Life Sciences Commons^™

Improving Collaborations Between Empiricists And Modelers To Advance Grassland Community Dynamics In Ecosystem Models, Kevin R. Wilcox, Kimberly J. Komatsu, Meghan L. Avolio, Nathan P. Lemoine

Biological Sciences Faculty Research and Publications

No abstract provided.

The Response Of Lianas To 20 Yr Of Nutrient Addition In A Panamanian Forest, Stefan A. Schnitzer, Sergio Estrada Villegas, S. Joseph Wright

Biological Sciences Faculty Research and Publications

Over the past two decades, liana density and basal area have been increasing in many tropical forests, which has profound consequences for forest diversity and functioning. One hypothesis to explain increasing lianas is elevated nutrient deposition in tropical forests resulting from fossil fuels, agricultural fertilizer, and biomass burning. We tested this hypothesis by surveying all lianas ≥1 cm in diameter (n = 3,967) in 32 plots in a fully factorial nitrogen (N), phosphorus (P), and potassium (K) addition experiment in a mature tropical forest in central Panama. We conducted the nutrient-addition experiment from 1998 until present and we first …

Lianas Maintain Insectivorous Bird Abundance And Diversity In A Neotropical Forest, Stefan A. Schnitzer, Nicole L. Michel, Jennifer S. Powers, W. Douglas Robinson

Biological Sciences Faculty Research and Publications

The spatial habitat heterogeneity hypothesis posits that habitat complexity increases the abundance and diversity of species. In tropical forests, lianas add substantial habitat heterogeneity and complexity throughout the vertical forest profile, which may maintain animal abundance and diversity. The effects of lianas on tropical animal communities, however, remain poorly understood. We propose that lianas have a positive effect on animals by enhancing habitat complexity. Lianas may have a particularly strong influence on the forest bird community, providing nesting substrate, protection from predators, and nutrition (food). Understory insectivorous birds, which forage for insects that specialize on lianas, may particularly benefit. Alternatively, …

Challenges Facing Young Scientists In Academia And Industry In The United States From The Lens Of A Millennial Academic, Joseph R. Clark

Biological Sciences Faculty Research and Publications

Rising to the challenge: Pictured from left to right: Salma L. Nuñez, Albert Reyes and Lisandra Santiago-Capeles, Ph.D. The challenges that young scientists face in academia and industry in the United States are discussed. Prof. Joseph Clark provides insight about how social media, funding, diversity, natural disasters, COVID-19 and student loan debt are impacting young scientists. A discussion of strategies to meet these challenges and support young scientists are presented.

Multi-Scale 3d Cryo-Correlative Microscopy For Vitrified Cells, Gong-Her Wu, Patrick G. Mitchell, Jesus G. Galaz-Montoya, Corey W. Hecksel, Emily M. Sontag, Vimal Gangadharan, Jeffrey Marshman, David Mankus, Margaret E. Bisher, Abigail K.R. Lytton-Jean, Judith Frydman, Kirk Czymmek, Wah Chiu

Biological Sciences Faculty Research and Publications

Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could …

Temporal Variability In Production Is Not Consistently Affected By Global Change Drivers Across Herbaceous-Dominated Ecosystems, Meghan L. Avolio, Kevin R. Wilcox, Kimberly J. Komatsu, Nathan P. Lemoine, William D. Bowman, Scott L. Collins, Alan K. Knapp, Sally E. Koerner, Melinda D. Smith, Sara G. Baer, Katherine Gross, Forest Isbell, Jennie R. Mclaren, Peter B. Reich, Katherine Suding, K. Blake Suttle, David Tilman, Zhuwen Xu, Qiang Yu

Biological Sciences Faculty Research and Publications

Understanding how global change drivers (GCDs) affect aboveground net primary production (ANPP) through time is essential to predicting the reliability and maintenance of ecosystem function and services in the future. While GCDs, such as drought, warming and elevated nutrients, are known to affect mean ANPP, less is known about how they affect inter-annual variability in ANPP. We examined 27 global change experiments located in 11 different herbaceous ecosystems that varied in both abiotic and biotic conditions, to investigate changes in the mean and temporal variability of ANPP (measured as the coefficient of variation) in response to different GCD manipulations, including …

Survivor Microbial Populations In Post-Chlorinated Wastewater Are Strongly Associated With Untreated Hospital Sewage And Include Ceftazidime And Meropenem Resistant Populations, Rachelle E. Beattie, Troy Skwor, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Wastewater treatment plant (WWTP) effluent has been implicated in the spread of antibiotic resistant bacteria (ARB), including pathogens, as the WWTP environment contains multiple selective pressures that may increase mutation rates, pathogen survivability, and induce gene transfer between bacteria. In WWTPs receiving hospital sewage, this selective effect may be more pronounced due to increased concentrations of antibiotics, ARB, and clinical pathogens from hospital sewage. To determine the extent to which hospital sewage contributes to the microbial community of disinfected wastewater which is released into the environment, we used 16S rRNA sequencing of hospital sewage, WWTP influent, primary effluent, Post-Chlorinated Effluent, …

Freshwater Sediment Microbial Communities Are Not Resilient To Disturbance From Agricultural Land Runoff, Rachelle E. Beattie, Aditya Bandla, Sanjay Swarup, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a …

Effects Of Low-Level Artificial Light At Night On Kentucky Bluegrass And Introduced Herbivore, Morgan Crump, Cassandra Brown, Robert J. Griffin-Nolan, Lisa Angeloni, Nathan P. Lemoine, Brett Seymoure

Biological Sciences Faculty Research and Publications

Increasing evidence suggests that artificial light at night (ALAN) can negatively impact organisms. However, most studies examine the impacts of ALAN on a single species or under high levels of artificial light that are infrequent or unrealistic in urban environments. We currently have little information on how low levels of artificial light emanating from urban skyglow affect plants and their interactions with herbivores. We examined how low levels of ALAN affect grass and insects, including growth rate, photosynthesis, and stomatal conductance in grass, and foraging behavior and survival in crickets. We compared growth and leaf-level gas exchange of Kentucky Bluegrass …

Can Functional Traits Explain Plant Coexistence? A Case Study With Tropical Lianas And Trees, Felipe N. A. Mello, Sergio Estrada Villegas, David M. Defilippis, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Organisms are adapted to their environment through a suite of anatomical, morphological, and physiological traits. These functional traits are commonly thought to determine an organism’s tolerance to environmental conditions. However, the differences in functional traits among co-occurring species, and whether trait differences mediate competition and coexistence is still poorly understood. Here we review studies comparing functional traits in two co-occurring tropical woody plant guilds, lianas and trees, to understand whether competing plant guilds differ in functional traits and how these differences may help to explain tropical woody plant coexistence. We examined 36 separate studies that compared a total of 140 …

Conserved Zz/Zw Sex Chromosomes In Caribbean Croaking Geckos (Aristelliger: Sphaerodactylidae), Shannon E. Keating, Aaron H. Griffing, Stuart V. Nielsen, Daniel P. Scantlebury, Tony Gamble

Biological Sciences Faculty Research and Publications

Current understanding of sex chromosome evolution is largely dependent on species with highly degenerated, heteromorphic sex chromosomes, but by studying species with recently evolved or morphologically indistinct sex chromosomes we can greatly increase our understanding of sex chromosome origins, degeneration and turnover. Here, we examine sex chromosome evolution and stability in the gecko genus Aristelliger. We used RADseq to identify sex‐specific markers and show that four Aristelliger species, spanning the phylogenetic breadth of the genus, share a conserved ZZ/ZW system syntenic with avian chromosome 2. These conserved sex chromosomes contrast with many other gecko sex chromosome systems by showing …

Bk Potassium Currents Contribute Differently To Action Potential Waveform And Firing Rate As Rat Hippocampal Neurons Mature In The First Postnatal Week, Michael Hunsberger, Michelle Mynlieff

Biological Sciences Faculty Research and Publications

The large-conductance calcium-activated potassium (BK) channel is a critical regulator of neuronal action potential firing and follows two distinct trends in early postnatal development: an increase in total expression and a shift from the faster activating STREX isoform to the slower ZERO isoform. We analyzed the functional consequences of developmental trends in BK channel expression in hippocampal neurons isolated from neonatal rats aged 1 to 7 days. Following overnight cultures, action potentials and currents were recorded using whole cell patch-clamp electrophysiology. These neurons undergo a steady increase in excitability during this time, and the effect of blockade of BK channel …

The Defining Genomic And Predicted Metabolic Features Of The Acetobacterium Genus, Daniel E. Ross, Christopher Marshall, Djuna Gulliver, Harold D. May, R. Sean Norman

Biological Sciences Faculty Research and Publications

Acetogens are anaerobic bacteria capable of fixing CO₂ or CO to produce acetyl coenzyme A (acetyl-CoA) and ultimately acetate using the Wood-Ljungdahl pathway (WLP). Acetobacterium woodii is the type strain of the Acetobacterium genus and has been critical for understanding the biochemistry and energy conservation in acetogens. Members of the Acetobacterium genus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done on the unique and various metabolisms of the genus. To gain a better appreciation for the metabolic breadth of the genus, we sequenced the …

The Negative Effect Of Lianas On Tree Growth Varies With Tree Species And Season, Alejandro Venegas-Gonzalez, Felipe N. A. Mello, Stefan A. Schnitzer, Ricardo G. Cesar, Mario Tomazello-Filho

Biological Sciences Faculty Research and Publications

Lianas reduce tree growth, reproduction, and survival in tropical forests. Liana competition can be particularly intense in isolated forest fragments, where liana densities are high, and thus, host tree infestation is common. Furthermore, lianas appear to grow particularly well during seasonal drought, when they may compete particularly intensely with trees. Few studies, however, have experimentally quantified the seasonal effects of liana competition on multiple tree species in tropical forests. We used a liana removal experiment in a forest fragment in southeastern Brazil to test whether the effects of lianas on tree growth vary with season and tree species identity. We …

The Actin Cytoskeletal Network Plays A Role In Yeast Prion Transmission And Contributes To Prion Stability, Jane E. Dorweiler, Mitchell J. Oddo, Douglas R. Lyke, Jacob A. Reilly, Brett T. Wisniewski, Emily E. Davis, Abigail M. Kuborn, Stephen J. Merrill, Anita L. Manogaran

Biological Sciences Faculty Research and Publications

Chaperone networks are required for the shearing and generation of transmissible propagons from pre‐existing prion aggregates. However, other cellular networks needed for maintaining yeast prions are largely uncharacterized. Here, we establish a novel role for actin networks in prion maintenance. The [PIN ⁺] prion, also known as [RNQ ⁺], exists as stable variants dependent upon the chaperone machinery for the transmission of propagons to daughter cells during cell division and cytoplasmic transfer. Loss of the Hsp104 molecular chaperone leads to the growth of prion particles until they are too large to be transmitted. Here, we isolated …

The Structure And Symmetry Of The Radial Spoke Protein Complex In Chlamydomonas Flagella, Emiliya Poghosyan, Ioan Iacovache, Lenka Faltova, Alexander Leitner, Pinfen Yang, Dennis R. Diener, Ruedi Aebersold, Benoit Zuber, Takashi Ishikawa

Biological Sciences Faculty Research and Publications

The radial spoke is a key element in a transducer apparatus controlling the motility of eukaryotic cilia. The transduction biomechanics is a long-standing question in cilia biology. The radial spoke has three regions – a spoke head, a bifurcated neck and a stalk. Although the neck and the stalk are asymmetric, twofold symmetry of the head has remained controversial. In this work we used single particle cryo-electron microscopy (cryo-EM) analysis to generate a 3D structure of the whole radial spoke at unprecedented resolution. We show the head region at 15 Å (1.5 nm) resolution and confirm twofold symmetry. Using distance …

Multiple Cold Tolerance Trait Phenotyping Reveals Shared Quantitative Trait Loci In Oryza Sativa, Naoki Shimoyama, Melineeh Johnson, André Beaumont, Michael Schläppi

Biological Sciences Faculty Research and Publications

Background

Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species.

Results

The Rice Diversity Panel 1 (RDP1) was used to investigate …

Individual Learning Phenotypes Drive Collective Behavior, Chelsea N. Cook, Natalie J. Lemanski, Thiago Mosqueiro, Cahit Ozturk, Jürgen Gadau, Noa Pinter-Wollman, Brian H. Smith

Biological Sciences Faculty Research and Publications

Individual differences in learning can influence how animals respond to and communicate about their environment, which may nonlinearly shape how a social group accomplishes a collective task. There are few empirical examples of how differences in collective dynamics emerge from variation among individuals in cognition. Here, we use a naturally variable and heritable learning behavior called latent inhibition (LI) to show that interactions among individuals that differ in this cognitive ability drive collective foraging behavior in honey bee colonies. We artificially selected two distinct phenotypes: high-LI bees that ignore previously familiar stimuli in favor of novel ones and low-LI bees …

Human Health, Interagency Coordination, And The Need For Biodiversity Data, Jennifer M. Zaspel, Julie M. Allen, Christopher D. Tyrrell, Nathan P. Lemoine, Luke M. Jacobus, Crystal Klem, Jillian Goodwin, John M. Bates

Biological Sciences Faculty Research and Publications

No abstract provided.

Potent Inhibition Of Mandelate Racemase By Boronic Acids: Boron As A Mimic Of A Carbon Acid Center, Amar Nath Sharma, Lia Grandinetti, Erin R. Johnson, Martin St. Maurice, Stephen L. Bearne

Biological Sciences Faculty Research and Publications

Boronic acids have been successfully employed as inhibitors of hydrolytic enzymes. Typically, an enzymatic nucleophile catalyzing hydrolysis adds to the electrophilic boron atom forming a tetrahedral species that mimics the intermediate(s)/transition state(s) for the hydrolysis reaction. We show that para-substituted phenylboronic acids (PBAs) are potent competitive inhibitors of mandelate racemase (MR), an enzyme that catalyzes a 1,1-proton transfer rather than a hydrolysis reaction. The K_i value for PBA was 1.8 ± 0.1 μM, and p-Cl-PBA exhibited the most potent inhibition (K_i = 81 ± 4 nM), exceeding the binding affinity of the substrate by ∼4 …

Allometric Scaling Laws Linking Biomass And Rooting Depth Vary Across Ontogeny And Functional Groups In Tropical Dry Forest Lianas And Trees, Chris M. Smith-Martin, Xiangtao Xu, David Medvigy, Stefan A. Schnitzer, Jennifer S. Powers

Biological Sciences Faculty Research and Publications

• There are two theories about how allocation of metabolic products occurs. The allometric biomass partitioning theory (APT) suggests that all plants follow common allometric scaling rules. The optimal partitioning theory (OPT) predicts that plants allocate more biomass to the organ capturing the most limiting resource.
• Whole-plant harvests of mature and juvenile tropical deciduous trees, evergreen trees, and lianas and model simulations were used to address the following knowledge gaps: (1) Do mature lianas comply with the APT scaling laws or do they invest less biomass in stems compared to trees? (2) Do juveniles follow the same allocation patterns as mature …

First Report Of Sex Chromosomes In Night Lizards (Scincoidea: Xantusiidae), Stuart V. Nielsen, Brendan John Pinto, IráN Andira Guzmán-Méndez, Tony Gamble

Biological Sciences Faculty Research and Publications

Squamate reptiles (lizards, snakes, and amphibians) are an outstanding group for studying sex chromosome evolution—they are old, speciose, geographically widespread, and exhibit myriad sex-determining modes. Yet, the vast majority of squamate species lack heteromorphic sex chromosomes. Cataloging the sex chromosome systems of species lacking easily identifiable, heteromorphic sex chromosomes, therefore, is essential before we are to fully understand the evolution of vertebrate sex chromosomes. Here, we use restriction site-associated DNA sequencing (RADseq) to classify the sex chromosome system of the granite night lizard, Xantusia henshawi. RADseq is an effective alternative to traditional cytogenetic methods for determining a species’ sex …

Parallel Evolution Of Tobramycin Resistance Across Species And Environments, Michelle R. Scribner, Alfonso Santos-Lopez, Christopher Marshall, Christopher Deitrick, Vaughn S. Cooper

Biological Sciences Faculty Research and Publications

Different species exposed to a common stress may adapt by mutations in shared pathways or in unique systems, depending on how past environments have molded their genomes. Understanding how diverse bacterial pathogens evolve in response to an antimicrobial treatment is a pressing example of this problem, where discovery of molecular parallelism could lead to clinically useful predictions. Evolution experiments with pathogens in environments containing antibiotics, combined with periodic whole-population genome sequencing, can be used to identify many contending routes to antimicrobial resistance. We separately propagated two clinically relevant Gram-negative pathogens, Pseudomonas aeruginosa and Acinetobacter baumannii, in increasing concentrations of …

Lianas Reduce Biomass Accumulation In Early Successional Tropical Forests, Sergio Estrada Villegas, Jefferson S. Hall, Michiel Van Breugel, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Early successional tropical forests could mitigate climate change via rapid accumulation of atmospheric carbon. However, liana (woody vine) abundance and biomass has been increasing in many tropical forests over the past decades, which may slow the speed at which secondary forests accumulate biomass. Lianas decrease biomass accumulation in tropical forests, and may have a particularly strong effect on young forests by stalling tree growth. As forests mature, trees may outgrow or shed lianas, thus escaping some of the negative effects of lianas. Alternatively, lianas may have the strongest effect in older successional forests if the effect of lianas is commensurate …

Macroborer Presence On Corals Increases With Nutrient Input And Promotes Parrotfish Bioerosion, Mallory M. Rice, Rebecca L. Maher, Adrienne M.S. Correa, Holly V. Moeller, Nathan P. Lemoine, Andrew A. Shantz, Deron E. Burkepile, Nyssa J. Silbiger

Biological Sciences Faculty Research and Publications

Bioerosion by reef-dwelling organisms influences net carbonate budgets on reefs worldwide. External bioeroders, such as parrotfish and sea urchins, and internal bioeroders, including sponges and lithophagid bivalves, are major contributors to bioerosion on reefs. Despite their importance, few studies have examined how environmental (e.g., nutrients) or biological drivers (e.g., the actions of other bioeroders) may influence bioeroder dynamics on reefs. For example, internal bioeroders could promote external bioerosion by weakening the coral skeletal matrix. Our study investigated: ( 1) whether nutrient supply influences the dynamics between internal and external bioeroders and ( 2) how the presence of a boring bivalve, …

Local Species Diversity, Β-Diversity And Climate Influence The Regional Stability Of Bird Biomass Across North America, Christopher P. Catano, Trevor S. Fristoe, Joseph A. Lamanna, Jonathan A. Myers

Biological Sciences Faculty Research and Publications

Biodiversity often stabilizes aggregate ecosystem properties (e.g. biomass) at small spatial scales. However, the importance of species diversity within communities and variation in species composition among communities (β-diversity) for stability at larger scales remains unclear. Using a continental-scale analysis of 1657 North American breeding-bird communities spanning 20-years and 35 ecoregions, we show local species diversity and β-diversity influence two components of regional stability: local stability (stability of bird biomass within sites) and spatial asynchrony (asynchronous fluctuations in biomass among sites). We found spatial asynchrony explained three times more variation in regional stability of bird biomass than did local stability. This …

Optimizing Phylogenomics With Rapidly Evolving Long Exons: Comparison With Anchored Hybrid Enrichment And Ultraconserved Elements, Benjamin R. Karin, Tony Gamble, Todd R. Jackman

Biological Sciences Faculty Research and Publications

Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), …

Experimental Psychology Meets Behavioral Ecology: What Laboratory Studies Of Learning Polymorphisms Mean For Learning Under Natural Conditions, And Vice Versa, Brian H. Smith, Chelsea N. Cook

Biological Sciences Faculty Research and Publications

Behavior genetics, and specifically the study of learning and memory, has benefitted immensely from the development of powerful forward- and reverse-genetic methods for investigating the relationships between genes and behavior. Application of these methods in controlled laboratory settings has led to insights into gene–behavior relationships. In this perspective article, we argue that the field is now poised to make significant inroads into understanding the adaptive value of heritable variation in behavior in natural populations. Studies of natural variation with several species, in particular, are now in a position to complement laboratory studies of mechanisms, and sometimes this work can lead …

The Development Of Cephalic Armor In The Tokay Gecko (Squamata: Gekkonidae: Gekko Gecko), Rebecca J. Laver, Cristian H. Morales, Matthew P. Heinicke, Tony Gamble, Kristin Longoria, Aaron M. Bauer, Juan D. Daza

Biological Sciences Faculty Research and Publications

Armored skin resulting from the presence of bony dermal structures, osteoderms, is an exceptional phenotype in gekkotans (geckos and flap-footed lizards) only known to occur in three genera: Geckolepis, Gekko, and Tarentola. The Tokay gecko (Gekko gecko LINNAEUS 1758) is among the best-studied geckos due to its large size and wide range of occurrence, and although cranial dermal bone development has previously been investigated, details of osteoderm development along a size gradient remain less well-known. Likewise, a comparative survey of additional species within the broader Gekko clade to determine the uniqueness of this trait has not …

Distinct Patterns Of Pigment Development Underlie Convergent Hyperpigmentation Between Nocturnal And Diurnal Geckos (Squamata: Gekkota), Aaron H. Griffing, Tony Gamble, Aaron M. Bauer

Biological Sciences Faculty Research and Publications

Background

Evolutionary transitions in temporal niche necessitates specialized morphology, physiology, and behaviors. Diurnal, heliothermic squamates (lizards and snakes) that bask require protection from ultraviolet radiation (UV) that can damage internal organs such as the brain, viscera, and gonads. Many smaller squamates have accomplished this protection by hyperpigmentation of the peritoneum and subcutaneous dorsum. Typically, nocturnal species do not require these protections from ultraviolet light. However, some nocturnal species that exhibit extreme crypsis may be exposed to sunlight and UV and require some means of mediating that damage. One such species is Gekko (Ptychozoon) kuhli, a nocturnal, arboreal …