroon, Eelke Jongejans, S. Joseph Wright

Biological Sciences Faculty Research and Publications

1. Lianas are structural parasites of trees that reduce the growth, survival and reproduction of their hosts. Given that co‐occurring tree species differ strongly in the proportion of individuals that are infested by lianas (liana prevalence), lianas could differentially impact tree species and thereby influence tree community composition. Surprisingly, little is known about what governs variation in liana prevalence.
2. Here, we apply an approach inspired by disease ecology to investigate the dynamics of liana prevalence over 11 years on Barro Colorado Island, Panama. We followed the fate of 1,938 individual trees from 21 tree species, recording deaths and change in liana …

Testing Ecological Theory With Lianas, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Lianas constitute a diverse polyphyletic plant group that is advancing our understanding of ecological theory. Specifically, lianas are providing new insights into the mechanisms that control plant distribution and diversity maintenance. For example, there is now evidence that a single, scalable mechanism may explain local, regional, and pan‐tropical distribution of lianas, as well as the maintenance of liana species diversity. The ability to outcompete trees under dry, stressful conditions in seasonal forests provides lianas a growth advantage that, over time, results in relatively high abundance in seasonal forests and low abundance in aseasonal forests. Lianas may also gain a similar …

Effects Of Elevated H+ And PI On The Contractile Mechanics Of Skeletal Muscle Fibres From Young And Old Men: Implications For Muscle Fatigue In Humans, Christopher W. Sundberg, Sandra K. Hunter, Todd A. Trappe, Carolyn S. Smith, Robert H. Fitts

Biological Sciences Faculty Research and Publications

The present study aimed to identify the mechanisms responsible for the loss in muscle power and increased fatigability with ageing by integrating measures of whole‐muscle function with single fibre contractile mechanics. After adjusting for the 22% smaller muscle mass in old (73–89 years, n = 6) compared to young men (20–29 years, n = 6), isometric torque and power output of the knee extensors were, respectively, 38% and 53% lower with age. Fatigability was ∼2.7‐fold greater with age and strongly associated with reductions in the electrically‐evoked contractile properties. To test whether cross‐bridge mechanisms could explain age‐related decrements in knee extensor …

Agricultural Contamination Impacts Antibiotic Resistance Gene Abundances In River Bed Sediment Temporally, Rachelle E. Beattie, Michael P. Walsh, Mercedes Cecilia Cruz, L. Rex Mcaliley, Laurel Dodgen, Wei Zheng, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Kewaunee County, Wisconsin is an agricultural area dominated by concentrated animal feeding operations and manure fertilized cropland. The objective of this study was to characterize chemical and antibiotic resistance gene (ARG) profiles of 20 surface water locations in Kewaunee County to better understand relationships between agricultural contamination and ARG abundance over one year. Surface water (n = 101) and bed sediment (n = 93) were collected from 20 sites during five timepoints between July 2016 and May 2017. Samples were analyzed for six genes (erm(B), tet(W), sul1, qnrA, intI1 and 16S rRNA) and water chemistry …

Effects Of Lianas And Hurricane Wilma On Tree Damage In The Yucatan Peninsula, Mexico, Edgardo I. Garrido-Pérez, Juan Manuel Dupuy, Rafael Durán-García, Mario Ucan-May, Stefan A. Schnitzer, Gerhard Gerold

Biological Sciences Faculty Research and Publications

Climate change may increase the intensity of hurricanes (Emanuel 1987, 2003), and thus the size of disturbance in tropical forests. As a consequence, disturbance-specialist plants, such as lianas, may increase in abundance there (Phillips & Gentry 1994). Putz (1984) hypothesized that lianas create larger treefall gaps by connecting trees together and pulling down multiple trees during storms. This positive-feedback cycle may increase the prevalence of lianas in disturbed tropical forests (Schnitzer & Bongers 2002, Schnitzer & Carson 2001). Alternatively, Putz (1984) proposed that lianas tie and stabilize canopies together, resulting in less disturbance. Forest age may determine the role of …