Biology Commons^™

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 …

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 …

Mechanisms Of Atp-Dependent Substrate Reduction In The Nitrogenase-Like Dpor Complex, Elliot Irwin Corless

Dissertations (1934 -)

Iron-Sulfur ([Fe-S]) clusters are the most common transient electron carriers in cells and are necessary for basic metabolism of all life. Bacterial systems use two operons (isc and suf ) for the biogenesis and delivery of [Fe-S] clusters to various proteins. Once delivered, they serve as transient electron carriers necessary for both heterotrophic and autotrophic metabolism and reduction/oxidation chemistry. This work utilizes the hetero-octameric Dark operative Protochlorophyllide Oxido-Reductase (DPOR) complex as a platform to investigate [Fe-S] cluster biogenesis and the concerted action of its multiple [Fe-S] clusters and protein subunits. DPOR catalyzes the penultimate step in bacterial chlorophyll synthesis and …

Characterization Of The Mir-44 Family Of Micrornas In The C. Elegans Germline, Katherine Ann Maniates

Dissertations (1934 -)

While numerous individual miRNAs have been detected in the germline, the functions of most other specific miRNAs remain largely unknown. Functions of miRNAs have been difficult to determine as miRNAs often modestly repress target mRNAs and are suggested to sculpt or fine tune gene expression to allow for the robust expression of cell fates. Analysis of newly generated mir-44 family mutants has identified a group of miRNAs that modulate the pathway of germline sex determination in C. elegans. Mutants produce fewer sperm and display an earlier switch to producing oocytes. In the germline, cell fate decisions are made for germline …

Characterizing The Mechanisms Of Ectopic Expression Of Dream Complex Target Genes And The Hta Phenotype In C. Elegans, Jerrin Roy Cherian

Dissertations (1934 -)

It is important for organisms to establish and maintain proper gene expression for normal growth and development. In C. elegans, the DREAM repressor complex helps maintain proper gene expression in somatic cells by repressing germline genes. DREAM complex mutants show close to normal gene expression at 20°C; however, at 26°C, DREAM complex mutants display increased misexpression of germline genes ectopically in the soma and display a distinct High Temperature larval Arrest (HTA) phenotype. It is unclear what gene regulatory mechanisms lead to misexpression of germline genes in somatic cells of DREAM complex mutants. My dissertation research investigated three aspects of …

Anthropogenic Drivers And Ecological Concepts Of Antimicrobial Resistance, Rachelle E. Beattie

Dissertations (1934 -)

Antimicrobial resistance (AMR) is a ubiquitous global health issue driven by the overuse and misuse of antimicrobial compounds in healthcare and veterinary medicine. Both natural and built environments have been recognized as reservoirs of antimicrobial resistant bacteria, genes, and pathogens but the factors that drive increases in their abundance are not well understood, especially in natural environments. The primary goal of this work is to characterize the ecological drivers of antimicrobial resistance in freshwater ecosystems impacted by intensive livestock farms, known contributors of environmental resistance. Kewaunee County, Wisconsin served as an ideal study site for the investigation of the impact …

Investigating The Role Of Lin-35 And The Dream Complex In Preserving Fertility Under Stress In C. Elegans, Frances Virginia Compere

Master's Theses (2009 -)

Organisms are subjected to environments that can fluctuate and cause them stress. Therefore, organisms must have the ability to adapt to the stress to survive and propagate. Temperature stress is becoming an increasingly relevant type of stress due to climate change and is known to affect fertility in many types of organisms including the model organism Caenorhabditis elegans. Here we examine the role of LIN-35, the single C. elegans homolog of the tumor suppressor Retinoblastoma (pRB), in fertility under moderate temperature stress. We found that lin-35 mutants lose fertility more drastically under moderate temperature stress than wildtype worms, and that …

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.

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 …

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 …

Establishing The Roles Of The Dna Binding Domains Of Replication Protein A (Rpa), Nilisha Pokhrel

Dissertations (1934 -)

During DNA metabolic processes such as replication and repair, double-stranded DNA is transiently unwound to expose single-stranded DNA (ssDNA). Such ssDNA intermediates are immediately coated by Replication Protein A (RPA), an essential single-stranded DNA binding protein present in all eukaryotes. RPA binding to ssDNA fulfills four goals: 1. The ssDNA is protected from degradation by endo- and exo-nucleases. 2. A cell-cycle checkpoint signaling cascade is triggered to indicate the presence of ssDNA. 3. RPA recruits other DNA metabolic enzymes on to the ssDNA. 4. Finally, RPA promotes the catalytic activity of the recruited enzyme. The overall objective of my thesis …

Characterization Of De Novo Protein Aggregate Formation In S. Cerevisiae, Douglas Lyke

Dissertations (1934 -)

Misfolded proteins are commonly refolded to a functional conformation or degraded by quality control mechanisms. When misfolded proteins evade quality control, they often form aggregates that are sequestered to specific sites in the cell. The proper sequestration of aggregates is thought to prevent potential dysfunction, toxicity and disease that is often associated with the presence of aggregates. However, the cellular mechanisms that underlie the management of newly formed protein aggregates are unclear. To understand the cellular response to protein aggregate formation, I used the aggregation prone prion domain of the Sup35 protein (Sup35NM) in yeast. Previous work observing GFP-tagged Sup35NM …

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 …

Edaphic Factors And Initial Conditions Influence Successional Trajectories Of Early Regenerating Tropical Dry Forests, Sergio Estrada Villegas, Mario Bailón, Jefferson S. Hall, Stefan A. Schnitzer, Benjamin L. Turner, Trevor Caughlin, Michiel Van Breugel

Biological Sciences Faculty Research and Publications

1. Edaphic factors and initial conditions can regulate the speed of forest succession. Edaphic factors, which include soil chemistry and topography, determine soil resource availability and can filter species as forests mature. Initial plant cover early in succession can determine the rates at which secondary forests change in structure, richness, biomass and composition over time. While some of the effects of edaphic factors and initial conditions on forest succession have been studied, how they simultaneously modify young regenerating tropical forest has rarely been examined.
2. We surveyed 22 young forests plots in Panama for 7 years (11, 6 and 3‐year‐old stands when …

Bromocriptine Improves Glucose Tolerance Independent Of Circadian Timing, Prolactin, Or The Melanocortin-4 Receptor, Sarah N. Framnes-Deboer, Ellen Bakke, Suma Yalamanchili, Hannah Peterson, Darleen A. Sandoval, Randy J. Seeley, Deanna M. Arble

Biological Sciences Faculty Research and Publications

Bromocriptine, a dopamine D2 receptor agonist originally used for the treatment of hyperprolactinemia, is largely successful in reducing hyperglycemia and improving glucose tolerance in type 2 diabetics. However, the mechanism behind bromocriptine’s effect on glucose intolerance is unclear. Here, we tested three hypotheses, that bromocriptine may exert its effects on glucose metabolism by 1) decreasing prolactin secretion, 2) indirectly increasing activity of key melanocortin receptors in the central nervous system, or 3) improving/restoring circadian rhythms. Using a diet-induced obese (DIO) mouse model, we established that a 2-wk treatment of bromocriptine is robustly effective at improving glucose tolerance. …

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 …

Defects In Mating Behavior And Tail Morphology Are The Primary Cause Of Sterility In Caenorhabditis Elegans Males At High Temperature, Emily M. Nett, Nicholas B. Sepulveda, Lisa N. Petrella

Biological Sciences Faculty Research and Publications

Reproduction is a fundamental imperative of all forms of life. For all the advantages sexual reproduction confers, it has a deeply conserved flaw: it is temperature sensitive. As temperatures rise, fertility decreases. Across species, male fertility is particularly sensitive to elevated temperature. Previously, we have shown in the model nematode Caenorhabditis elegans that all males are fertile at 20°C, but almost all males have lost fertility at 27°C. Male fertility is dependent on the production of functional sperm, successful mating and transfer of sperm, and successful fertilization post-mating. To determine how male fertility is impacted by elevated temperature, we analyzed …

Transcriptomic Data Support A Nocturnal Bottleneck In The Ancestor Of Gecko Lizards, Brendan J. Pinto, Stuart V. Nielsen, Tony Gamble

Biological Sciences Faculty Research and Publications

Gecko lizards are a species-rich clade of primarily-nocturnal squamate reptiles. In geckos, adaptations to nocturnality have dramatically reshaped the eye. Perhaps the most notable change is the loss of rod cells in the retina and subsequent “transmutation” of cones into a rod-like morphology and physiology. While many studies have noted the absence of some rod-specific genes, such as the visual pigment Rhodopsin (RH1), these studies have focused on just a handful of species that are nested deep in the gecko phylogeny. Thus, it is not clear whether these changes arose through convergence, are homologous and ubiquitous across geckos, or restricted …

Hypoxia-Inducible Gene Domain 1 Proteins In Yeast Mitochondria Protect Against Proton Leak Through Complex Iv, Ngoc H. Hoang, Vera Strogolova, Jaramys J. Mosley, Rosemary A. Stuart, Jonathan Hosler

Biological Sciences Faculty Research and Publications

Hypoxia-inducible gene domain 1 (HIGD1) proteins are small integral membrane proteins, conserved from bacteria to humans, that associate with oxidative phosphorylation supercomplexes. Using yeast as a model organism, we have shown previously that its two HIGD1 proteins, Rcf1 and Rcf2, are required for the generation and maintenance of a normal membrane potential (ΔΨ) across the inner mitochondrial membrane (IMM). We postulated that the lower ΔΨ observed in the absence of the HIGD1 proteins may be due to decreased proton pumping by complex IV (CIV) or enhanced leak of protons across the IMM. Here we measured the ΔΨ generated by complex …

Embryonic Development Of A Parthenogenetic Vertebrate, The Mourning Gecko (Lepidodactylus Lugubris), Aaron H. Griffing, Thomas J. Sanger, Juan D. Daza, Stuart V. Nielsen, Brendan J. Pinto, Edward L. Stanley, Tony Gamble

Biological Sciences Faculty Research and Publications

Background

One goal of evolutionary developmental biology is to understand the role of development in the origin of phenotypic novelty and convergent evolution. Geckos are an ideal system to study this topic, as they are species‐rich and exhibit a suite of diverse morphologies—many of which have independently evolved multiple times within geckos.

Results

We characterized and discretized the embryonic development of Lepidodactylus lugubris—an all‐female, parthenogenetic gecko species. We also used soft‐tissue μCT to characterize the development of the brain and central nervous system, which is difficult to visualize using traditional microscopy techniques. Additionally, we sequenced and assembled a de …

Do Lianas Shape Ant Communities In An Early Successional Tropical Forest?, Benjamin J. Adams, Evan M. Gora, Michiel Van Breugel, Sergio Estrada-Villegas, Stefan A. Schnitzer, Jefferson S. Hall, Stephen P. Yanoviak

Biological Sciences Faculty Research and Publications

Almost half of lowland tropical forests are at various stages of regeneration following deforestation or fragmentation. Changes in tree communities along successional gradients have predictable bottom‐up effects on consumers. Liana (woody vine) assemblages also change with succession, but their effects on animal succession remain unexplored. Here we used a large‐scale liana removal experiment across a forest successional chronosequence (7–31 years) to determine the importance of lianas to ant community structure. We conducted 1,088 surveys of ants foraging on and living in trees using tree trunk baiting and hand‐collecting techniques at 34 paired forest plots, half of which had all lianas …

C. Elegans Synmuv B Proteins Regulate Spatial And Temporal Chromatin Compaction During Development, Meghan Elizabeth Costello, Lisa N. Petrella

Biological Sciences Faculty Research and Publications

Tissue-specific establishment of repressive chromatin through creation of compact chromatin domains during development is necessary to ensure proper gene expression and cell fate. Caenorhabditis elegans synMuv B proteins are important for the soma/germline fate decision and mutants demonstrate ectopic germline gene expression in somatic tissue, especially at high temperature. We show that C. elegans synMuv B proteins regulate developmental chromatin compaction and that the timing of chromatin compaction is temperature sensitive in both wild type and synMuv B mutants. Chromatin compaction in mutants is delayed into developmental time periods when zygotic gene expression is upregulated and demonstrates an anterior-to-posterior pattern. …

Escaping The Evolutionary Trap? Sex Chromosome Turnover In Basilisks And Related Lizards (Corytophanidae: Squamata), Stuart V. Nielsen, Irán Andira Guzmán-Méndez, Tony Gamble, Madison Blumer, Brendan J. Pinto, Lukáš Kratochvíl, Michail Rovatsos

Biological Sciences Faculty Research and Publications

Most pleurodont lizard families (anoles, iguanas and their relatives), with the exception of the basilisks and casquehead lizards (family Corytophanidae), share homologous XX/XY sex chromosomes, syntenic with chicken chromosome 15. Here, we used a suite of methods (i.e. RADseq, RNAseq and qPCR) to identify corytophanid sex chromosomes for the first time. We reveal that all examined corytophanid species have partially degenerated XX/XY sex chromosomes, syntenic with chicken chromosome 17. Transcriptomic analyses showed that the expression of X-linked genes in the corytophanid, Basiliscus vittatus, is not balanced between the sexes, which is rather exceptional under male heterogamety, and unlike the dosage-balanced …