Life Sciences Commons^™

Copper Oxide Nanoparticles Impact Several Toxicological Endpoints And Cause Neurodegeneration In Caenorhabditis Elegans, Michael Joseph Mashock, Tyler Zanon, Anthony D. Kappell, Lisa N. Petrella, Erik C. Andersen, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Engineered nanoparticles are becoming increasingly incorporated into technology and consumer products. In 2014, over 300 tons of copper oxide nanoparticles were manufactured in the United States. The increased production of nanoparticles raises concerns regarding the potential introduction into the environment or human exposure. Copper oxide nanoparticles commonly release copper ions into solutions, which contribute to their toxicity. We quantified the inhibitory effects of both copper oxide nanoparticles and copper sulfate on C. elegans toxicological endpoints to elucidate their biological effects. Several toxicological endpoints were analyzed in C. elegans, including nematode reproduction, feeding behavior, and average body length. We examined three …

Sleeve Gastrectomy Leads To Weight Loss In The Magel2 Knockout Mouse, Deanna M. Arble, Joshua W. Pressler, Joyce Sorrell, Rachel Wevrick, Darleen A. Sandoval

Biological Sciences Faculty Research and Publications

Background

Prader-Willi syndrome (PWS) is a genetic disorder characterized by hyperphagia, obesity, cardiopulmonary diseases, and increased mortality. Although successful weight loss improves health in PWS, few treatments cause sustained weight loss in obese patients let alone obese individuals with PWS.

Objectives

The present study uses the Magel2 knockout (KO) mouse, an animal model of PWS, to conduct a preclinical study on the efficacy of sleeve gastrectomy(SG) in PWS.

Setting

Academic research laboratory, United States.

Methods

We performed sham or SG surgeries in 24- to 28-week-old male Magel2 KO and wild-type littermate control mice (WT) who had been …

Contribution Of Lianas To Plant Area Index And Canopy Structure In A Panamanian Forest, M. Elizabeth Rodríguez-Ronderos, Gil Bohrer, Arturo Sanchez-Azofeifa, Jennifer S. Powers, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Lianas are an important component of tropical forests, where they reduce tree growth, fecundity, and survival. Competition for light from lianas may be intense; however, the amount of light that lianas intercept is poorly understood. We used a large-scale liana-removal experiment to quantify light interception by lianas in a Panamanian secondary forest. We measured the change in plant area index (PAI) and forest structure before and after cutting lianas (for 4 yr) in eight 80 m × 80 m plots and eight control plots (16 plots total). We used ground-based LiDAR to measure the 3-dimensional canopy structure before cutting lianas, …

Draft Genome Of The Leopard Gecko, Eublepharis Macularius, Zijun Xiong, Fang Li, Qiye Li, Long Zhou, Jiao Zheng, Tony Gamble, Ling Kui, Cai Li, Shengbin Li, Huanming Yang, Guojie Zhang

Biological Sciences Faculty Research and Publications

Background

Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these ‘rules’ and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in ‘typical’ geckos.

Findings

We report high-depth genome sequencing, assembly, and …

Draft Genome Of The Leopard Gecko, Eublepharis Macularius, Zijun Xiong, Fang Li, Long Zhou, Tony Gamble, Jiao Zheng, Ling Kui, Cai Li, Shengbin Li, Huanming Yang, Guojie Zhang

Biological Sciences Faculty Research and Publications

Background

Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these ‘rules’ and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in ‘typical’ geckos.

Findings

We report high-depth genome sequencing, assembly, and …

Muscle Fatigue From The Perspective Of A Single Crossbridge, Edward Patrick Debold, Robert H. Fitts, Christopher W. Sundberg, Thomas M. Nosek

Biological Sciences Faculty Research and Publications

The repeated intense stimulation of skeletal muscle rapidly decreases its force- and motion-generating capacity. This type of fatigue can be temporally correlated with the accumulation of metabolic by-products, including phosphate (P_i) and protons (H⁺). Experiments on skinned single muscle fibers demonstrate that elevated concentrations of these ions can reduce maximal isometric force, unloaded shortening velocity, and peak power, providing strong evidence for a causative role in the fatigue process. This seems to be due, in part, to their direct effect on muscle’s molecular motor, myosin, because in assays using isolated proteins, these ions directly inhibit myosin’s …

The Role Of Acidosis In Fatigue: Pro Perspective, Robert Fitts

Biological Sciences Faculty Research and Publications

No abstract provided.

Negative Cooperativity In The Nitrogenase Fe Protein Electron Delivery Cycle, Karamatullah Danyal, Sudipta Shaw, Taylor R. Page, Simon Duval, Masaki Horitani, Amy R. Marts, Dmitriy Lukoyanov, Dennis R. Dean, Simone Raugei, Brian M. Hoffman, Lance C. Seefeldt, Edwin Antony

Biological Sciences Faculty Research and Publications

Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N₂) to two ammonia (NH₃) molecules through the participation of its two protein components, the MoFe and Fe proteins. Electron transfer (ET) from the Fe protein to the catalytic MoFe protein involves a series of synchronized events requiring the transient association of one Fe protein with each αβ half of the α₂β₂ MoFe protein. This process is referred to as the Fe protein cycle and includes binding of two ATP to an Fe protein, association of an Fe protein with the MoFe protein, ET from the …

The Urea Carboxylase And Allophanate Hydrolase Activities Of Urea Amidolyase Are Functionally Independent, Yi Lin, Cody J. Boese, Martin St. Maurice

Biological Sciences Faculty Research and Publications

Urea amidolyase (UAL) is a multifunctional biotin-dependent enzyme that contributes to both bacterial and fungal pathogenicity by catalyzing the ATP-dependent cleavage of urea into ammonia and CO₂. UAL is comprised of two enzymatic components: urea carboxylase (UC) and allophanate hydrolase (AH). These enzyme activities are encoded on separate but proximally related genes in prokaryotes while, in most fungi, they are encoded by a single gene that produces a fusion enzyme on a single polypeptide chain. It is unclear whether the UC and AH activities are connected through substrate channeling or other forms of direct communication. Here, we use …

Destabilization Of The Ornithine Decarboxylase Mrna Transcript By The Rna-Binding Protein Tristetraprolin, Shannon L. Nowotarski, Sofia Origanti, Suzanne Sass-Kuhn, Lisa M. Shantz

Biological Sciences Faculty Research and Publications

Ornithine decarboxylase (ODC) is the first and usually rate-limiting enzyme in the polyamine biosynthetic pathway. In a normal physiological state, ODC is tightly regulated. However, during neoplastic transformation, ODC expression becomes upregulated. The studies described here show that the ODC mRNA transcript is destabilized by the RNA-binding protein tristetraprolin (TTP). We show that TTP is able to bind to the ODC mRNA transcript in both non-transformed RIE-1 cells and transformed Ras12V cells. Moreover, using mouse embryonic fibroblast cell lines that are devoid of a functional TTP protein, we demonstrate that in the absence of TTP both ODC mRNA stability and …

Effect Of Benzene And Ethylbenzene On The Transcription Of Methyl-Tert-Butyl Ether Degradation Genes Of Methylibium Petroleiphilum Pm1, Geetika Joshi, Radomir Schmidt, Kate M. Scow, Michael S. Denison, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds’ impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes …

Hypothalamic Vitamin D Improves Glucose Homeostasis And Reduces Weight, Stephanie R. Sisley, Deanna M. Arble, Adam P. Chambers, Ruth Gutierrez-Aguilar, Yanlin He, Yong Xu, David Gardner, David D. Moore, Randy J. Seeley, Darleen A. Sandoval

Biological Sciences Faculty Research and Publications

Despite clear associations between vitamin D deficiency and obesity and/or type 2 diabetes, a causal relationship is not established. Vitamin D receptors (VDRs) are found within multiple tissues, including the brain. Given the importance of the brain in controlling both glucose levels and body weight, we hypothesized that activation of central VDR links vitamin D to the regulation of glucose and energy homeostasis. Indeed, we found that small doses of active vitamin D, 1α,25-dihydroxyvitamin D₃ (1,25D₃) (calcitriol), into the third ventricle of the brain improved glucose tolerance and markedly increased hepatic insulin sensitivity, an effect that is …

Trade-Offs Between Water Transport Capacity And Drought Resistance In Neotropical Canopy Liana And Tree Species, Mark E. De Guzman, Louis S. Santiago, Stefan A. Schnitzer, Leonor Álvarez-Cansino

Biological Sciences Faculty Research and Publications

In tropical forest canopies, it is critical for upper shoots to efficiently provide water to leaves for physiological function while safely preventing loss of hydraulic conductivity due to cavitation during periods of soil water deficit or high evaporative demand. We compared hydraulic physiology of upper canopy trees and lianas in a seasonally dry tropical forest to test whether trade-offs between safety and efficiency of water transport shape differences in hydraulic function between these two major tropical woody growth forms. We found that lianas showed greater maximum stem-specific hydraulic conductivity than trees, but lost hydraulic conductivity at less negative water potentials …

Rad51 Nucleoprotein Filament Disassembly Captured Using Fluorescent Plasmodium Falciparum Ssb As A Reporter For Single-Stranded Dna, Eric Parker Davenport, Derek F. Harris, Sofia Origanti, Edwin Antony

Biological Sciences Faculty Research and Publications

Single-stranded DNA binding (SSB) proteins coordinate DNA replication, repair, and recombination and are critical for maintaining genomic integrity. SSB binds to single-stranded DNA (ssDNA) rapidly and with very high affinity making it a useful molecular tool to detect free ssDNA in solution. We have labeled SSB from Plasmodium falciparum (Pf-SSB) with the MDCC (7-diethylamino-3-((((2-maleimidyl)ethyl)amino)-carbonyl)coumarin) fluorophore which yields a four-fold increase in fluorescence upon binding to ssDNA. Pf-SSB^MDCC binding to DNA is unaffected by NaCl or Mg²⁺ concentration and does not display salt-dependent changes in DNA binding modes or cooperative binding on long DNA substrates. These …

Lianas And Soil Nutrients Predict Fine‐Scale Distribution Of Above‐Ground Biomass In A Tropical Moist Forest, Alicia Ledo, Janine B. Illian, Stefan A. Schnitzer, S. Joseph Wright, James W. Dalling, David F.R.P. Burslem

Biological Sciences Faculty Research and Publications

Summary

1. Prediction of carbon dynamics in response to global climate change requires an understanding of the processes that govern the distribution of carbon stocks. Above‐ground biomass (AGB) in tropical forests is regulated by variation in soil fertility, climate, species composition and topography at regional scales, but the drivers of fine‐scale variation in tropical forest AGB are poorly understood. The factors that control the growth and mortality of individual trees may be obscured by the low resolution of studies at regional scales.
2. In this paper, we evaluated the effects of soil nutrients, topography and liana abundance on the fine‐scale spatial distribution …

Evidence That The PI Release Event Is The Rate-Limiting Step In The Nitrogenase Catalytic Cycle, Zhi-Yong Yang, Rhesa Ledbetter, Sudipta Shaw, Natasha Pence, Monika Tokmina-Lukaszewska, Brian Eilers, Qingjuan Guo, Nilisha Pokhrel, Valerie L. Cash, Dennis R. Dean, Edwin Antony, Brian Bothner, John W. Peters, Lance C. Seefeldt

Biological Sciences Faculty Research and Publications

Nitrogenase reduction of dinitrogen (N₂) to ammonia (NH₃) involves a sequence of events that occur upon the transient association of the reduced Fe protein containing two ATP molecules with the MoFe protein that includes electron transfer, ATP hydrolysis, P_i release, and dissociation of the oxidized, ADP-containing Fe protein from the reduced MoFe protein. Numerous kinetic studies using the nonphysiological electron donor dithionite have suggested that the rate-limiting step in this reaction cycle is the dissociation of the Fe protein from the MoFe protein. Here, we have established the rate constants for each of the key …

Supercomplex-Associated Cox26 Protein Binds To Cytochrome C Oxidase, Valentina Strecker, Zibirnisa Kadeer, Juliana Heidler, Cristina-Maria Cruciat, Heike Angerer, Heiko Giese, Kathy Pfeiffer, Rosemary A. Stuart, Ilka Wittig

Biological Sciences Faculty Research and Publications

Here we identified a hydrophobic 6.4 kDa protein, Cox26, as a novel component of yeast mitochondrial supercomplex comprising respiratory complexes III and IV. Multi-dimensional native and denaturing electrophoretic techniques were used to identify proteins interacting with Cox26. The majority of the Cox26 protein was found non-covalently bound to the complex IV moiety of the III–IV supercomplexes. A population of Cox26 was observed to exist in a disulfide bond partnership with the Cox2 subunit of complex IV. No pronounced growth phenotype for Cox26 deficiency was observed, indicating that Cox26 may not play a critical role in the COX enzymology, and we …

Using Rad‐Seq To Recognize Sex‐Specific Markers And Sex Chromosome Systems, Tony Gamble

Biological Sciences Faculty Research and Publications

Next‐generation sequencing methods have initiated a revolution in molecular ecology and evolution (Tautz et al. 2010). Among the most impressive of these sequencing innovations is restriction site‐associated DNA sequencing or RAD‐seq (Baird et al. 2008; Andrews et al. 2016). RAD‐seq uses the Illumina sequencing platform to sequence fragments of DNA cut by a specific restriction enzyme and can generate tens of thousands of molecular genetic markers for analysis. One of the many uses of RAD‐seq data has been to identify sex‐specific genetic markers, markers found in one sex but not the other (Baxter et …

Spa47 Is An Oligomerization-Activated Type Three Secretion System (T3ss) Atpase From Shigella Flexneri, Jamie L. Burgess, Heather B. Jones, Prashant Kumar, Ronald T. Toth Iv, C. Russell Middaugh, Edwin Antony, Nicholas E. Dickenson

Biological Sciences Faculty Research and Publications

Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa47 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 with …

Sexual Differentiation Of Circadian Clock Function In The Adrenal Gland, Ian Kloehn, Savin B. Pillai, Laurel Officer, Claire Klement, Paul J. Gasser, Jennifer A. Evans

Biological Sciences Faculty Research and Publications

Sex differences in glucocorticoid production are associated with increased responsiveness of the adrenal gland in females. However, the adrenal-intrinsic mechanisms that establish sexual dimorphic function remain ill defined. Glucocorticoid production is gated at the molecular level by the circadian clock, which may contribute to sexual dimorphic adrenal function. Here we examine sex differences in the adrenal gland using an optical reporter of circadian clock function. Adrenal glands were cultured from male and female Period2::Luciferase (PER2::LUC) mice to assess clock function in vitro in real time. We confirm that there is a pronounced sex difference in the intrinsic capacity to …

Relating Anaerobic Digestion Microbial Community And Process Function, Kaushik Venkiteshwaran, Benjamin T.W. Bocher, James Maki, Daniel Zitomer

Biological Sciences Faculty Research and Publications

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production …

Liana Canopy Cover Mapped Throughout A Tropical Forest With High-Fidelity Imaging Spectroscopy, David C. Marvin, Gregory P. Asner, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Increasing size and abundance of lianas relative to trees are pervasive changes in Neotropical forests that may lead to reduced forest carbon stocks. Yet the liana growth form is chronically understudied in large-scale tropical forest censuses, resulting in few data on the scale, cause, and impact of increasing lianas. Satellite and airborne remote sensing provide potential tools to map and monitor lianas at much larger spatial and rapid temporal scales than are possible with plot-based forest censuses. We combined high-resolution airborne imaging spectroscopy and a ground-based tree canopy census to investigate whether tree canopies supporting lianas could be discriminated from …

Using Alien Resources: Caribbean Dwarf Geckos Nesting Communally In Invasive Flora, Justin M. Bernstein, Aaron H. Griffing, Juan D. Daza, Tony Gamble, Aaron M. Bauer

Biological Sciences Faculty Research and Publications

No abstract provided.

Would Ecology Fail The Repeatability Test?, Stefan A. Schnitzer, Walter P. Carson

Biological Sciences Faculty Research and Publications

No abstract provided.

Mcra Gene Abundance Correlates With Hydrogenotrophic Methane Production Rates In Full-Scale Anaerobic Waste Treatment Systems, R. L. Morris, Vaibhav Panjabrao Tale, P. P. Mathai, Daniel Zitomer, James Maki

Biological Sciences Faculty Research and Publications

Anaerobic treatment is a sustainable and economical technology for waste stabilization and production of methane as a renewable energy. However, the process is under-utilized due to operational challenges. Organic overload or toxicants can stress the microbial community that performs waste degradation, resulting in system failure. In addition, not all methanogenic microbial communities are equally capable of consistent, maximum biogas production. Opinion varies as to which parameters should be used to monitor the fitness of digester biomass. No standard molecular tools are currently in use to monitor and compare full-scale operations. It was hypothesized that determining the number of gene copies …

Lianas Suppress Seedling Growth And Survival Of 14 Tree Species In A Panamanian Tropical Forest, Laura Martinez Izquierdo, Maria M. Garcia, Jennifer S. Powers, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Lianas are a common plant growth form in tropical forests, where they compete intensely with trees, decreasing tree recruitment, growth, and survival. If the detrimental effects of lianas vary significantly with tree species identity, as is often assumed, then lianas may influence tree species diversity and community composition. Furthermore, recent studies have shown that liana abundance and biomass are increasing relative to trees in neotropical forests, which will likely magnify the detrimental effects of lianas and may ultimately alter tree species diversity, relative abundances, and community composition. Few studies, however, have tested the responses of multiple tree species to the …

Mutations In Mtr4 Structural Domains Reveal Their Important Role In Regulating TrnaI Met Turnover In Saccharomyces Cerevisiae And Mtr4p Enzymatic Activities In Vitro, Yan Li, Joseph Burclaff, James T. Anderson

Biological Sciences Faculty Research and Publications

RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH …

Single-Particle Imaging Reveals Intraflagellar Transport–Independent Transport And Accumulation Of Eb1 In Chlamydomonas Flagella, J. Aaron Harris, Yi Liu, Pinfen Yang, Peter Kner, Karl F. Lechtreck

Biological Sciences Faculty Research and Publications

The microtubule (MT) plus-end tracking protein EB1 is present at the tips of cilia and flagella; end-binding protein 1 (EB1) remains at the tip during flagellar shortening and in the absence of intraflagellar transport (IFT), the predominant protein transport system in flagella. To investigate how EB1 accumulates at the flagellar tip, we used in vivo imaging of fluorescent protein–tagged EB1 (EB1-FP) in Chlamydomonas reinhardtii. After photobleaching, the EB1 signal at the flagellar tip recovered within minutes, indicating an exchange with unbleached EB1 entering the flagella from the cell body. EB1 moved independent of IFT trains, and EB1-FP recovery did …

Copper Oxide Nanoparticles Inhibit The Metabolic Activity Of Saccharomyces Cerevisiae , Michael Joseph Mashock, Anthony D. Kappell, Nadia Hallaj, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Copper oxide nanoparticles (CuO NPs) are used increasingly in industrial applications and consumer products and thus may pose risk to human and environmental health. The interaction of CuO NPs with complex media and the impact on cell metabolism when exposed to sublethal concentrations are largely unknown. In the present study, the short-term effects of 2 different sized manufactured CuO NPs on metabolic activity of Saccharomyces cerevisiae were studied. The role of released Cu²⁺ during dissolution of NPs in the growth media and the CuO nanostructure were considered. Characterization showed that the 28 nm and 64 nm CuO NPs used …

A Reply To Verbeeck And Kearsley: Addressing The Challenges Of Including Lianas In Global Vegetation Models, Stefan A. Schnitzer, Geertje M. F. Van Der Heijden, Jennifer S. Powers

Biological Sciences Faculty Research and Publications

Verbeeck and Kearsley (1) rightfully point out that global vegetation models would greatly benefit from implicitly including the effects of lianas. Recent experimental evidence that lianas substantially reduce the capacity of tropical forests to uptake and store carbon is compelling (2, 3). Furthermore, lianas are increasing relative to trees rapidly in many neotropical forests (4), which will further change the way that forests uptake, cycle, and store carbon.