Life Sciences Commons^™

An Archaeal Trna-Synthetase Complex That Enhances Aminoacylation Under Extreme Conditions, Vlatka Godinic-Mikulcic, Jelena Jaric, Corinne D. Hausmann, Michael Ibba, Ivana Weygand-Durasevic

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacyl-tRNA synthetases (aaRSs) play an integral role in protein synthesis, functioning to attach the correct amino acid with its cognate tRNA molecule. AaRSs are known to associate into higher-order multi-aminoacyl-tRNA synthetase complexes (MSC) involved in archaeal and eukaryotic translation, although the precise biological role remains largely unknown. To gain further insights into archaeal MSCs, possible protein-protein interactions with the atypical Methanothermobacter thermautotrophicus seryl-tRNA synthetase (MtSerRS) were investigated. Yeast two-hybrid analysis revealed arginyl-tRNA synthetase (MtArgRS) as an interacting partner of MtSerRS. Surface plasmon resonance confirmed stable complex formation, with a dissociation constant (KD) of 250 nm. Formation of the MtSerRS·MtArgRS complex …

A Fish Out Of Water: Gill And Skin Remodeling Promotes Osmo- And Ionoregulation In The Mangrove Killifish Kryptolebias Marmoratus, Danielle M. Leblanc, Chris M. Wood, Douglas S. Fudge, Patricia A. Wright

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The euryhaline, amphibious mangrove killifish Kryptolebias marmoratus is known to survive weeks out of water in moist environments. We tested the hypothesis that the skin is a site of osmo- and ionoregulation in K. marmoratus. We predicted that under terrestrial conditions, gill and skin remodeling would result in an enhanced role for skin and a diminished role for the gills in osmo- and ionoregulation. Fish were exposed to water—either freshwater (FW, 1‰) or hypersaline water (saltwater [SW], 45‰)—or air over a moist surface of FW or SW for 9 d and then recovered in water. When fish were emersed …

Poxa, Yjek And Elongation Factor P Coordinately Modulate Virulence And Drug Resistance In Salmonella Enterica, William Wiley Navarre, Shicong Zou, Hervé Roy, Jinglin Lucy Xie, Alexei Savchenko, Alexander Singer, Elena Edvokimova, Lynne R. Prost, Runjun Kumar, Michael Ibba, Ferric C. Fang

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report an interaction between poxA, encoding a paralog of lysyl tRNA-synthetase, and the closely linked yjeK gene, encoding a putative 2,3-β-lysine aminomutase, that is critical for virulence and stress resistance in Salmonella enterica. Salmonella poxA and yjeK mutants share extensive phenotypic pleiotropy, including attenuated virulence in mice, an increased ability to respire under nutrient-limiting conditions, hypersusceptibility to a variety of diverse growth inhibitors, and altered expression of multiple proteins, including several encoded on the SPI-1 pathogenicity island. PoxA mediates posttranslational modification of bacterial elongation factor P (EF-P), analogous to the modification of the eukaryotic EF-P homolog, eIF5A, with …

Redox Status Affects The Catalytic Activity Of Glutamyl-Trna Synthetase, Assaf Katz, Ranat Banerjee, Merly De Armas, Michael Ibba, Omar Orellana

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Glutamyl-tRNA synthetases (GluRS) provide Glu-tRNA for different processes including protein synthesis, glutamine transamidation and tetrapyrrole biosynthesis. Many organisms contain multiple GluRSs, but whether these duplications solely broaden tRNA specificity or also play additional roles in tetrapyrrole biosynthesis is not known. Previous studies have shown that GluRS1, one of two GluRSs from the extremophile Acidithiobacillus ferrooxidans, is inactivated when intracellular heme is elevated suggesting a specific role for GluRS1 in the regulation of tetrapyrrole biosynthesis. We now show that, in vitro, GluRS1 activity is reversibly inactivated upon oxidation by hemin and hydrogen peroxide. The targets for oxidation-based inhibition were …

Effects Of Variable Oceanographic Conditions On Forage Fish Lipid Content And Fatty Acid Composition In The Northern California Current, Marisa N. C. Litz, Richard D. Brodeur, Robert L. Emmett, Selina S. Heppell, Rosalee S. Hellberg, Linda O'Higgins, Matthew S. Morris

Food Science Faculty Articles and Research

Lipids and fatty acids (FA) were investigated in 4 species of forage fish: northern anchovy Engraulis mordax, Pacific sardine Sardinops sagax, Pacific herring Clupea pallasi, and whitebait smelt Allosmerus elongatus, for their ability to serve as biological indicators of ocean conditions in the California Current large marine ecosystem (CCLME). Samples were collected during the oceanographically contrasting years of 2005 and 2006. Upwelling was severely curtailed in the spring and early summer of 2005, leading to delayed biological productivity, whereas upwelling was relatively normal in spring 2006. Principal components analysis described 78% of the variance within the …

Protein Evolution Via Amino Acid And Codon Elimination, Lise Goltermann, Marie Sofie Yoo Larsen, Ranat Banerjee, Andreas C. Joerger, Michael Ibba, Thomas Bentin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background
Global residue-specific amino acid mutagenesis can provide important biological insight and generate proteins with altered properties, but at the risk of protein misfolding. Further, targeted libraries are usually restricted to a handful of amino acids because there is an exponential correlation between the number of residues randomized and the size of the resulting ensemble. Using GFP as the model protein, we present a strategy, termed protein evolution via amino acid and codon elimination, through which simplified, native-like polypeptides encoded by a reduced genetic code were obtained via screening of reduced-size ensembles.

Methodology/Principal Findings
The strategy involves combining a sequential …

How The Sequence Of A Gene Can Tune Its Translation, Kurt Fredrick, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Sixty-one codons specify 20 amino acids, offering cells many options for encoding a polypeptide sequence. Two new studies (Cannarrozzi et al., 2010, Tuller et al., 2010) now foster the idea that patterns of codon usage can control ribosome speed, fine-tuning translation to increase the efficiency of protein synthesis.

Distribution Of Allatostatin C-Like Immunoreactivity In The Central Nervous System Of The Copepod Crustacean Calanus Finmarchicus, Caroline H. Wilson, Andrew E. Christie

Health Sciences and Kinesiology Faculty Articles

The C-type allatostatins (C-ASTs) are a family of highly pleiotropic arthropod neuropeptides. In crustaceans, transcriptomic/mass spectral studies have identified C-ASTs in the nervous systems of many species; the cellular distributions of these peptides remain unknown. Here, the distribution of C-AST was mapped in the nervous system of the copepod Calanus finmarchicus, the major contributor to the North Atlantic’s zooplanktonic biomass; C-AST-immunopositive neurons were identified in the protocerebrum, in several peripheral ganglia associated with feeding appendages, and in the ganglia controlling the swimming legs, with immunopositive axons present throughout the ventral nerve cord. In addition, axons innervating the dorsal longitudinal …

Family Members' Influence On Family Meal Vegetable Choices, Tionni R. Wenrich, J. Lynne Brown, Michelle Miller-Day, Kevin J. Kelley, Eugene J. Lengerich

Communication Faculty Articles and Research

Objective—Characterize the process of family vegetable selection (especially cruciferous, deep orange, and dark green leafy vegetables); demonstrate the usefulness of Exchange Theory (how family norms and past experiences interact with rewards and costs) for interpreting the data.

Design—Eight focus groups, two with each segment (men/women vegetable-likers/dislikers based on a screening form). Participants completed a vegetable intake form.

Setting—Rural Appalachian Pennsylvania.

Participants—61 low-income, married/cohabiting men (n=28) and women (n=33).

Analysis—Thematic analysis within Exchange Theory framework for qualitative data. Descriptive analysis, t-tests and chi-square tests for quantitative data.

Results—Exchange Theory proved useful for understanding that regardless …

Different Training Volumes Yield Equivalent Increases In Bmd, R. A. Pierce, L. C. Lee, C. P. Ahles, S. M. Shdo, S. V. Jaque, Ken D. Sumida

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The purpose of this study was to determine if an exercise threshold existed in stimulating an elevation in bone mineral density (BMD), via resistance training, during the growth period in male rats. 27 male rats were randomly divided into Control (Con, n = 9), 3 ladder climb resistance trained group (3LC, n = 9), and 6 ladder climb resistance trained group (6LC, n = 9). The 3LC and 6LC groups were conditioned to climb a vertical ladder with weights appended to their tail 3 days/wk for a total of 6 wks, but the 6LC group performed significantly more work than …

Web-Based, Participant-Driven Studies Yield Novel Genetic Associations For Common Traits, Nicholas Eriksson, J. Michael Macpherson, Joyce Y. Tung, Lawrence S. Hon, Brian Naughton, Serge Saxonov, Linda Avey, Anne Wojcicki, Itsik Pe'er, Joanna Mountain

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design. Here …

Harvesting Victory: Education, Student/Farmworker Solidarity, And The Growth Of An Organizing Model, Melody González, Natasha Noriega-Goodwin, Marc Rodrigues, Jorge Rodríguez, Marina Sáenz-Luna, Sean Sellers, John-Michael Torres, Kandace Vallejo

Education Faculty Books and Book Chapters

"On May 23, 2008, farmworkers and student activists gathered with corporate executives, U.S. Senator Bernie Sanders (Vermont), and dozens of members of the local and national media for a standing room-only press conference under the dome of the U.S. Capitol announcing an accord between the Burger King fast food corporation and a Florida farmworker organization, the Coalition of lmmokalee Workers (CIW). Weeks earlier, Burger King made headlines when a spate of malicious Internet postings defaming the CIW and its supporters were traced back to a company executive, and news surfaced that the company hired an unlicensed private investigator to infiltrate …

Equal Bmd After Daily Or Triweekly Exercise In Growing Rats, B. D. Kayser, J. K. Godfrey, R. M. Cunningham, R. A. Pierce, S. V. Jaque, Ken D. Sumida

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The purpose of this study was to examine the efficacy of continuous resistance training (3 days/wk) compared to interrupted resistance training where 20-24 h separated an exercise bout (i.e. 6 days/wk) for enhancing bone mineral density (BMD) in growing male rats. The total volume of work performed per week between the two resistance training programs was equivalent by design. Young male rats were randomly divided into Control (Con, n = 9), 3 days/wk resistance trained group (RT3, n = 9), and 6 days/wk resistance trained group (RT6, n = 9). The RT3 and RT6 groups were conditioned to climb a …

Interspecific Variation In Palatability Suggests Cospecialization Of Antipredator Defenses In Sea Hares, Kimberly K. Takagi, Nadia N. Ono, William G. Wright

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Prey species often deploy different kinds of antipredator defenses, which can interact with each other in ways that are not yet completely understood. Much research into these interactions has utilized gastropod mollusks, usually focusing (in part) on the protective utility of the gastropod shell. This makes the evolutionary reduction of the shell in the opisthobranch gastropods (marine slugs) particularly interesting. This loss of protective function of the shell is associated with the evolution of alternative defenses. Particularly well studied are chemical defenses, especially those using secondary metabolites derived from food resources. As a first step toward understanding interspecific variation in …

Gene Delivery In The Equine Cornea: A Novel Therapeutic Strategy, Dylan G. Buss, Ajay Sharma, Elizabeth A. Giuliano, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

Objective—To determine if hybrid adeno-associated virus serotype 2/5 (AAV5) vector can effectively deliver foreign genes into the equine cornea without causing adverse side effects. The aims of this study were to: (i) evaluate efficacy of AAV5 to deliver therapeutic genes into equine corneal fibroblasts (ECFs) using enhanced green fluorescent protein (EGFP) marker gene and (ii) establish the safety of AAV5 vector for equine corneal gene therapy.

Animal Material—Primary ECF cultures were harvested from healthy donor equine corneas. Cultures were maintained at 370C in humidified atmosphere with 5% CO2.

Procedure—AAV5 vector expressing EGFP under control of hybrid cytomegalovirus (CMV) + chicken …

Vector Delivery Technique Affects Gene Transfer In The Cornea In Vivo, Rajiv R. Mohan, Ajay Sharma, Tyler C. Cebulko, Ashish Tandon

Pharmacy Faculty Articles and Research

Purpose: This study tested whether controlled drying of the cornea increases vector absorption in mouse and rabbit corneas in vivo and human cornea ex vivo, and studied the effects of corneal drying on gene transfer, structure and inflammatory reaction in the mouse cornea in vivo.

Methods: Female C57 black mice and New Zealand White rabbits were used for in vivo studies. Donor human corneas were used for ex vivo experiments. A hair dryer was used for drying the corneas after removing corneal epithelium by gentle scraping. The corneas received no, once, twice, thrice, or five times warm air for …

Impaired M3 And Enhanced M2 Muscarinic Receptor Contractile Function In A Streptozotocin Model Of Mouse Diabetic Urinary Bladder, K. J. Pak, Rennolds S. Ostrom, M. Matsui, F. J. Ehlert

Pharmacy Faculty Articles and Research

We investigated the contractile roles of M2 and M3 muscarinic receptors in urinary bladder from streptozotocin-treated mice. Wild-type and M2 muscarinic receptor knockout (M2 KO) mice were given a single injection of vehicle or streptozotocin (125 mg kg−1) 2–24 weeks prior to bladder assays. The effect of forskolin on contractions elicited to the muscarinic agonist, oxotremorine-M, was measured in isolated urinary bladder (intact or denuded of urothelium). Denuded urinary bladder from vehicle-treated wild-type and M2 KO mice exhibited similar contractile responses to oxotremorine-M, when contraction was normalized relative to that elicited by KCl (50 mM). Eight to 9 weeks after …

Aav Serotype Influences Gene Transfer In Corneal Stroma In Vivo, Ajay Sharma, Jonathan C. K. Tovey, Arkasubhra Ghosh, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

This study evaluated the cellular tropism and relative transduction efficiency of three AAV serotypes, AAV6, AAV8 and AAV9, for corneal gene delivery using mouse cornea in vivo and donor human cornea ex vivo. The AAV6, AAV8 and AAV9 serotypes having AAV2 plasmid encoding for alkaline phosphatase (AP) gene were generated by transfecting HEK293 cell line with pHelper, pARAP4 and pRep/Cap plasmids. Viral vectors (109 vg/μl) were topically applied onto mouse cornea in vivo and human cornea ex vivo after removing the epithelium. Human corneas were processed for transgene delivery at day 5 after viral vector application. Mouse corneas were harvested …

Estimation Of Effective Plant Area Index For South Korean Forests Using Lidar System, D. A. Kwak, W. K. Lee, Menas Kafatos, Y. Son, H. K. Cho, S. H. Lee

Mathematics, Physics, and Computer Science Faculty Articles and Research

Light Detection and Ranging (LiDAR) systems can be used to estimate both vertical and horizontal forest structure. Woody components, the leaves of trees and the understory can be described with high precision, using geo-registered 3D-points. Based on this concept, the Effective Plant Area Indices (PAIe) for areas of Korean Pine (Pinus koraiensis), Japanese Larch (Larix leptolepis) and Oak (Quercus spp.) were estimated by calculating the ratio of intercepted and incident LIDAR laser rays for the canopies of the three forest types. Initially, the canopy gap fraction (GLiDAR) was generated by extracting the LiDAR data reflected from the canopy surface, or …

Major Challenges For The Modern Chemistry In Particular And Science In General, Vuk Uskoković

Pharmacy Faculty Articles and Research

In the past few hundred years, science has exerted an enormous influence on the way the world appears to human observers. Despite phenomenal accomplishments of science, science nowadays faces numerous challenges that threaten its continued success. As scientific inventions become embedded within human societies, the challenges are further multiplied. In this critical review, some of the critical challenges for the field of modern chemistry are discussed, including: (a) interlinking theoretical knowledge and experimental approaches; (b) implementing the principles of sustainability at the roots of the chemical design; (c) defining science from a philosophical perspective that acknowledges both pragmatic and realistic …

Efficacy And Safety Of Mitomycin C As An Agent To Treat Corneal Scarring In Horses Using An In Vitro Model, Dylan G. Buss, Ajay Sharma, Elizabeth A. Giuliano, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

Objective—Mitomycin C (MMC) is used clinically to treat corneal scarring in human patients. We investigated the safety and efficacy of MMC to treat corneal scarring in horses by examining its effects at the early and late stages of disease using an in-vitro model.

Procedure—An in-vitro model of equine corneal fibroblast (ECF) developed was used. The equine corneal fibroblast or myofibroblast cultures were produced by growing primary ECF in the presence or absence of transforming growth factor beta-1 (TGFβ1) under serum-free conditions. The MMC dose for the equine cornea was defined with dose-dependent trypan blue exclusion and MTT [(3-4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assays …

Functionality, Parsimony, Discovery, Avoiding Hamartia: How Evolutionary Perspectives Are Changing Psychology, Brooke N. Jenkins, Aaron T. Goetz

Psychology Faculty Articles and Research

Evolutionary psychology offers an important perspective to scientific psychology. Evolutionary psychology, in its short existence, has added an abundance of knowledge to the social sciences, let alone psychology. The study of human cognition and behavior remains incomplete without an evolutionary perspective. Here, we argue that evolutionary psychology uniquely provides a complete understanding of scientific psychology because it explains the functions of our psychological traits, provides us with the most parsimonious explanation of many psychological phenomena, predicts undocumented phenomena, and possibly allows us to avoid the downfalls of some of our contemptible evolved psychological mechanisms.

Prospects And Pits On The Path Of Biomimetics: The Case Of Tooth Enamel, Vuk Uskoković

Pharmacy Faculty Articles and Research

This review presents a discourse on challenges in understanding and imitating the process of amelogenesis in vitro on the molecular scale. In light of the analysis of imitation of the growth of dental enamel, it also impends on the prospects and potential drawbacks of the biomimetic approach in general. As the formation of enamel proceeds with the protein matrix guiding the crystal growth, while at the same time conducting its own degradation and removal, it is argued that three aspects of amelogenesis need to be induced in parallel: a) crystal growth; b) protein assembly; c) proteolytic degradation. A particular emphasis …

Isolation And Cultivation Of Equine Corneal Keratocytes, Fibroblasts And Myofibroblasts, Dylan G. Buss, Elizabeth A. Giuliano, Ajay Sharma, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

Objective—To establish an in vitro model for the investigation of equine corneal wound healing. To accomplish this goal, a protocol to isolate and culture equine corneal keratocytes, fibroblasts and myofibroblasts was developed.

Animal material—Equine corneal buttons were aseptically harvested from healthy research horses undergoing humane euthanasia for reasons unrelated to this study. Slit-lamp biomicroscopy was performed prior to euthanasia by a board-certified veterinary ophthalmologist to ensure that all samples were harvested from horses free of anterior segment disease.

Procedure—Equine corneal stroma was isolated using mechanical techniques and stromal subsections were then cultured. Customized media at different culture conditions was used …

Localization Of Angiotensin Converting Enzyme In Rabbit Cornea And Its Role In Controlling Corneal Angiogenesis In Vivo, Ajay Sharma, Daniel I. Bettis, John W. Cowden, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

Purpose: The renin angiotensin system (RAS) has been shown to modulate vascular endothelial growth factor and angiogenesis. In this study we investigated (i) the existence of the RAS components angiotensin converting enzyme (ACE) and angiotensin II receptors (AT1 and AT2) in the rabbit cornea using in vitro and ex vivo models and (ii) the effect of enalapril, an ACE inhibitor, to inhibit angiogenesis in rabbit cornea in vivo.

Methods: New Zealand White rabbits were used. Cultured corneal fibroblasts and corneal epithelial cells were used for RNA isolation and cDNA preparation using standard molecular biology techniques. PCR was performed to …

Chemosensitization Of Cancer Cells By Sirna Using Targeted Nanogel Delivery, Erin B. Dickerson, William H. Blackburn, Michael H. Smith, Laura B. Kapa, L. Andrew Lyon, John F. Mcdonald

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background: Chemoresistance is a major obstacle in cancer treatment. Targeted therapies that enhance cancer cell sensitivity to chemotherapeutic agents have the potential to increase drug efficacy while reducing toxic effects on untargeted cells. Targeted cancer therapy by RNA interference (RNAi) is a relatively new approach that can be used to reversibly silence genes in vivo by selectively targeting genes such as the epidermal growth factor receptor (EGFR), which has been shown to increase the sensitivity of cancer cells to taxane chemotherapy. However, delivery represents the main hurdle for the broad development of RNAi therapeutics.

Methods: We report here …

Lobster Attack Induces Sensitization In The Sea Hare, Aplysia Californica, Amanda J. Watkins, Daniel A. Goldstein, Lucy C. Lee, Christina J. Pepino, Scott L. Tillett, Francis E. Ross, Elizabeth M. Wilder, Virginia A. Zachary, William G. Wright

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Studies of the neural mechanisms of learning, especially of sensitization, have benefitted from extensive research on the model species, Aplysia californica (hereafter Aplysia). Considering this volume of literature on mechanisms, it is surprising that our understanding of the ecological context of sensitization in Aplysia is completely lacking. Indeed, the widespread use of strong electric shock to induce sensitization (an enhancement of withdrawal reflexes following noxious stimulation) is completely unnatural and leaves unanswered the question of whether this simple form of learning has any ecological relevance. We hypothesized that sublethal attack by a co-occurring predator, the spiny lobster, Panulirus interruptus, might …