Digital Commons Network^™

Modulation Of Yeast Genome Expression In Response To Defective Rna Polymerase Iii-Dependent Transcription, Christine Conesa, Roberta Ruotolo, Pascal Soularue, Tiffany A. Simms, David Donze, André Sentenac, Giorgio Dieci

Faculty Publications

We used genome-wide expression analysis in Saccharomyces cerevisiae to explore whether and how the expression of protein-coding, RNA polymerase (Pol) II-transcribed genes is influenced by a decrease in RNA Pol III-dependent transcription. The Pol II transcriptome was characterized in four thermosensitive, slow-growth mutants affected in different components of the RNA Pol III transcription machinery. Unexpectedly, we found only a modest correlation between altered expression of Pol II-transcribed genes and their proximity to class III genes, a result also confirmed by the analysis of single tRNA gene deletants. Instead, the transcriptome of all of the four mutants was characterized by increased …

Cellular Efflux Of Auxin Catalyzed By The Arabidopsis Mdr/Pgp Transporter Atpgp1, Markus Geisler, Joshua J. Blakeslee, Rodolphe Bouchard, Ok Ran Lee, Vincent Vincenzetti, Anindita Bandyopadhyay, Boosaree Titapiwatanakun, Wendy Ann Peer, Aurèlien Bailly, Elizabeth L. Richards, Karin F.K. Ejendal, Aaron P. Smith, Célia Baroux, Ueli Grossniklaus, Axel Müller, Christine A. Hrycyna, Robert Dudler, Angus S. Murphy, Enrico Martinoia

Faculty Publications

Directional transport of the phytohormone auxin is required for the establishment and maintenance of plant polarity, but the underlying molecular mechanisms have not been fully elucidated. Plant homologs of human multiple drug resistance/P-glycoproteins (MDR/PGPs) have been implicated in auxin transport, as defects in MDR1 (AtPGP19) and AtPGP1 result in reductions of growth and auxin transport in Arabidopsis (atpgp1, atpgp19), maize (brachytic2) and sorghum (dwarf3). Here we examine the localization, activity, substrate specificity and inhibitor sensitivity of AtPGP1. AtPGP1 exhibits non-polar plasma membrane localization at the shoot and root apices, as well as polar localization above the root apex. Protoplasts from …

Is Adventist Theology Compatible With Evolutionary Theory?, Fernando L. Canale

Faculty Publications

No abstract provided.

Phylogenetic Analysis Of Large Sequence Data Sets, Hyrum Carroll, Mark J. Clement, Keith Crandall, Quinn O. Snell

Faculty Publications

Phylogenetic analysis is an integral part of biological research. As the number of sequenced genomes increases, available data sets are growing in number and size. Several algorithms have been proposed to handle these larger data sets. A family of algorithms known as disc covering methods (DCMs), have been selected by the NSF funded CIPRes project to boost the performance of existing phylogenetic algorithms. Recursive Iterative Disc Covering Method 3 (Rec-I-DCM3), recursively decomposes the guide tree into subtrees, executing a phylogenetic search on the subtree and merging the subtrees, for a set number of iterations. This paper presents a detailed analysis …

Structure Of Human Thymidylate Synthase Under Low-Salt Conditions, Leslie L. Lovelace, Wladek Minor, Lukasz Lebioda

Faculty Publications

Human thymidylate synthase, a target in cancer chemotherapy, was crystallized from PEG 3350 with 30 mM ammonium sulfate (AS) in the crystallization medium. The crystals are isomorphous with the high-salt crystals (~2.0 M AS) and the structure has been solved and refined (R = 22.6%, Rfree = 24.3%) at 1.8 Å resolution. The high- and low-AS-concentration structures are quite similar, with loop 181-197 is in the inactive conformation. Also, residues 95-106 and 129-135 (eukaryotic inserts region) show high mobility as assessed by poor electron density and high values of crystallographic temperature factors (residues 1-25 and 108-129 are disordered in both …

Hurricane-Forced Upwelling And Chlorophyll A Enhancement Within Cold-Core Cyclones In The Gulf Of Mexico, Nan D. Walker, Robert R. Leben, Shreekanth Balasubramanian

Faculty Publications

Clear skies, subsequent to Hurricane Ivan's passage across the Gulf of Mexico in September 2004, provided a unique opportunity to investigate upper ocean responses to a major hurricane. Oceanic cyclonic circulation was rapidly intensified by the hurricane's wind field (59-62 m s^-1), maximizing upwelling and surface cooling (3-7°C) in two large areas along Ivan's track. Upward isothermal displacements of 50-65 m, computed from wind stress and sea surface height changes, caused rapid ventilation of thermoclines and nutriclines, leading to phytoplankton blooms with peak concentrations 3-4 days later. Wind speed changes along Ivan's track demonstrated that the cool waters …

Distribution Of Hydrogen Peroxide In The Northwest Pacific Ocean, Jinchun Yuan, Alan M. Shiller

Faculty Publications

[1] Hydrogen peroxide (H2O2) is a reactive oxygen intermediate involved in the cycling of metals and dissolved organic matter. Because little is known of its distribution in the North Pacific Ocean, we determined H2O2 in surface waters continuously and obtained vertical profiles at nine stations during a cruise from Japan to Hawaii. Surface water H2O2 varied from less than 10 to more than 250 nmol dm(-3). A diel cycle in surface water H2O2 (similar to 25 nmol dm(-3)) was observed only on one day during the monthlong cruise. This is contrary to expectations based on the usual assumption of photo-production …

The Emergence Of The Social Brain Network: Evidence From Typical And Atypical Development, Mark H. Johnson, Richard Griffin, Gergely Csibra, Hanife Halit, Teresa Farroni, Michelle Dehaan, Leslie A. Tucker, Simon Baron-Cohen, John E. Richards

Faculty Publications

Several research groups have identified a network of regions of the adult cortex that are activated during social perception and cognition tasks. In this paper we focus on the development of components of this social brain network during early childhood and test aspects of a particular viewpoint on human functional brain development: “interactive specialization.” Specifically, we apply new data analysis techniques to a previously published data set of event-related potential ~ERP! studies involving 3-, 4-, and 12-month-old infants viewing faces of different orientation and direction of eye gaze. Using source separation and localization methods, several likely generators of scalp recorded …

Modulation Of Synaptic Function In Retinal Amacrine Cells, Brian K. Hoffpauir, Evanna L. Gleason

Faculty Publications

Amacrine cells are interneurons that have diverse functions in retinal signal processing. In order to study signaling and modulation in retinal amacrine cells, we employ a simplified culture system containing identifiable GABAergic amacrine cells. Immunocytochemistry experiments indicate that GABAergic amacrine cells express metabotropic glutamate receptor 5 (mGluR5), a group I mGluR usually linked to the IP3 signaling pathway. Ca2+ imaging experiments using an mGluR5-specific agonist indicate that these receptors are functional and when activated, can stimulate temporally diverse Ca2+ elevations. To begin to establish the role of these receptors in modulating amacrine cell function, we have used electrophysiological methods to …

A Climate-Based Approach To The Restoration Of Fire-Dependent Ecosystems, Brian Beckage, William J. Platt, Bob Panko

Faculty Publications

Recurrent fires are integral to the function of many ecosystems worldwide. The management of fire-frequented ecosystems requires the application of fire at the appropriate frequency and seasonally, but establishing the natural fire regime for an ecosystem can be problematic. Historical records of fires are often not available, and surrogates for past fires may not exist. We suggest that the relationship between climate and fire can provide an alternative means for inferring past fire regimes in some ecosystems. © 2005 Society for Ecological Restoration International.

Analysis Of The Distribution And Diversity In Recent Hawaiian Volcanic Deposits Of A Putative Carbon Monoxide Dehydrogenase Large Subunit Gene, Kari E. Dunfield, Gary M. King

Faculty Publications

A putative carbon monoxide dehydrogenase large subunit gene (BMS putative coxL) was amplified from genomic DNA extracts of four recent (42-300 year old) Hawaiian volcanic deposits by polymerase chain reaction (PCR). Sequence databases derived from clone libraries constructed using PCR products were analysed phylogenetically and statistically. These analyses indicated that each of the deposits supported distinct BMS putative coxL gene assemblages. Statistical analyses also showed that the youngest deposit (42 years old) contained the least diverse sequences (P < 0.05), but that diversity did not vary significantly among three older deposits with ages from about 108-300 years. Although diversity indices did not vary among the older deposits, mismatch analyses suggested population structures increased in complexity with increasing deposit age. At each of the sites, most of the clone sequences appeared to originate from Proteobacteria not currently represented in culture or recognized as CO oxidizers. © 2005 Society for Applied Microbiology and Blackwell Publishing Ltd.

Status, Trends And Management Of Sturgeon And Paddlefish Fisheries, Ellen K. Pikitch, Phaedra Doukakis, Liz Lauck, Prosanta Chakrabarty, Daniel L. Erickson

Faculty Publications

The 27 extant species of sturgeons and paddlefishes (Order Acipenseriformes) represent a unique and relict lineage of fishes. Producers of coveted black caviar, sturgeons are one of the most valuable wildlife commodities on earth. The group is among the most endangered fishes with all species listed under Convention on International Trade in Endangered Species (CITES) Appendix I (two species) or II (25 species), only two species considered Lower Risk by IUCN, four of the nine US taxa and one Caspian species protected under the Endangered Species Act, and local extinctions recorded for 19 of 27 species. Despite their well-publicized imperilled …

A Global Regulatory Role Of Gluconeogenic Genes In Escherichia Coli Revealed By Transcriptome Network Analysis, Katy Kao, Linh Tran, James Liao

Faculty Publications

In bacterial adaptation to the dynamic environment, metabolic genes are typically thought to be the executors, whereas global transcription regulators are regarded as the decision makers. Although the feedback from metabolic consequence is believed to be important, much less is understood. This work demonstrates that the gluconeogenic genes in Escherichia coli, ppsA, sfcA, and maeB, provide a feedback loop to the global regulator, cAMP receptor protein (CRP), in carbon source transition. Disruption of one of the gluconeogenic pathways has no phenotype in balanced growth, but causes a significant delay in the diauxic transition from glucose to acetate. To investigate the …

Thioredoxin Reductase System Mediates Iron Binding In Isca And Iron Delivery For The Iron-Sulfur Cluster Assembly In Iscu, Huangen Ding, Karyn Harrison, Jianxin Lu

Faculty Publications

IscA is a key member of the iron-sulfur cluster assembly machinery found in bacteria and eukaryotes. Previously, IscA was characterized as an alternative iron-sulfur cluster assembly scaffold, as purified IscA can host transient iron-sulfur clusters. However, recent studies indicated that IscA is an iron-binding protein that can provide iron for the iron-sulfur cluster assembly in a proposed scaffold IscU (Ding H., Clark, R. J., and Ding, B. (2004) J. Biol. Chem. 279, 37499-37504). To further elucidate the roles of IscA in the biogenesis of iron-sulfur clusters, we reevaluate the iron binding activity of IscA under physiologically relevant conditions. The results …

Soy Isoflavone Glycitein Protects Against Beta Amyloid-Induced Toxicity And Oxidative Stress In Transgenic Caenorhabditis Elegans, Astrid Gutierrez-Zepeda, Ross Santell, Zhixin Wu, Marishka Brown, Yanjue Wu, Ikhlas Khan, Christopher D. Link, Baolu Zhao, Yuan Luo

Faculty Publications

Background

Epidemiological studies have associated estrogen replacement therapy with a lower risk of developing Alzheimer's disease, but a higher risk of developing breast cancer and certain cardiovascular disorders. The neuroprotective effect of estrogen prompted us to determine potential therapeutic impact of soy-derived estrogenic compounds. Transgenic C. elegans, that express human beta amyloid (Aβ), were fed with soy derived isoflavones genistein, daidzein and glycitein (100 μg/ml) and then examined for Aβ-induced paralysis and the levels of reactive oxygen species.

Results

Among the three compounds tested, only glycitein alleviated Aβ expression-induced paralysis in the transgenic C. elegans. This activity of …

Animal Virus Replication And Rnai-Mediated Antiviral Silencing In Caenorhabditis Elegans, R. Lu, M. Maduro, F. Li, H. W. Li, G. Broitman-Maduro, W. X. Li, S. W. Ding

Faculty Publications

The worm Caenorhabditis elegans is a model system for studying many aspects of biology, including host responses to bacterial pathogens, but it is not known to support replication of any virus. Plants and insects encode multiple Dicer enzymes that recognize distinct precursors of small RNAs and may act cooperatively. However, it is not known whether the single Dicer of worms and mammals is able to initiate the small RNA-guided RNA interference (RNAi) antiviral immunity as occurs in plants and insects. Here we show complete replication of the Flock house virus (FHV) bipartite, plus-strand RNA genome in C. elegans. We show …

Surface Salt Bridges Modulate The Dna Site Size Of Bacterial Histone-Like Hu Proteins, Edwin Kamau, Nick D. Tsihlis, L. Alice Simmons, Anne Grove

Faculty Publications

Bacterial histone-like DNA-binding proteins are best known for their role in compacting the genomic DNA. Of these proteins, HU is ubiquitous and highly conserved across the eubacterial kingdom. Using the HBsu (Bacillus subtilis-encoded HU homologue) as a model, we explore here the molecular basis for the ability of some HU homologues to engage a longer approx. 35 bp DNA site as opposed to the much shorter sites reported for other homologues. Using electrophoretic mobility-shift assays, we show that the DNA site size for HBsu is approx. 10-13 bp and that a specific surface salt bridge limits the DNA site size …

Tandem Repetitive Transgenes And Fluorescent Chromatin Tags Alter Local Interphase Chromosome Arrangement In Arabidopsis Thaliana, Ales Pecinka, Naohiro Kato, Armin Meister, Aline V. Probst, Ingo Schubert, Eric Lam

Faculty Publications

Fluorescent protein chromatin tagging as achieved by the lac operator/lac repressor system is useful to trace distinct chromatin domains in living eukaryotic nuclei. To interpret the data correctly, it is important to recognize influences of the tagging system on nuclear architecture of the host cells. Within an Arabidopsis line that carries lac operator/lac repressor/GFP transgenes, the transgene loci frequently associate with each other and with heterochromatic chromocenters. Accumulation of tagged fusion protein further enhances the association frequency. Independent experiments with a transgenic plant carrying another multi-copy transgene also revealed, independent of its transcriptional state, unusually high frequencies of association with …

Toward Sequencing The Sorghum Genome: A U.S. National Science Foundation-Sponsored Workshop Report, Stephen Kresovich, Brad Barbazuk, Joseph A. Bedell, Andrew Borrell, C. Robin Buell, John Burke, Sandra Clifton, Marie-Michéle Cordonnier-Ptratt, Stan Cox, Jeff Dahlberg, John Erpelding, Theresa M. Fulton, Bob Fulton, Lucinda Fulton, Alan R. Gingle, C. Tom Hash, Yinghua Huang, David Jordan, Patricia E. Klein, Robert R. Klein, Jurandir Magalhaes, Richard Mccombie, Paul Moore, John E. Mullet, Peggy Ozias-Akins, Andrew H. Paterson, Kay Porter, Lee Pratt, Bruce Roe, William Rooney, Patrick S. Schnable, David M. Stelly, Mitchell Tuinstra, Doreen Ware, Ujwala Warek

Faculty Publications

Members of the worldwide sorghum (Sorghum spp.) community, including private sector and international scientists as well as community representatives from closely related crops such as sugarcane (Saccharum spp.) and maize (Zea mays), met in St. Louis, Missouri, on November 9, 2004, to lay the groundwork for future advances in sorghum genomics and, in particular, to coordinate plans for sequencing of the sorghum genome. Key developments that made this workshop timely included advances in knowledge of the sorghum genome that provide for the development of a genetically anchored physical map to guide sequence assembly and annotation, the …

Highly Water-Soluble Thermally Responsive Poly(Thiophene)-Based Brushes, Sreelatha S. Balamurugan, Grigor B. Bantchev, Yuming Yang, Robin L. Mccarley

Faculty Publications

(Figure Presented) A brush with success: Responsive brushes composed of poly(N-isopropylacrylamide) grafted onto a poly(thiophene) backbone display the highest water solubility ever reported for a neutral poly(thiophene) as well as temperature-dependent optical properties and water solubilities (see picture). The graft polymer exhibits shifts in the π-π* transition of the poly(thiophene) backbone near the collapse temperature of the poly(N-isopropylacrylamide) chains. © 2005 Wiley-VCH Verlag GmbH & Co. KGaA.

A Mechanism For Assembly Of Complexes Of Vitronectin And Plasminogen Activator Inhibitor-1 From Sedimentation Velocity Analysis, Kenneth H. Minor, Christine R. Schar, Grant E. Blouse, Joseph D. Shore, Daniel A. Lawrence, Peter Schuck, Cynthia B. Peterson

Faculty Publications

Plasminogen activator inhibitor-1 (PAI-1) and vitronectin are cofactors involved in pathological conditions such as injury, inflammation, and cancer, during which local levels of PAI-1 are increased and the active serpin forms complexes with vitronectin. These complexes become deposited into surrounding tissue matrices, where they regulate cell adhesion and pericellular proteolysis. The mechanism for their co-localization has not been elucidated. We hypothesize that PAI-1-vitronectin complexes form in a stepwise and concentration-dependent fashion via 1:1 and 2:1 intermediates, with the 2:1 complex serving a key role in assembly of higher order complexes. To test this hypothesis, sedimentation velocity experiments in the analytical …

Mobilization Of The Iron Centre In Isca For The Iron-Sulphur Cluster Assembly In Iscu, Baojin Ding, Edward S. Smith, Huangen Ding

Faculty Publications

The biogenesis of iron-sulphur clusters requires the co-ordinated delivery of both iron and sulphur. It is now clear that sulphur in iron-sulphur clusters is derived from L-cysteine by cysteine desulphurases. However, the iron donor for the iron-sulphur cluster assembly still remains elusive. Our previous studies indicated that Escherichia coli IscA, a member of the iron-sulphur cluster assembly machinery, is an iron-binding protein that can provide iron for the iron-sulphur cluster assembly in a proposed scaffold IscU. To determine how the iron centre in IscA is transferred for the iron-sulphur cluster assembly in IscU, we explore the mobility of the iron …

Altering The Tropism Of Lentiviral Vectors Through Pseudotyping, James Cronin, Xian Yang Zhang, Jakob Reiser

Faculty Publications

The host range of retroviral vectors including lentiviral vectors can be expanded or altered by a process known as pseudotyping. Pseudotyped lentiviral vectors consist of vector particles bearing glycoproteins (GPs) derived from other enveloped viruses. Such particles possess the tropism of the virus from which the GP was derived. For example, to exploit the natural neural tropism of rabies virus, vectors designed to target the central nervous system have been pseudotyped using rabies virus-derived GPs. Among the first and still most widely used GPs for pseudotyping lentiviral vectors is the vesicular stomatitis virus GP (VSV-G), due to the very broad …

From The Margins Of The Genome: Mobile Elements Shape Primate Evolution, Dale J. Hedges, Mark A. Batzer

Faculty Publications

As is the case with mammals in general, primate genomes are inundated with repetitive sequence. Although much of this repetitive content consists of "molecular fossils" inherited from early mammalian ancestors, a significant portion of this material comprises active mobile element lineages. Despite indications that these elements played a major role in shaping the architecture of the genome, there remain many unanswered questions surrounding the nature of the host-element relationship. Here we review advances in our understanding of the host-mobile element dynamic and its overall impact on primate evolution. © 2005 Wiley Periodicals, Inc.

Phylogeny And Comparative Biogeography Of Pionopsitta Parrots And Pteroglossus Toucans, Jessica R. Eberhard, Eldredge Bermingham

Faculty Publications

Studies of Neotropical birds, and their distributions and areas of endemism, in particular, have been central in the formulation of hypotheses proposed to explain the high species diversity in the Neotropics. We used mtDNA sequence data (ATPase 6 and 8, COI, and cyt b) to reconstruct the species-level phylogenies for two genera, Pionopsitta (Aves: Psittacidae) and Pteroglossus (Aves: Ramphastidae), compare our results with previous morphology-based phylogenetic analyses, and estimate the absolute timing of lineage and biogeographic divergences. Both the Pionopsitta and Pteroglossus phylogenies support a hypothesis of area relationships in which a divergence of the Serra do Mar (Atlantic Forest, …

Extraocular Muscle Activity, Rapid Eye Movements And The Development Of Active And Quiet Sleep, Adele M. H. Seelke, Andrew J. Gall, Karl Æ. Karlsson, Mark S. Blumberg

Faculty Publications

Rapid eye movements (REMs), traditionally measured using the electrooculogram (EOG), help to characterize active sleep in adults. In early infancy, however, they are not clearly expressed. Here we measured extraocular muscle activity in infant rats at 3 days of age (P3), P8 and P14-15 in order to assess the ontogeny of REMs and their relationship with other forms of sleep-related phasic activity. We found that the causal relationship between extraocular muscle twitches and REMs strengthened during the first two postnatal weeks, reflecting increased control of the extraocular muscles over eye movements. As early as P3, however, phasic bursts of extraocular …

Bioluminescence Intensity Modeling And Sampling Strategy Optimization, I. Shulman, D.J. Mcgillicuddy Jr., M.A. Moline, S.H.D. Haddock, J.C. Kindle, D. Nechaev

Faculty Publications

The focus of this paper is on the development of methodology for short-term (1-3 days) oceanic bioluminescence (BL) predictions and the optimization of spatial and temporal bioluminescence sampling strategies. The approach is based on predictions of bioluminescence with an advection-diffusion-reaction (tracer) model with velocities and diffusivities from a circulation model. In previous research, it was shown that short-term changes in some of the salient features in coastal bioluminescence can be explained and predicted by using this approach. At the same time, it was demonstrated that optimization of bioluminescence sampling prior to the forecast is critical for successful short-term BL predictions …

Loss Of Outer Membrane Proteins Without Inhibition Of Lipid Export In An Escherichia Coli Yaet Mutant, William T. Doerrler, Christian R.H. Raetz

Faculty Publications

Escherichia coli yaeT encodes an essential, conserved outer membrane (OM) protein that is an ortholog of Neisseria meningitidis Omp85. Conflicting data with TV. meningitidis indicate that Omp85 functions either in assembly of OM proteins or in export of OM lipids. The role of YaeT in E. coli was investigated with a new temperature-sensitive mutant harboring nine amino acid substitutions. The mutant stops growing after 60 min at 44 °C. After 30 min at 44 °C, incorporation of [35S]methionine into newly synthesized OM proteins is selectively inhibited. Synthesis and export of OM phospholipids and lipopolysaccharide are not impaired. OM protein levels …

Cardiorespiratory Fitness Is Inversely Associated With The Incidence Of Metabolic Syndrome: A Prospective Study Of Men And Women, Michael J. Lamonte, Carolyn E. Barlow, Radim Jurca, James B. Kampert, Timothy S. Church, Steven N. Blair

Faculty Publications

Background - Few studies have reported the relationship between cardiorespiratory fitness and metabolic syndrome incidence, particularly in women.

Methods and Results - We prospectively studied 9007 men (mean±SD, age, 44±9 years; body mass index, 25±3 kg/m²) and 1491 women (age, 44±9 years; body mass index, 22±2 kg/m²) who were free of metabolic syndrome and for whom measures of waist girth, resting blood pressure, fasting lipids, and glucose were taken during baseline and follow-up examinations. Baseline cardiorespiratory fitness was quantified as duration of a maximal treadmill test. Metabolic syndrome was defined with NCEP ATP-III criteria. During a …

A Modified Poisson–Boltzmann Analysis Of The Capacitance Behavior Of The Electric Double Layer At Low Temperatures, Douglas Henderson, L. B. Bhuiyan, C. W. Outhwaite

Faculty Publications

The modified Poisson–Boltzmann theory is used to analyze the anomalous behavior of the electric double layer capacitance for small surface charge at low temperatures and densities. Good agreement is found with simulation and recent density-functional theory results. Negative adsorption is also found in line with theory and simulation. An unsatisfactory feature is the relatively poor structure in this region due to the inherent approximations in the theory. This feature is unimportant in relation to the capacitance results but has implications when calculating adsorption properties.