Biology Commons^™

Mutational Analysis Of The Qrrq Motif In The Yeast Hig1 Type 2 Protein Rcf1 Reveals A Regulatory Role For The Cytochrome C Oxidase Complex, Joshua Garlich, Valentina Strecker, Ilka Wittig, Rosemary A. Stuart

Biological Sciences Faculty Research and Publications

The yeast Rcf1 protein is a member of the conserved family of proteins termed the hypoxia-induced gene (domain) 1 (Hig1 or HIGD1) family. Rcf1 interacts with components of the mitochondrial oxidative phosphorylation system, in particular the cytochrome bc₁(complex III)-cytochrome c oxidase (complex IV) supercomplex (termed III-IV) and the ADP/ATP carrier proteins. Rcf1 plays a role in the assembly and modulation of the activity of complex IV; however, the molecular basis for how Rcf1 influences the activity of complex IV is currently unknown. Hig1 type 2 isoforms, which include the Rcf1 protein, are characterized in part by the presence …

Loss Of The Rna Helicase Skiv2l2 Impairs Mitotic Progression And Replication-Dependent Histone Mrna Turnover In Murine Cell Lines, Alexis Marie Onderak, James T. Anderson

Biological Sciences Faculty Research and Publications

RNA surveillance via the nuclear exosome requires cofactors such as the helicase SKIV2L2 to process and degrade certain noncoding RNAs. This research aimed to characterize the phenotype associated with RNAi knockdown of Skiv2l2 in two murine cancer cell lines: Neuro2A and P19. SKIV2L2 depletion in Neuro2A and P19 cells induced changes in gene expression indicative of cell differentiation and reduced cellular proliferation by 30%. Propidium iodide-based cell-cycle analysis of Skiv2l2 knockdown cells revealed defective progression through the G2/M phase and an accumulation of mitotic cells, suggesting SKIV2L2 contributes to mitotic progression. Since SKIV2L2 targets RNAs to the nuclear exosome for …

De Novo [Psi+] Prion Formation Involves Multiple Pathways To Form Infectious Oligomers, Jaya Sharma, Grett T. Wisniewski, Emily Paulson, Joanna O. Obaoye, Stephen J. Merrill, Anita L. Manogaran

Biological Sciences Faculty Research and Publications

Prion and other neurodegenerative diseases are associated with misfolded protein assemblies called amyloid. Research has begun to uncover common mechanisms underlying transmission of amyloids, yet how amyloids form in vivo is still unclear. Here, we take advantage of the yeast prion, [PSI ⁺], to uncover the early steps of amyloid formation in vivo. [PSI ⁺] is the prion form of the Sup35 protein. While [PSI ⁺] formation is quite rare, the prion can be greatly induced by overexpression of the prion domain of the Sup35 protein. This de novo induction of [PSI …

Two Adjacent Phenylalanines In The Nmda Receptor Glun2a Subunit M3 Domain Interactively Regulate Alcohol Sensitivity And Ion Channel Gating, Hong Ren, Yulin Zhao, Man Wu, Donard S. Dwyer, Robert W. Peoples

Biological Sciences Faculty Research and Publications

The N-methyl-d-aspartate (NMDA) receptor is a key target of ethanol action in the central nervous system. Alcohol inhibition of NMDA receptor function involves small clusters of residues in the third and fourth membrane-associated (M) domains. Previous results from this laboratory have shown that two adjacent positions in the M3 domain, F636 and F637, can powerfully regulate alcohol sensitivity and ion channel gating. In this study, we report that these positions interact with one another in the regulation of both NMDA receptor gating and alcohol action. Using dual mutant cycle analysis, we detected interactions among various substitution mutants at these …

On The Origin Of Frictional Adhesion In Geckos: Small Morphological Changes Lead To A Major Biomechanical Transition In The Genus Gonatodes, Timothy E. Higham, Tony Gamble, Anthony P. Russell

Biological Sciences Faculty Research and Publications

The evolutionary history of vertebrate locomotion is punctuated by innovations that have permitted expansion into novel ecological niches. Frictional adhesion of geckos is an innovation renowned for enabling locomotion on vertical and inverted smooth surfaces. Much is known about the microstructure and function of the fully-expressed gekkotan adhesive apparatus, although how it originated is poorly understood. Therefore, identifying species that exhibit the earliest stages of expression of frictional adhesion will provide significant insights into the evolution of this trait. Our previous investigation of digital proportions, shape, scalation, skeletal form, and subdigital epidermal micro-ornamentation in the genus Gonatodes led us to …

Physiological Regulation And Efficient Xylem Water Transport Regulate Diurnal Water And Carbon Balances Of Tropical Lianas, Ya-Jun Chen, Stefan A. Schnitzer, Yongg-Jiang Zhang, Ze-Xin Fan, Guillermo Goldstein, Kyle W. Tomlinson, Hua Lin, Jiao-Lin Zhang, Kun-Fang Cao

Biological Sciences Faculty Research and Publications

No abstract provided.

Calsequestrin Depolymerizes When Calcium Is Depleted In The Sarcoplasmic Reticulum Of Working Muscle, Carlo Manno, Lourdes Figueroa, Dirk Gillespie, Robert H. Fitts, Chul-Hee Kang, Clara Franzini-Armstrong, Eduardo Rios

Biological Sciences Faculty Research and Publications

Calsequestrin, the only known protein with cyclical storage and supply of calcium as main role, is proposed to have other functions, which remain unproven. Voluntary movement and the heart beat require this calcium flow to be massive and fast. How does calsequestrin do it? To bind large amounts of calcium in vitro, calsequestrin must polymerize and then depolymerize to release it. Does this rule apply inside the sarcoplasmic reticulum (SR) of a working cell? We answered using fluorescently tagged calsequestrin expressed in muscles of mice. By FRAP and imaging we monitored mobility of calsequestrin as [Ca²⁺] in the …

Network Dynamics Mediate Circadian Clock Plasticity, Abdelhalim Azzi, Jennifer A. Evans, Tanya Leise, Jihwan Myung, Toru Takumi, Alec J. Davidson, Steven A. Brown

Biological Sciences Faculty Research and Publications

A circadian clock governs most aspects of mammalian behavior. Although its properties are in part genetically determined, altered light-dark environment can change circadian period length through a mechanism requiring de novo DNA methylation. We show here that this mechanism is mediated not via cell-autonomous clock properties, but rather through altered networking within the suprachiasmatic nuclei (SCN), the circadian “master clock,” which is DNA methylated in region-specific manner. DNA methylation is necessary to temporally reorganize circadian phasing among SCN neurons, which in turn changes the period length of the network as a whole. Interruption of neural communication by inhibiting neuronal firing …

H+- And Na+- Elicited Rapid Changes Of The Microtubule Cytoskeleton In The Biflagellated Green Alga Chlamydomonas, Yi Liu, Mike Visetsouk, Michelle Mynlieff, Hongmin Qin, Karl F. Lechtreck, Pinfen Yang

Biological Sciences Faculty Research and Publications

Although microtubules are known for dynamic instability, the dynamicity is considered to be tightly controlled to support a variety of cellular processes. Yet diverse evidence suggests that this is not applicable to Chlamydomonas, a biflagellate fresh water green alga, but intense autofluorescence from photosynthesis pigments has hindered the investigation. By expressing a bright fluorescent reporter protein at the endogenous level, we demonstrate in real time discreet sweeping changes in algal microtubules elicited by rises of intracellular H⁺ and Na⁺. These results from this model organism with characteristics of animal and plant cells provide novel explanations regarding …

Spatial Sequestration And Oligomer Remodeling During De Novo [Psi+] Formation, Douglas Lyke, Anita L. Manogaran

Biological Sciences Faculty Research and Publications

Prions are misfolded, aggregated, infectious proteins found in a range of organisms from mammals to bacteria. In mammals, prion formation is difficult to study because misfolding and aggregation take place prior to symptom presentation. The study of the yeast prion [PSI⁺], which is the misfolded infectious form of Sup35p, provides a tractable system to monitor prion formation in real time. Recently, we showed that the de novo formation of prion aggregates begins with the appearance of highly mobile cytoplasmic foci, called early foci, which assemble into larger ring or dot structures. We also observed SDS-resistant oligomers during …

Effects Of Fatigue And Recovery On Contractile Properties Of Frog Muscle, Robert H. Fitts, J. O. Holloszy

Biological Sciences Faculty Research and Publications

The contractile properties of frog sartorius muscles were evaluated during development of fatigue and recovery. Muscles were stimulated under anaerobic conditions at a rate of 30 stimuli/min. Twitch tension (P_t) decreased 59% and tetanic tension (P_o) decreased 52% during 15 min of stimulation. Contraction time and one-half relaxation time increased markedly during the first 6 min and then leveled off. The peak rate of twitch tension development (dP/dt) progressively declined to 33% of its initial value. Maximum shortening velocity did not change significantly. Large increases in P_t and twitch dP/dt occurred during …

Stage-Specific Timing Of The Microrna Regulation Of Lin-28 By The Heterochronic Gene Lin-14 In Caenorhabditis Elegans, Jennifer Tsialikas, Mitchell A. Romens, Allison L. Abbott, Eric G. Moss

Biological Sciences Faculty Research and Publications

In normal development, the order and synchrony of diverse developmental events must be explicitly controlled. In the nematode Caenorhabditis elegans, the timing of larval events is regulated by hierarchy of proteins and microRNAs (miRNAs) known as the heterochronic pathway. These regulators are organized in feedforward and feedback interactions to form a robust mechanism for specifying the timing and execution of cell fates at successive stages. One member of this pathway is the RNA binding protein LIN-28, which promotes pluripotency and cell fate decisions in successive stages. Two genetic circuits control LIN-28 abundance: it is negatively regulated by the miRNA …

Synthesis Of N-Acetyl-ᴅ-Quinovosamine In Rhizobium Etli Ce3 Is Completed After Its 4-Keto-Precursor Is Linked To A Carrier Lipid, Tiezheng Li, K. Dale Noel

Biological Sciences Faculty Research and Publications

Bacterial O-antigens are synthesized on lipid carriers before being transferred to lipopolysaccharide core structures. Rhizobium etli CE3 lipopolysaccharide is a model for understanding O-antigen biological function. CE3 O-antigen structure and genetics are known. However, proposed enzymology for CE3 O-antigen synthesis has been examined very little in vitro, and even the sugar added to begin the synthesis is uncertain. A model based on mutagenesis studies predicts that 2-acetamido-2,6-dideoxy-d-glucose (QuiNAc) is the first O-antigen sugar and that genes wreV, wreQ and wreU direct QuiNAc synthesis and O-antigen initiation. Previously, synthesis of UDP-QuiNAc was shown to occur in vitro with a WreV …

Identification Of Multiple Functional Receptors For Tyramine On An Insect Secretory Epithelium, Haiying Zhang, Edward M. Blumenthal

Biological Sciences Faculty Research and Publications

The biogenic amine tyramine (TA) regulates many aspects of invertebrate physiology and development. Although three TA receptor subtypes have been identified (TAR1-3), specific receptors have not been linked to physiological responses in native tissue. In the Malpighian (renal) tubule of Drosophila melanogaster, TA activates a transepithelial chloride conductance, resulting in diuresis and depolarization of the transepithelial potential. In the current work, mutation or RNAi-mediated knockdown in the stellate cells of the tubule of TAR2 (tyrR, CG7431) resulted in a dramatic reduction, but not elimination, of the TA-mediated depolarization. Mutation or knockdown of TAR3 (tyrRII, …

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 …

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 …

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 syndrom (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 maintained on …

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

Biological Sciences Faculty Research and Publications

No abstract provided.

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 …

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 …

Characterization Of The Rcf1 Q-X3-R-X-R-X3-Q Motif And Its Role In Supporting Oxidative Phosphorylation Enzyme Complexes, Joshua Garlich

Dissertations (1934 -)

Mitochondrial respiratory complexes are critical components of cellular energy production that require tight regulation to ensure optimal function. Rcf1 and Rcf2 are mitochondrial proteins that can physically associate with the yeast respiratory complexes III and IV, and the higher-ordered III-IV respiratory supercomplex that also contains the ADP/ATP translocase, AAC. Rcf1 can physically associate with both complex III and IV independently, and can be chemically crosslinked to AAC, indicating a close physical proximity to a predominant regulator of energy flux within the cell. It was therefore hypothesized that Rcf1, through its physical association with complexes III and IV, and its close …

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 …

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 …

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 …

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 …

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 …