Biology Commons^™

Adenosine Triphosphate (Atp) Is A Candidate Signaling Molecule In The Mitochondria-To-Nucleus Retrograde Response Pathway, Feng Zhang, Tammy Pracheil, Janet Thornton, Zhengchang Liu

Biological Sciences Faculty Publications

Intracellular communication from the mitochondria to the nucleus is achieved via the retrograde response. In budding yeast, the retrograde response, also known as the RTG pathway, is regulated positively by Rtg1, Rtg2, Rtg3 and Grr1 and negatively by Mks1, Lst8 and two 14-3-3 proteins, Bmh1/2. Activation of retrograde signaling leads to activation of Rtg1/3, two basic helix-loop-helix leucine zipper transcription factors. Rtg1/3 activation requires Rtg2, a cytoplasmic protein with an N-terminal adenosine triphosphate (ATP) binding domain belonging to the actin/Hsp70/sugar kinase superfamily. The critical regulatory step of the retrograde response is the interaction between Rtg2 and Mks1. Rtg2 binds to …

Matrix Adhesion Polarizes Heart Progenitor Induction In The Invertebrate Chordate Ciona Intestinalis, J. Norton, J. Cooley, A. Islam, C. D. Cota, Bradley Justin Davidson , '91

Biology Faculty Works

Cell-matrix adhesion strongly influences developmental signaling. Resulting impacts on cell migration and tissue morphogenesis are well characterized. However, the in vivo impact of adhesion on fate induction remains ambiguous. Here, we employ the invertebrate chordate Ciona intestinalis to delineate an essential in vivo role for matrix adhesion in heart progenitor induction. In Ciona pre-cardiac founder cells, invasion of the underlying epidermis promotes localized induction of the heart progenitor lineage. We found that these epidermal invasions are associated with matrix adhesion along the pre-cardiac cell/epidermal boundary. Through targeted manipulations of RAP GTPase activity, we were able to manipulate pre-cardiac cell-matrix adhesion. …

Confocal Imaging Of Transmembrane Voltage By Seer Of Di-8-Anepps, Carlo Manno, Lourdes Figueroa, Robert H. Fitts, Eduardo Rios

Biological Sciences Faculty Research and Publications

Imaging, optical mapping, and optical multisite recording of transmembrane potential (V_m) are essential for studying excitable cells and systems. The naphthylstyryl voltage-sensitive dyes, including di-8-ANEPPS, shift both their fluorescence excitation and emission spectra upon changes in V_m. Accordingly, they have been used for monitoring V_m in nonratioing and both emission and excitation ratioing modes. Their changes in fluorescence are usually much less than 10% per 100 mV. Conventional ratioing increases sensitivity to between 3 and 15% per 100 mV. Low sensitivity limits the value of these dyes, especially when imaged with low light systems …

Additional Routes To Staphylococcus Aureus Daptomycin Resistance As Revealed By Comparative Genome Sequencing, Transcriptional Profiling, And Phenotypic Studies, Yang Song, Aileen Rubio, Radheshyam K. Jayaswal, Jared A. Silverman, Brian J. Wilkinson

Faculty Publications – Biological Sciences

Daptomycin is an extensively used anti-staphylococcal agent due to the rise in methicillin-resistant Staphylococcus aureus, but the mechanism(s) of resistance is poorly understood. Comparative genome sequencing, transcriptomics, ultrastructure, and cell envelope studies were carried out on two relatively higher level (4 and 8 mu g/ml(-1)) laboratory-derived daptomycin-resistant strains (strains CB1541 and CB1540 respectively) compared to their parent strain (CB1118; MW2). Several mutations were found in the strains. Both strains had the same mutations in the two-component system genes waIK and agrA. In strain CB1540 mutations were also detected in the ribose phosphate pyrophosphokinase (prs) and polyribonucleotide nucleotidyltransferase genes (pnpA), a …

Cns Control Of Glucose Metabolism: Response To Environmental Challenges, Deanna M. Arble, Darleen A. Sandoval

Biological Sciences Faculty Research and Publications

Over the last 15 years, considerable work has accumulated to support the role of the CNS in regulating postprandial glucose levels. As discussed in the first section of this review, the CNS receives and integrates information from afferent neurons, circulating hormones, and postprandially generated nutrients to subsequently direct changes in glucose output by the liver and glucose uptake by peripheral tissues. The second major component of this review focuses on the effects of external pressures, including high fat diet and changes to the light:dark cycle on CNS-regulating glucose homeostasis. We also discuss the interaction between these different pressures and how …

Microbial Biomineralization Of Iron, Wen Fang

Dissertations and Theses

Iron is a common cation in biomineral sand; it is present for example in magnetite produced by magnetotactic bacteria and in iron sulfides produced by sulfate reducing microorganisms. The work presented in this thesis focused on two types of microorganisms capable of forming iron biominerals. In the first project I have studied the effect of O2 on the respiratory physiology and the formation of magnetosomes by Magnetospirillum magneticum AMB-1. In the second project I have studied the relationship between olivine and the activity of dissimilatory sulfate reducing (DSR) microorganisms. For the first project, I grew cells of AMB-1 in cultures …

Estimated Losses Of Plant Biodiversity Across The U.S. From Historical N Deposition From 1985—2010., Christopher M. Clark, Philip E. Morefield, Frank S. Gilliam, Linda H. Pardo

Biological Sciences Faculty Research

Although nitrogen (N) deposition is a significant threat to herbaceous plant biodiversity worldwide, it is not a new stressor for many developed regions. Only recently has it become possible to estimate historical impacts nationally for the United States. We used 26 years (1985–2010) of deposition data, with ecosystem-specific functional responses from local field experiments and a national critical loads (CL) database, to generate scenario-based estimates of herbaceous species loss. Here we show that, in scenarios using the low end of the CL range, N deposition exceeded critical loads over 0.38, 6.5, 13.1, 88.6, and 222.1 million ha for the Mediterranean …

The Advertisement Call Of The Poorly Known Leptodactylus Tapiti (Anura, Leptodactylidae), Reuber Albuquerque Brandão, Guilherme Fajardo Roldão Álvares, Rafael O. De Sá

Biology Faculty Publications

The genus Leptodactylus consists of approximately 80 species distributed in four nominal groups (Frost 2011). The fuscus group harbors approximately 30 small species with terrestrial nests, deposited in male built burrows on soft soils. Leptodactylus tapiti Sazima & Bokermann 1978 was described from Veadeiros, currently Alto Paraíso municipality, Goiás State, Brazil. The species is restricted to the region of Chapada dos Veadeiros (Frost 2011), where it occurs in areas of water-saturated soils associated with open fields (Sazima & Bokermann 1978). Since its original description, nothing was published about the species, and its advertisement call remains unknown. Herein, we describe its …

Mechanisms Of Signal Transduction By Ethylene: Overlapping And Non-Overlapping Signalling Roles In A Receptor Family, Samina N. Shakeel, Xiaomin Wang, Brad M. Binder, G. Eric Schaller

Dartmouth Scholarship

The plant hormone ethylene regulates growth and development as well as responses to biotic and abiotic stresses. Over the last few decades, key elements involved in ethylene signal transduction have been identified through genetic approaches, these elements defining a pathway that extends from initial ethylene perception at the endoplasmic reticulum to changes in transcriptional regulation within the nucleus. Here, we present our current understanding of ethylene signal transduction, focusing on recent developments that support a model with overlapping and non-overlapping roles for members of the ethylene receptor family. We consider the evidence supporting this model for sub-functionalization within the receptor …

Genomic Reconstruction Of Transcriptional Regulatory Networks In Lactic Acid Bacteria, Dmitri A. Ravcheev, Aaron A. Best, Natalia V. Sernova, Marat D. Kazanov, Pavel S. Novichkov, Dmitri A. Rodionov

Faculty Publications

Background

Genome scale annotation of regulatory interactions and reconstruction of regulatory networks are the crucial problems in bacterial genomics. The Lactobacillales order of bacteria collates various microorganisms having a large economic impact, including both human and animal pathogens and strains used in the food industry. Nonetheless, no systematic genome-wide analysis of transcriptional regulation has been previously made for this taxonomic group.

Results

A comparative genomics approach was used for reconstruction of transcriptional regulatory networks in 30 selected genomes of lactic acid bacteria. The inferred networks comprise regulons for 102 orthologous transcription factors (TFs), including 47 novel regulons for previously uncharacterized …

Traversing Swanton Road, 12th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Dna Damage Repair Genes Controlling Human Papillomavirus (Hpv) Episome Levels Under Conditions Of Stability And Extreme Instability, Terri Edwards, Thomas Vidmar, Kevin Koeller, James Bashkin, Chris Fisher

Chemistry & Biochemistry Faculty Works

DNA damage response (DDR) genes and pathways controlling the stability of HPV episomal DNA are reported here. We set out to understand the mechanism by which a DNA-binding, N-methylpyrrole-imidazole hairpin polyamide (PA25) acts to cause the dramatic loss of HPV DNA from cells. Southern blots revealed that PA25 alters HPV episomes within 5 hours of treatment. Gene expression arrays identified numerous DDR genes that were specifically altered in HPV16 episome-containing cells (W12E) by PA25, but not in HPV-negative (C33A) cells or in cells with integrated HPV16 (SiHa). A siRNA screen of 240 DDR genes was then conducted to identify enhancers …

Undergraduate Research In Biology: Field Studies, Eric Walters

Undergraduate Research Symposium

Chair: Eric Walters, Department of Biological Sciences

Undergraduate Research In Biology: Ticks, Holly Gaff

Undergraduate Research Symposium

Chair: Dr. Holly Gaff, Department of Biological Sciences

Undergraduate Research In Biology: Aquatic, David Gauthier

Undergraduate Research Symposium

Chair: Dr. David Gauthier, Department of Biological Sciences

Isoflurane Increases Neuronal Cell Death Vulnerability By Downregulating Mir-214, Hailiang Yan, Tao Xu, Hongfeng Zhao, Kuo-Chieh Lee, Hoau-Yan Wang, Yan Zhang

Publications and Research

Since accumulating evidence suggests the application of anesthetics may increase the risk of Alzheimer’s disease (AD), we investigated the cytotoxicity of inhaled general anesthesia in neurons and its underlying mechanism. Using primary cultured rat hippocampal neurons as the study model, here we show that isoflurane increases vulnerability to intracellular or extracellular amyloid b with or without serum deprivation. This isoflurane-induced effect is mediated by the downregulation of miR-214 level that lead to an elevated expression of Bax, a prominent target for miR-214. We conclude that isoflurane increases cell death in the presence of amyloid b by increasing Bax level through …

Pb Distribution In Bones From The Franklin Expedition: Synchrotron X-Ray Fluorescence And Laser Ablation/Mass Spectroscopy, Ronald Martin, Steven Naftel, Sheila Macfie, Keith Jones, Andrew J. Nelson

Biology Publications

Synchrotron micro-X-ray Fluorescence has been used to map the metal distribution in selected bone fragments representative of remains associated with the Franklin expedition. In addition, laser ablation mass spectroscopy using a 25 μm diameter circular spot was employed to compare the Pb isotope distributions in small regions within the bone fragments. The X-ray Fluorescence mapping shows Pb to be widely distributed in the bone while the Pb isotope ratios obtained by laser ablation within small areas representative of bone with different Pb exchange rates do not show statistically significant differences. These results are inconsistent with the hypothesis that faulty solder …

Immobile Myosin-Ii Plays A Scaffolding Role During Cytokinesis In Budding Yeast, C. Wloka, Elizabeth Ann Vallen, Lydia Thé , '08, X. Fang, Y. Oh, E. Bi

Biology Faculty Works

Core components of cytokinesis are conserved from yeast to human, but how these components are assembled into a robust machine that drives cytokinesis remains poorly understood. In this paper, we show by fluorescence recovery after photobleaching analysis that Myo1, the sole myosin-II in budding yeast, was mobile at the division site before anaphase and became immobilized shortly before cytokinesis. This immobility was independent of actin filaments or the motor domain of Myo1 but required a small region in the Myo1 tail that is thought to be involved in higher-order assembly. As expected, proteins involved in actin ring assembly (tropomyosin and …

Release Of Avian Neurotensin In Response To Intraluminal Contents In The Duodenum Of Chickens, Teresa F. Degolier, Robert E. Carraway

Biological Sciences Faculty Publications

Peripheral and hepatic-portal plasma levels of neurotensin (NT) in fed and fasted chickens were determined using RIA. Portal levels of NT1-13 (fed = 61.3 ± 3.9 fmol/mL; fasted = 44.5 ± 3.9 fmol/mL) were significantly higher than peripheral levels (fed = 8.2 ± 3.3 fmol/mL; fasted = 7.8 ± 3.0 fmol/mL) collected from the wing vein, indicating that some NT is metabolized in the liver. Portal plasma levels of NT collected from fed birds were also significantly higher than portal plasma levels of NT collected from fasted birds. Neurotensin, as identified by HPLC, exhibited a 2-fold increase in plasma extracts …

S-Adenosyl-L-Methionine Protects The Probiotic Yest, Saccharomyces Boulardii, From Acid-Induced Cell Death, Nicanor Austriaco, Vincent Cascio, Daniel Gittings, Kristen Merloni, David Laprade

Biology Faculty Publications

Background

Saccharomyces boulardii is a probiotic yeast routinely used to prevent and to treat gastrointestinal disorders, including the antibiotic-associated diarrhea caused by Clostridium difficile infections. However, only 1-3% of the yeast administered orally is recovered alive in the feces suggesting that this yeast is unable to survive the acidic environment of the gastrointestinal tract.

Results

We provide evidence that suggests that S. boulardii undergoes programmed cell death (PCD) in acidic environments, which is accompanied by the generation of reactive oxygen species and the appearance of caspase-like activity. To better understand the mechanism of cell death at the molecular level, we …

Honokiol Blocks Store Operated Calcium Entry In Cho Cells Expressing The M3 Muscarinic Receptor: Honokiol And Muscarinic Signaling, Hsiu-Jen Wang, Alexis Martin, Po-Kuan Chao, Rhett A. Reichard, Adam L. Martin, Yue-Wern Huang, Ming-Huan Chan, Robert Aronstam

Biological Sciences Faculty Research & Creative Works

Background: Honokiol, a cell-permeable phenolic compound derived from the bark of magnolia trees and present in Asian herbal teas, has a unique array of pharmacological actions, including the inhibition of multiple autonomic responses. We determined the effects of honokiol on calcium signaling underlying transmission mediated by human M3 muscarinic receptors expressed in Chinese hamster ovary (CHO) cells. Receptor binding was determined in radiolabelled ligand binding assays; changes in intracellular calcium concentrations were determined using a fura-2 ratiometric imaging protocol; cytotoxicity was determined using a dye reduction assay.

Results: Honokiol had a potent (EC50 ≈ 5 μmol/l) inhibitory effect on store …

Poised To Prosper? A Cross-System Comparison Of Climate Change Effects On Native And Non-Native Species Performance, Cascade J. B. Sorte, Ines Ibáñez, Dana M. Blumenthal, Nicole A. Molinari, Luke P. Miller, Edwin D. Grosholz, Jeffrey M. Diez, Carla M. D'Antonio, Julian D. Olden, Sierra J. Jones, Jeffrey S. Dukes

Faculty Publications, Biological Sciences

Climate change and biological invasions are primary threats to global biodiversity that may interact in the future. To date, the hypothesis that climate change will favour non-native species has been examined exclusively through local comparisons of single or few species. Here, we take a meta-analytical approach to broadly evaluate whether non-native species are poised to respond more positively than native species to future climatic conditions. We compiled a database of studies in aquatic and terrestrial ecosystems that reported performance measures of non-native (157 species) and co-occurring native species (204 species) under different temperature, CO2 and precipitation conditions. Our analyses revealed …

A Socratic Method For Surveying Students’ Readiness To Study Evolution, William D. Stansfield

Biological Sciences

Before beginning a series of presentations on evolution, it would be prudent to survey the general level of students’ understanding of prerequisite basic concepts of reproduction, heredity, ontology, and phenotypic diversity so that teachers can avoid devoting time to well-known subjects of general knowledge and can spend more time on subjects that are unknown, forgotten, or misunderstood by most students. This article outlines a Socratic method for surveying and teaching to address these concerns.

Sensory Exploitation And Indicator Models May Explain Red Pelvic Spines In The Brook Stickleback, Culaea Inconstans, Andrew Hodgson, A. Ross Black, Ryan Hull

Biology Faculty Publications

Background: Sensory bias models explaining the evolution of sexually selected traits predict that trait preferences evolve as an artifact of a pre-existing preference for certain components of the environment such as specifically coloured prey. Indicator models, in contrast, predict that sexually selected traits indicate mate condition. We investigate the potential for sensory exploitation and condition indication models to explain the evolution of what appears to be a recently evolved sexually selected trait. Question: Did red pelvic spine coloration in male Turnbull National Wildlife Refuge (TNWR) brook stickleback (Culaea inconstans) evolve to exploit a pre-existing sensory bias for red prey, thus …

Teaching Evolution & The Nature Of Science Via The History Of Debates About The Levels At Which Natural Selection Operates, William D. Stansfield

Biological Sciences

Students should not graduate from high school without understanding that scientific debates are essential components of scientific methodology. This article presents a brief history of ongoing debates regarding the hypothesis that group selection is an evolutionary mechanism, and it serves as an example of the role that debates play in correcting faulty ideas and stimulating new research in the pursuit of extending scientific knowledge.

Ecological Divergence Of A Novel Group Of Chloroflexus Strains Along A Geothermal Gradient, Michael L. Weltzer, Scott R. Miller

Biological Sciences Faculty Publications

Environmental gradients are expected to promote the diversification and coexistence of ecological specialists adapted to local conditions. Consistent with this view, genera of phototrophic microorganisms in alkaline geothermal systems generally appear to consist of anciently divergent populations which have specialized on different temperature habitats. At White Creek (Lower Geyser Basin, Yellowstone National Park), however, a novel, 16S rRNA-defined lineage of the filamentous anoxygenic phototroph Chloroflexus (OTU 10, phylum Chloroflexi) occupies a much wider thermal niche than other 16S rRNA-defined groups of phototrophic bacteria. This suggests that Chloroflexus OTU 10 is either an ecological generalist or, alternatively, a group of cryptic …

A Systematic Revision Of Operclipygus Marseul (Coleoptera, Histeridae, Exosternini), Michael S. Caterino, Alexey K. Tishechkin

Publications

We revise the large Neotropical genus Operclipygus Marseul, in the histerid tribe Exosternini (Histeridae: Histerinae). We synonymize 3 species, move 14 species from other genera, sink the genus Tribalister Horn into Operclipygus, and describe 138 species as new, bringing the total to 177 species of Operclipygus. Keys are provided for the identification of all species, and the majority of the species are illustrated by habitus and male genitalia illustrations. The species are diverse throughout tropical South and Central America, with only a few species extending into the temperate parts of North America. The majority of species can be recognized by …

Comparative Phyloclimatic Analysis And Evolution Of Ecological Niches In The Scimitar Babblers (Aves: Timaliidae: Pomatorhinus), Arpad S. Nyari, Sushma Reddy

Biology: Faculty Publications and Other Works

We present the first extensive and integrative analysis of niche evolution based on climatic variables and a dated molecular phylogeny of a heterogeneous avian group of Southeast Asian scimitar babblers of the genus Pomatorhinus. The four main clades of scimitar babblers have species that co-occur in similar areas across southern Asia but some have diverged at different timeframes, with the most recently evolved clade harboring the highest number of species. Ecological niche models and analysis of contributing variables within a phylogenetic framework indicate instances of convergent evolution of members of different clades onto similar ecological parameter space, as well …

Phytochemistry Predicts Habitat Selection By An Avian Herbivore At Multiple Spatial Scales, Graham G. Frye, John W. Connelly, David D. Musil, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Animal habitat selection is a process that functions at multiple, hierarchically structured spatial scales. Thus multi-scale analyses should be the basis for inferences about factors driving the habitat selection process. Vertebrate herbivores forage selectively on the basis of phytochemistry, but few studies have investigated the influence of selective foraging (i.e., fine-scale habitat selection) on habitat selection at larger scales. We tested the hypothesis that phytochemistry is integral to the habitat selection process for vertebrate herbivores. We predicted that habitats selected at three spatial scales would be characterized by higher nutrient concentrations and lower concentrations of plant secondary metabolites (PSMs) than …

Inhibition Of Herpes Simplex Virus Type 1 With The Modified Green Tea Polyphenol Palmitoyl-Epigallocatechin Gallate, Aline De Oliveira, Sandra Adams, Lee Lee, Sean R. Murray, Stephen D. Hsu, Jeffrey R. Hammond, Douglas Dickinson, Ping Chen, Tin Chun Chu

Department of Biology Faculty Scholarship and Creative Works

Green tea polyphenol epigallocatechin gallate (EGCG) is a strong antioxidant that has previously been shown to reduce the number of plaques in HIV-infected cultured cells. Modified EGCG, palmitoyl-EGCG (p-EGCG), is of interest as a topical antiviral agent for herpes simplex virus (HSV-1) infections. This study evaluated the effect of p-EGCG on HSV-infected Vero cells. Results of cell viability and cell proliferation assays indicate that p-EGCG is not toxic to cultured Vero cells and show that modification of the green tea polyphenol epigallocatechin gallate (EGCG) with palmitate increases the effectiveness of EGCG as an antiviral agent. Furthermore, p-EGCG is a more …