Biology Commons^™

Welcome To Microbial Informatics And Experimentation, Michael J. Wise, Barry L. Wanner

Department of Biological Sciences Faculty Publications

Microbial Informatics and Experimentation (MIE) is a journal about computers and microbes. We created a new journal to fill a gap for which there is no publication avenue that is particularly geared to computationally-oriented, strongly biologically motivated, pragmatic articles focused on microbes. On the one hand, the bioinformatics journals are generally very computer technical and unlikely to be read by the diverse community of microbiologists. There is also a strong emphasis in bioinformatics literature on human/mammalian systems, though this is a secondary issue. On the other hand, microbial informatics work has appeared in a variety of microbiological publications, but it …

Cooperative And Antagonistic Contributions Of Two Heterochromatin Proteins To Transcriptional Regulation Of The Drosophila Sex Determination Decision, Hui Li, Janel Rodriguez, Youngdong Yoo, Momin Mohammed Shareef, Ramakrishna Badugu, Jamila I. Horabin, Rebecca Kellum

Biology Faculty Publications

Eukaryotic nuclei contain regions of differentially staining chromatin (heterochromatin), which remain condensed throughout the cell cycle and are largely transcriptionally silent. RNAi knockdown of the highly conserved heterochromatin protein HP1 in Drosophila was previously shown to preferentially reduce male viability. Here we report a similar phenotype for the telomeric partner of HP1, HOAP, and roles for both proteins in regulating the Drosophila sex determination pathway. Specifically, these proteins regulate the critical decision in this pathway, firing of the establishment promoter of the masterswitch gene, Sex-lethal (Sxl). Female-specific activation of this promoter, Sxl(Pe), is essential to females, as it provides SXL …

Aintegumenta And Aintegumenta-Like6 Regulate Auxin-Mediated Flower Development In Arabidopsis, Beth A. Krizek

Faculty Publications

Background: Two related genes encoding AP2/ERF-type transcription factors, AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6 (AIL6), are important regulators of floral growth and patterning in Arabidopsis. Evidence suggests that these genes promote several aspects of flower development in response to auxin. To investigate the interplay of ANT, AIL6 and auxin during floral development, I have examined the phenotypic consequences of disrupting polar auxin transport in ant, ail6 and ant ail6 mutants by either genetic or chemical means.

Results: Plants containing mutations in ANT or AIL6 alone or in both genes together exhibit increased sensitivity to disruptions in polar auxin transport. …

Efficient Unfolding Pattern Recognition In Single Molecule Force Spectroscopy Data, Bill Andreopoulos, Dirk Labudde

Faculty Publications, Computer Science

BackgroundSingle-molecule force spectroscopy (SMFS) is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance (F-D) curves. A statistical analysis of a set of F-D curves reveals different unfolding pathways. Information on protein structure, conformation, functional states, and inter- and intra-molecular interactions can be derived.ResultsIn the present work, we propose a pattern recognition algorithm and apply our algorithm to datasets from SMFS experiments on the membrane protein bacterioRhodopsin (bR). We discuss the unfolding pathways found in bR, which are characterised by main peaks and side peaks. A main peak is the result of the pairwise …

Growth Phase-Dependent Gene Regulation In Vivo In Sulfolobus Solfataricus, Melissa Deyoung, Michelle Thayer, John Van Der Oost, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Ribosomal genes are strongly regulated dependent on growth phase in all organisms, but this regulation is poorly understood in Archaea. Moreover, very little is known about growth phase-dependent gene regulation in Archaea. SSV1- based lacS reporter gene constructs containing the Sulfolobus 16S/23S rRNA gene core promoter, the TF55a core promoter, or the native lacS promoter were tested in Sulfolobus solfataricus cells lacking the lacS gene. The 42-bp 16S/23S rRNA gene and 39-bp TF55a core promoters are sufficient for gene expression in S. solfataricus. However, only gene expression driven by the 16S/23S rRNA gene core promoter is dependent on …

Distant Positioning Of Proteasomal Proteolysis Relative To Actively Transcribed Genes, Andrea Scharf, Petar N. Grozdanov, Roman Veith, Ulrich Kubitscheck, U. Thomas Meier, Anna Von Mikecz

Biological Sciences Faculty Research & Creative Works

While it is widely acknowledged that the ubiquitin-proteasome system plays an important role in transcription, little is known concerning the mechanistic basis, in particular the spatial organization of proteasome-dependent proteolysis at the transcription site. Here, we show that proteasomal activity and tetraubiquitinated proteins concentrate to nucleoplasmic microenvironments in the euchromatin. Such proteolytic domains are immobile and distinctly positioned in relation to transcriptional processes. Analysis of gene arrays and early genes in Caenorhabditis elegans embryos reveals that proteasomes and proteasomal activity are distantly located relative to transcriptionally active genes. In contrast, transcriptional inhibition generally induces local overlap of proteolytic microdomains with …

Yeast Bax Inhibitor, Bxi1p, Is An Er-Localized Protein That Links The Unfolded Protein Response And Programmed Cell Death In Saccharomyces Cerevisiae, Nicanor Austriaco, James Cebulski, Joshua Malouin, Nathan Pinches, Vincent Cascio

Biology Faculty Publications

Bax inhibitor-1 (BI-1) is an anti-apoptotic gene whose expression is upregulated in a wide range of human cancers. Studies in both mammalian and plant cells suggest that the BI-1 protein resides in the endoplasmic reticulum and is involved in the unfolded protein response (UPR) that is triggered by ER stress. It is thought to act via a mechanism involving altered calcium dynamics. In this paper, we provide evidence that the Saccharomyces cerevisiae protein encoded by the open reading frame, YNL305C, is a bona fide homolog for BI-1. First, we confirm that yeast cells from two different strain backgrounds lacking YNL305C, …

Camp And Calcium Interactions In Endocrine Cells, Colette Crane

Electronic Theses and Dissertations

Inhibitors of cAMP phosphodiestereses (PDEs) promoted an increase in intracellular [cAMP]_c and an influx of Ca²⁺, in both MMQ pituitary cells and α-Pancreatic cells. The specific targets for PDEs and the domains of PDEs are still unknown. Pituitary MMQ cells were used as a model to test modulation of calcium influx through the L-type calcium channel with PDE inhibitors. cAMP analogs were used to determine cAMP molecular targets. 8-cpt-cAMP initiated an Epac mediated pathway and had strong effects on calcium influx in the cell; suggesting, a relatively strong cAMP target. Experiments of α-Pancreatic cells were done in …

Importance Of Behavior And Morphological Traits For Controlling Body Temperature In Littorinid Snails, Luke Miller, Mark Denny

Faculty Publications, Biological Sciences

For organisms living in the intertidal zone, temperature is an important selective agent that can shape species distributions and drive phenotypic variation among populations. Littorinid snails, which occupy the upper limits of rocky shores and estuaries worldwide, often experience extreme high temperatures and prolonged aerial emersion during low tides, yet their robust physiology—coupled with morphological and behavioral traits—permits these gastropods to persist and exert strong grazing control over algal communities. We use a mechanistic heat-budget model to compare the effects of behavioral and morphological traits on the body temperatures of five species of littorinid snails under natural weather conditions. Model …

Camera Study For Mammalian Carnivore Presence Across Seasons In Montana De Oro State Park, San Luis Obispo County, Ca, Samuel R. Young

Natural Resources Management and Environmental Sciences

Montana de Oro (MDO) is one of the largest state parks in California. Little is known however about its wildlife or their habits. Large predators such as mountain lion (Puma concolor) and black bear (Ursus americanus), and non–native species such as red fox (Vulpes vulpes) and feral pig (Sus scropha) are of management concern because of their potentially dramatic ecological roles. Cameras were deployed at 5 sites along the Coon Creek hiking trail in spring (May 3–June 7), summer (July 15–August 19), and fall (October 10–November 23) sessions with the goal of …

Effects Of Canola And Corn Oil Mimetic On Jurkat Cells, Gabriela Ion, Kayla Fazio, Juliana A. Akinsete, W. Elaine Hardman

Biochemistry and Microbiology

BACKGROUND: The Western diet is high in omega-6 fatty acids and low in omega-3 fatty acids. Canola oil contains a healthier omega 3 to omega 6 ratio than corn oil. Jurkat T leukemia cells were treated with free fatty acids mixtures in ratios mimicking that found in commercially available canola oil (7% α-linolenic, 30% linoleic, 54% oleic) or corn oil (59% linoleic, 24% oleic) to determine the cell survival or cell death and changes in expression levels of inflammatory cytokines and receptors following oil treatment.

METHODS: Fatty acid uptake was assessed by gas chromatography. Cell survival and cell death were …

Isopods Failed To Acclimate Their Thermal Sensitivity Of Locomotor Performance During Predictable Or Stochastic Cooling, Michael W. Sears, Matthew S. Schuler, Brandon S. Cooper, Jonathan J. Storm, Michael J. Angilletta

Publications

Most organisms experience environments that vary continuously over time, yet researchers generally study phenotypic responses to abrupt and sustained changes in environmental conditions. Gradual environmental changes, whether predictable or stochastic, might affect organisms differently than do abrupt changes. To explore this possibility, we exposed terrestrial isopods (Porcellio scaber) collected from a highly seasonal environment to four thermal treatments: (1) a constant 20°C; (2) a constant 10°C; (3) a steady decline from 20° to 10°C; and (4) a stochastic decline from 20° to 10°C that mimicked natural conditions during autumn. After 45 days, we measured thermal sensitivities of running …

Intermittent Preventive Treatment With Sulfadoxine-Pyrimethamine Against Malaria And Anemia In Pregnant Women, Winston Anderson

Department of Biology Faculty Publications

The effectiveness of intermittent preventive treatment during pregnancy with sulfadoxine-pyrimethamine (IPTp-SP) against malaria and anemia is unclear because of the spread of SP-resistant Plasmodium falciparum. This study evaluates the effectiveness of IPTp-SP among pregnant women attending the antenatal clinic at Korle-Bu Teaching Hospital in Accra, Ghana. A cross-sectional study comparing malaria and anemia prevalence among pregnant women using IPTp-SP with non-IPTp-SP users was conducted during June-August 2009. A total of 363 pregnant women (202 of IPTp users and 161 non-IPTp users) were recruited. A total of 15.3% of IPTp users had malaria compared with 44.7% of non-IPTp users (P < 0.001). A total of 58.4% of non-IPTp users were anemic compared with 22.8% of IPTp users (P < 0.001). When we controlled for other variables, the difference in the prevalence of malaria (odds ratio = 0.18, 95% confidence interval = 0.08-0.37) and anemia (odds ratio = 0.20, 95% confidence interval = 0.12-0.34) remained significant. The recommended IPTp-SP regimen is useful in preventing malaria and anemia among pregnant women in Ghana.

A Cellular Automata Model Of Infection Control On Medical Implants, Alicia Prieto-Langarica, Hristo Kojouharov, Benito Chen-Charpentier, Liping Tang

Applications and Applied Mathematics: An International Journal (AAM)

S. epidermidis infections on medically implanted devices are a common problem in modern medicine due to the abundance of the bacteria. Once inside the body, S. epidermidis gather in communities called biofilms and can become extremely hard to eradicate, causing the patient serious complications. We simulate the complex S. epidermidis-Neutrophils interactions in order to determine the optimum conditions for the immune system to be able to contain the infection and avoid implant rejection. Our cellular automata model can also be used as a tool for determining the optimal amount of antibiotics for combating biofilm formation on medical implants.

The Effects Of Neonatal Handling On Adrenocortical Responsiveness, Morphological Development And Corticosterone Binding Globulin In Nestling American Kestrels (Falco Sparverius), Buddy A. Whitman, Creagh W. Breuner, Alfred M. Dufty

Biology Faculty Publications and Presentations

Early developmental experiences play an important role in development of the adult phenotype. We investigated the effects of neonatal handling on the hypothalamic-pituitary-adrenal axis in a free-living avian species, the American kestrel (Falco sparverius). In the handled group (H), kestrel chicks were handled for 15 min/day from hatching until 26 days of age, after which time blood samples were collected for analysis of adrenal responsiveness and corticosterone binding globulin (CBG) levels. The non-handled control group (NH) was left undisturbed until 26 days of age when blood samples were collected and analyzed as above. Handled and NH kestrels did not differ …

Life History Benefits Of Residency In A Partially Migrating Pond-Breeding Amphibian, Kristine L. Grayson, Larissa L. Bailey, Henry M. Wilbur

Biology Faculty Publications

Species with partial migration, where a portion of a population migrates and the other remains residential, provide the opportunity to evaluate conditions for migration and test mechanisms influencing migratory decisions. We conducted a five-year study of two populations of red-spotted newts (Notophthalmus viridescens), composed of individuals that either remain as residents in the breeding pond over the winter or migrate to the terrestrial habitat. We used multistate mark-recapture methods to (1) test for differences in survival probability between migrants and residents, (2) determine if migrants breed every year or skip opportunities for reproduction, and (3) estimate the frequency …

Weaning Onto Solid Foods In Ireland: Some Of The Challenges, A. E. Bennett, A. O'Connor, N. J. Canning, E. M. Keaveney, Katherine Younger, M. Flynn

Conference Papers

No abstract provided.

Factors Affecting Phytoplankton Biodiversity And Toxin Production, Tracey Magrann

Loma Linda University Electronic Theses, Dissertations & Projects

This dissertation reports a survey of water quality, algal biodiversity, and toxin production in Southern California lakes, ponds, bays, and lagoons along the California coastline, in five counties from Santa Barbara to San Diego. Samples were analyzed for pH, electrical conductivity, total dissolved solids, dissolved oxygen, alkalinity, chlorophyll–a, total phosphorous, phosphate, total dissolved phosphorous, dissolved organic and inorganic phosphorous, particulate phosphorous, total nitrogen, total dissolved nitrogen, dissolved organic and inorganic nitrogen, nitrate, nitrite, and ammonium. Algal assays were conducted for phytoplankton identification and numbers, and indices of biodiversity (richness and evenness) were calculated to ascertain relationships between nutrients and algal …

Effects Of Heavy Metal Pollution On The Loggerhead Sea Turtle, Ashley L. Register

Loma Linda University Electronic Theses, Dissertations & Projects

Historically, heavy metal research on sea turtles has been focused on deceased specimens, limiting the ability to determine if the concentrations of heavy metals affected the health of the individuals. More recently, the collection and analysis of blood samples from live turtles has enabled the researcher to investigate the potential health implications of observed metal concentrations. In this thesis, I present two original studies on the blood concentrations of essential and non-essential heavy metals and their potential physiological correlates on the endangered loggerhead sea turtle (Caretta caretta). This work reflects analysis of archived samples collected in 2008 off the southeastern …

Behavioral Ecology, Taxonomy, And Conservation Genetics Of The Bahama Oriole (Icterus Northropi), Melissa R. Price

Loma Linda University Electronic Theses, Dissertations & Projects

In this dissertation, I examined the Bahama Oriole (Icterus northropi) at multiple scales, with the aim of developing a sound management plan for this critically endangered bird. In the first of five studies, I measured plumage variation among four allopatric populations of the former Icterus dominicensis complex in the Caribbean. Diagnosable plumage differences among populations contributed to the subsequent elevation of each of these populations (including northropi) to species status. In the second study, I examined molecular variation in subpopulations of 1. northropi on North Andros, Mangrove Cay, and South Andros, The Bahamas. I identified several patterns of genetic variation …

Shooting Neural Networks Algorithm For Solving Boundary Value Problems In Odes, Kais I. Ibraheem, Bashir M. Khalaf

Applications and Applied Mathematics: An International Journal (AAM)

The objective of this paper is to use Neural Networks for solving boundary value problems (BVPs) in Ordinary Differential Equations (ODEs). The Neural networks use the principle of Back propagation. Five examples are considered to show effectiveness of using the shooting techniques and neural network for solving the BVPs in ODEs. The convergence properties of the technique, which depend on the convergence of the integration technique and accuracy of the interpolation technique are considered.

The Amsterdam Declaration On Fungal Nomenclature, David L. Hawksworth, Pedro W. Crous, Scott A. Redhead, Don R. Reynolds, Robert A. Samson, Keith A. Seifert, John W. Taylor, Michael J. Wingfield, Özlem Abaci, Catherine Aime, Ahmet Asan, Feng Yan Bai, Z. Wilhelm De Beer, Dominik Begerow, Derya Berikten, Teun Boekhout, Peter K. Buchanan, Treena Burgess, Walter Buzina, Lei Cai, Paul F. Cannon, J. Leland Crane, Ulrike Damm, Heide Marie Daniel, Anne D. Van Diepeningen, Irina Druzhinina, Paul S. Dyer, Ursula Eberhardt, Jack W. Fell, Jens C. Frisvad, David M. Geiser, József Geml, David Hibbett

Biology

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes …

Fertilization Narratives In The Art Of Gustav Klimt, Diego Rivera And Frida Kahlo: Repression, Domination And Eros Among Cells, Scott F. Gilbert, S. Brauckmann

Biology Faculty Works

Fertilization narratives are powerful biological stories that can be used for social ends, and 20th-century artists have used fertilization-based imagery to convey political and social ideas. In Danae, Gustav Klimt used an esoteric stage of early human embryos to indicate successful fertilization and the inability of government repression to stifle creativity. In Man, Controller of the Universe, Diego Rivera painted a mural of a man controlling an ovulating ovary, depicting Trotsky's view that society will rationally regulate human fertilization. His former wife, Frida Kahlo, refuted this view in Moses: Nucleus of Creation, wherein she painted images of fertilization and embryo …

Unexpected Accumulation Of Ncm5U And Ncm5S2U In A Trm9 Mutant Suggests An Additional Step In The Synthesis Of Mcm5U And Mcm5S2U, Changchun Chen, Bo Huang, James T. Anderson, Anders S. Byström

Biological Sciences Faculty Research and Publications

Background

Transfer RNAs are synthesized as a primary transcript that is processed to produce a mature tRNA. As part of the maturation process, a subset of the nucleosides are modified. Modifications in the anticodon region often modulate the decoding ability of the tRNA. At position 34, the majority of yeast cytosolic tRNA species that have a uridine are modified to 5-carbamoylmethyluridine (ncm⁵U), 5-carbamoylmethyl-2′-O-methyluridine (ncm⁵Um), 5-methoxycarbonylmethyl-uridine (mcm⁵U) or 5-methoxycarbonylmethyl-2-thiouridine (mcm⁵s²U). The formation of mcm⁵ and ncm⁵ side chains involves a complex pathway, where the last step in formation of …

The Rna Helicase Mtr4p Modulates Polyadenylation In The Tramp Complex, Huijue Jia, Xuying Wang, Fei Liu, Ulf-Peter Guenther, Sukanya Srinivasan, James T. Anderson, Eckhard Jankowsky

Biological Sciences Faculty Research and Publications

Many steps in nuclear RNA processing, surveillance, and degradation require TRAMP, a complex containing the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for decay or trimming by the nuclear exosome. It has been unclear how polyadenylation by TRAMP differs from polyadenylation by conventional poly(A) polymerase, which produces poly(A) tails that stabilize RNAs. Using reconstituted S. cerevisiae TRAMP, we show that TRAMP inherently suppresses poly(A) addition after only 3–4 adenosines. This poly(A) tail length restriction is controlled by Mtr4p. The helicase detects the number of 3′-terminal adenosines and, over several adenylation steps, …

The Conservation And Habitat Ecology Of Antillean Manatees (Trichechus Manatus Manatus) In The Drowned Cayes Area Of Belize, Central America, Katherine Spencer Lacommare

Graduate Doctoral Dissertations

The Drowned Cayes area of Belize, Central America is regionally important for the conservation of Antillean manatees in the Caribbean (Lefebvre et al. 2001; Quintana-Rizzo & Reynolds 2008). These islands are increasingly threatened by human activities such as tourism, development and population growth. The objective of this dissertation is to evaluate manatee habitat use and status in this area. The 5 specific objectives are to examine manatee (1) distribution in the Drowned Cayes, (2) use of seagrass beds and forage selection, (3) resting habitat use and selection (4) response to disturbance, and (5) trends in abundance and to suggest a …

Evolutionary Patterns In Deep-Sea Mollusks, Elizabeth Ellen Boyle

Graduate Doctoral Dissertations

The evolution of deep-sea fauna is poorly known. We know little about the scales of population differentiation, radiation and colonization of the deep sea. This dissertation explores evolution in the deep sea at the level of population differentiation on ocean-wide scales in a gastropod species Benthonella tenella and phylogeny of a deep-sea subfamily of protobranch bivalves, Ledellinae. While working on the phylogeny of the Ledellinae the presence of mitochondrial heteroplasmy was discovered.

Genetic variation was quantified within and among populations of deep-sea gastropod Benthonella tenella to identify the extent of population differentiation and potential mechanisms that might isolate gene pools. …

Establishing An Interdepartmental Fluorescent Microscopy Facility, Marcy Kelly, David Zuzga

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Immunolocalization Of Influenza A Virus And Markers Of Inflammation In The Human Parkinson’S Disease Brain, Troy T. Rohn, Lindsey W. Catlin

Biology Faculty Publications and Presentations

Although much is known regarding the molecular mechanisms leading to neuronal cell loss in Parkinson’s disease (PD), the initiating event has not been identified. Prevailing theories including a chemical insult or infectious agent have been postulated as possible triggers, leading to neuroinflammation. We present immunohistochemical data indicating the presence of influenza A virus within the substantia nigra pars compacta (SNpc) from postmortem PD brain sections. Influenza A virus labeling was identified within neuromelanin granules as well as on tissue macrophages in the SNpc. Further supporting a role for neuroinflammation in PD was the identification of T-lymphocytes that colocalized with an …

Hivtoolbox, An Integrated Web Application For Investigating Hiv, David P. Sargeant, Sandeep Deverasetty, Yang Luo, Angel Villahoz Baleta, Stephanie Zobrist, Viraj Rathnayake, Jacqueline C. Russo, Jay Vyas, Mark A. Muesing, Martin Schiller

Life Sciences Faculty Research

Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid …