Digital Commons Network^™

A Systems Model Of Vesicle Trafficking In Arabidopsis Pollen Tubes, Naohiro Kato, Hongyu He, Alexander P. Steger

Faculty Publications

A systems model that describes vesicle trafficking during pollen tube growth in Arabidopsis (Arabidopsis thaliana) was constructed. The model is composed of ordinary differential equations that connect the molecular functions of genes expressed in pollen. The current model requires soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNAREs) and small GTPases, Arf or Rab, to reasonably predict tube growth as a function of time. Tube growth depends on vesicle trafficking that transports phospholipid and pectin to the tube tip. The vesicle trafficking genes identified by analyzing publicly available transcriptome data comprised 328 genes. Fourteen of them are up-regulated by the gibberellin …

Effects Of Transgenic Rice Expressing Bacillus Thuringiensis Cry1ab Protein On Ground-Dwelling Collembolan Community In Postharvest Seasons, Y. Y. Bai, R. H. Yan, G. Y. Ye, F. N. Huang, J. A. Cheng

Faculty Publications

During 20052008, field studies were conducted at two locations in Chongqing, China, to assess the potential effects of transgenic rice expressing Bacillus thuringiensis (Bt) Cry1Ab protein on the nontarget ground-dwelling collembolan community in three postharvest seasons. Collembolans in non-Bt and Bt rice fields were sampled with pitfall traps during each of two postharvest seasons of 2005/2006 and 2006/2007 and litterbag traps during each of three postharvest seasons of 2005/2006, 2006/2007, and 2007/2008. Ground-dwelling collembolans in rice fields during the postharvest seasons were abundant, whereas community densities varied considerably between the two locations and among the three seasons. A total of …

Inefficient Tat-Dependent Export Of Periplasmic Amidases In An Escherichia Coli Strain With Mutations In Two Deda Family Genes, Rakesh Sikdar, William T. Doerrler

Faculty Publications

The DedA family genes are found in most bacterial genomes. Two of these proteins are Escherichia coli YqjA and YghB, predicted inner membrane proteins of unknown function sharing 61% amino acid identity. The E. coli single deletion mutants are largely without phenotype, but the double mutant (BC202; ΔyqjA::Tetr ΔyghB::Kanr) is characterized by incomplete cell division, temperature sensitivity, and altered phospholipid levels (K. Thompkins et al., J. Bacteriol. 190:4489-4500, 2008). In this report, we have better characterized the cell division chaining defect of BC202. Fluorescence recovery after photobleaching indicates that 58% of the cells in chains are compartmentalized by at least …

Virus Discovery By Deep Sequencing And Assembly Of Virus-Derived Small Silencing Rnas, Qingfa Wu, Yingjun Luo, Rui Lu, Nelson Lau, Eric C. Lai, Wan Xiang Li, Shou Wei Ding

Faculty Publications

In response to infection, invertebrates process replicating viral RNA genomes into siRNAs of discrete sizes to guide virus clearance by RNA interference. Here, we show that viral siRNAs sequenced from fruit fly, mosquito, and nematode cells were all overlapping in sequence, suggesting a possibility of using siRNAs for viral genome assembly and virus discovery. To test this idea, we examined contigs assembled from published small RNA libraries and discovered five previously undescribed viruses from cultured Drosophila cells and adult mosquitoes, including three with a positive-strand RNA genome and two with a dsRNA genome. Notably, four of the identified viruses exhibited …

Structural Basis For The Photoconversion Of A Phytochrome To The Activated Pfr Form, Andrew T. Ulijasz, Gabriel Cornilescu, Claudia C. Cornilescu, Junrui Zhang, Mario Rivera, John L. Markley, Richard D. Vierstra

Faculty Publications

Phytochromes are a collection of bilin-containing photoreceptors that regulate numerous photoresponses in plants and microorganisms through their ability to photointerconvert between a red-light-absorbing, ground state (Pr) and a far-red-light-absorbing, photoactivated state (Pfr). Although the structures of several phytochromes as Pr have been determined, little is known about the structure of Pfr and how it initiates signalling. Here we describe the three-dimensional solution structure of the bilin-binding domain as Pfr, using the cyanobacterial phytochrome from Synechococcus OSB′. Contrary to predictions, light-induced rotation of the A pyrrole ring but not the Dring is the primary motion of the chromophore during photoconversion. Subsequent …

Psifr: An Integrated Resource For Prediction Of Protein Structure And Function, Shashi B. Pandit, Michal Brylinski, Hongyi Zhou, Mu Gao, Adrian K. Arakaki, Jeffrey Skolnick

Faculty Publications

In the post-genomic era, the annotation of protein function facilitates the understanding of various biological processes. To extend the range of function annotation methods to the twilight zone of sequence identity, we have developed approaches that exploit both protein tertiary structure and/or protein sequence evolutionary relationships. To serve the scientific community, we have integrated the structure prediction tools, TASSER, TASSER-Lite and METATASSER, and the functional inference tools, FINDSITE, a structure-based algorithm for binding site prediction, Gene Ontology molecular function inference and ligand screening, EFICAz2, a sequence-based approach to enzyme function inference and DBD-hunter, an algorithm for predicting DNA-binding proteins and …

Pyritization Of Trace Metals In Estuarine Sediments And The Controlling Factors: A Case In Jiaojiang Estuary Of Zhejiang Province, China, Siyuan Ye, Edward A. Laws, Qiang Wu, Shaojun Zhong, Xigui Ding, Guangming Zhao, Shaojun Gong

Faculty Publications

Three undisturbed sediment samples were collected from the intertidal zone of the Jiaojiang Estuary of Zhejiang Province, China. The sediments were found to contain remarkably low concentrations of organic carbon (< 0.6%) and acid volatile sulfide (AVS) (< 30 μmol g^-1). The availability of these two substrates likely constrained sulfate reduction and pyritization of several trace metals, respectively. This was especially true at one station where AVS concentrations in the upper 20 cm averaged less than 0.05 μmol g^-1. Although the depth dependence of the degree of trace metal pyritization was generally consistent with expectations based on redox conditions, depth profiles of reactive-metal and pyrite-metal concentrations …

Functional Characterization Of The Chlamydomonas Reinhardtii Erg3 Ortholog, A Gene Involved In The Biosynthesis Of Ergosterol, Kristy M. Brumfield, James V. Moroney, Thomas S. Moore, Tiffany A. Simms, David Donze

Faculty Publications

Background: The predominant sterol in the membranes of the alga Chlamydomonas reinhardtii is ergosterol, which is commonly found in the membranes of fungi, but is rarely found in higher plants. Higher plants and fungi synthesize sterols by different pathways, with plants producing cycloartenol as a precursor to end-product sterols, while nonphotosynthesizing organisms like yeast and humans produce lanosterol as a precursor. Analysis of the C. reinhardtii genome sequence reveals that this algae is also likely to synthesize sterols using a pathway resembling the higher plant pathway, indicating that its sterols are synthesized somewhat differently than in fungi. The work presented …

Bilitrienones From The Chemical Oxidation Of Dodecasubstituted Porphyrins, Owendi Ongayi, M. Graça H. Vicente, Brahma Ghosh, Frank R. Fronczek, Kevin M. Smith

Faculty Publications

The structure of the ring-opened product from direct oxidation of meso-tetra-arylporphyrins has been controversial for three decades. Herein we show that bilitrienones 2 are obtained from oxidation of metal-free dodecasubstituted porphyrins 1 in the presence of sodium nitrite, trifluoroacetic acid, and air oxygen. The presence of the para-nonyl groups in 1b stabilized the corresponding bilitrienone 2b, which was characterized by X-ray crystallography. In the absence of the para-nonyl groups bilitrienone 2a undergoes a rapid hydration reaction, giving biladienone 3a as the major isolated product. The molecular structures of 2b and 3a, and the photochemical isomerization of 3a are discussed. © …

Alum Application To Improve Water Quality In A Municipal Wastewater Treatment Wetland: Effects On Macrophyte Growth And Nutrient Uptake, Lynette M. Malecki-Brown, John R. White, Hans Brix

Faculty Publications

Application of low doses of alum to treatment wetlands to reduce elevated outflow winter phosphorus concentrations were tested in mesocosms vegetated with either Typha domingensis, Schoenoplectus californicus, or submerged aquatic vegetation (SAV) (Najas guadalupensis-dominated). Alum was pumped to experimental units at a rate of 0.91 g Al m^-2 d^-1 and water quality monitored for 3 months. The alum application significantly improved the outflow water quality and overall the growth of the plants was unaffected by the alum application. Biomass and growth varied between species and through time, but no significant effects of alum application were detected. The concentrations …

Dynamics And Distribution Of Natural And Human-Caused Hypoxia, N N. Rabalais, R J. Diaz, L A. Levin, R. Eugene Turner, N N. Rabalais, J Zhang

Faculty Publications

Water masses can become undersaturated with oxygen when natural processes alone or in combination with anthropogenic processes produce enough organic carbon that is aerobically decomposed faster than the rate of oxygen re-aeration. The dominant natural processes usually involved are photosynthetic carbon production and microbial respiration. The re-supply rate is indirectly related to its isolation from the surface layer. Hypoxic water masses (< 2 mg L-1, or approximately 30% saturation) can form, therefore, under 'natural' conditions, and are more likely to occur in marine systems when the water residence time is extended, water exchange and ventilation are minimal, stratification occurs, and where carbon production and export to the bottom layer are relatively high. Hypoxia has occurred through geological time and naturally occurs in oxygen minimum zones, deep basins, eastern boundary upwelling systems, and fjords. Hypoxia development and continuation in many areas of the world's coastal ocean is accelerated by human activities, especially where nutrient loading increased in the Anthropocene. This higher loading set in motion a cascading set of events related to eutrophication. The formation of hypoxic areas has been exacerbated by any combination of interactions that increase primary production and accumulation of organic carbon leading to increased respiratory demand for oxygen below a seasonal or permanent pycnocline. Nutrient loading is likely to increase further as population growth and resource intensification rises, especially with increased dependency on crops using fertilizers, burning of fossil fuels, urbanization, and waste water generation. It is likely that the occurrence and persistence of hypoxia will be even more widespread and have more impacts than presently observed. Global climate change will further complicate the causative factors in both natural and human-caused hypoxia. The likelihood of strengthened stratification alone, from increased surface water temperature as the global climate warms, is sufficient to worsen hypoxia where it currently exists and facilitate its formation in additional waters. Increased precipitation that increases freshwater discharge and flux of nutrients will result in increased primary production in the receiving waters up to a point. The interplay of increased nutrients and stratification where they occur will aggravate and accelerate hypoxia. Changes in wind fields may expand oxygen minimum zones onto more continental shelf areas. On the other hand, not all regions will experience increased precipitation, some oceanic water temperatures may decrease as currents shift, and frequency and severity of tropical storms may increase and temporarily disrupt hypoxia more often. The consequences of global warming and climate change are effectively uncontrollable at least in the near term. On the other hand, the consequences of eutrophication-induced hypoxia can be reversed if long-term, broad-scale, and persistent efforts to reduce substantial nutrient loads are developed and implemented. In the face of globally expanding hypoxia, there is a need for water and resource managers to act now to reduce nutrient loads to maintain, at least, the current status.

Potential Of Modis Evi In Identifying Hurricane Disturbance To Coastal Vegetation In The Northern Gulf Of Mexico, F. Wang, E.J. D'Sa

Faculty Publications

No abstract provided.

Assessment Of Particulate Absorption Properties In The Southeastern Bering Sea From In-Situ And Remote Sensing Data, P. Naik, E. D'Sa, J.I. Goés, H.D.R. Gomes

Faculty Publications

No abstract provided.

Recommendations For Interdisciplinary Study Of Tipping Points In Natural And Social Systems, T.E. Jordan, O.E. Sala, S.G. Stafford, J.L. Bubier, J.C. Crittenden, S.L. Cutter, A.C. Kay, G.D. Libecap, J.C. Moore, N.N. Rabalais, J.M. Shepherd, J. Travis

Faculty Publications

No abstract provided.

Natural And Human-Induced Hypoxia And Consequences For Coastal Areas: Synthesis And Future Development, J. Zhang, D. Gilbert, A.J. Gooday, L. Levin, S.W.A. Naqvi, J.J. Middelburg, M. Scranton, W. Ekau, A. Peña, B. Dewitte, T. Oguz, P.M.S. Monteiro, E. Urban, N.N. Rabalais, V. Ittekkot, W.M. Kemp, O. Ulloa, R. Elmgren, E. Escobar-Briones, A.K. Van Der Plas

Faculty Publications

No abstract provided.

Louisiana Universities Marine Consortium: Relatively New Kid On The Block, N.N. Rabalais

Faculty Publications

No abstract provided.

Effects Of Biological And Physical Factors On Seasonal Oxygen Dynamics In A Stratified, Eutrophic Coastal Ecosystem, Z.J. Quiñones-Rivera, B. Wissel, N.N. Rabalais, D. Justic

Faculty Publications

No abstract provided.

Evidence For Greater Oxygen Decline Rates In The Coastal Ocean Than In The Open Ocean, D. Gilbert, N.N. Rabalais, R.J. Díaz, J. Zhang

Faculty Publications

No abstract provided.

Synaptically Activated Burst-Generating Conductances May Underlie A Group-Pacemaker Mechanism For Respiratory Rhythm Generation In Mammals, Christopher A. Del Negro, John A. Hayes, Ryland W. Pace, Benjamin R. Brush, Ryoichi Teruyama, Jack L. Feldman

Faculty Publications

Breathing, chewing, and walking are critical life-sustaining behaviors in mammals that consist essentially of simple rhythmic movements. Breathing movements in particular involve the diaphragm, thorax, and airways but emanate from a network in the lower brain stem. This network can be studied in reduced preparations in vitro and using simplified mathematical models that make testable predictions. An iterative approach that employs both in vitro and in silico models argues against canonical mechanisms for respiratory rhythm in neonatal rodents that involve reciprocal inhibition and pacemaker properties. We present an alternative model in which emergent network properties play a rhythmogenic role. Specifically, …

Histone H2a.Z Regulates The Expression Of Several Classes Of Phosphate Starvation Response Genes But Not As A Transcriptional Activator, Aaron P. Smith, Ajay Jain, Roger B. Deal, Vinay K. Nagarajan, Michael D. Poling, Kashchandra G. Raghothama, Richard B. Meagher

Faculty Publications

Phosphate (Pi) availability is a major constraint to plant growth. Consequently, plants have evolved complex adaptations to tolerate low Pi conditions. Numerous genes implicated in these adaptations have been identified, but their chromatin-level regulation has not been investigated. The nuclear actin-related protein ARP6 is conserved among all eukaryotes and is an essential component of the SWR1 chromatin remodeling complex, which regulates transcription via deposition of the H2A.Z histone variant into chromatin. Here, we demonstrate that ARP6 is required for proper H2A.Z deposition at a number of Pi starvation response (PSR) genes in Arabidopsis (Arabidopsis thaliana). The loss of H2A.Z at …

Intracellular Ph Regulation In Isolated Trout Gill Mitochondrion-Rich (Mr) Cell Subtypes: Evidence For Na+/H+ Activity, Scott K. Parks, Martin Tresguerres, Fernando Galvez, Greg G. Goss

Faculty Publications

We have studied intracellular pH (pHi) recovery in isolated trout gill mitochondrion-rich (MR) cells following acidification by the NH4Cl pre-pulse technique. Within a mixed MR cell population, one cell type displayed Na+-independent pHi recovery while the other cell type lacked a Na+-independent pHi recovery. Cells displaying Na+ independent recovery exhibited a significantly higher buffering capacity compared to cells lacking Na+-independent pHi recovery. Cells displaying Na+ independent recovery were identified as PNA+ (peanut lectin agluttinin binding) MR cells while those unable to recover were identified as PNA- (non-peanut lectin agluttinin binding) MR cells. Therefore, recovery from acidification in the absence of …

Social Status Regulates Kisspeptin Receptor Mrna In The Brain Of Astatotilapia Burtoni, Brian P. Grone, Karen P. Maruska, Wayne J. Korzan, Russell D. Fernald

Faculty Publications

The brain controls reproduction in response to relevant external and internal cues. Central to this process in vertebrates is gonadotropin-releasing hormone (GnRH1) produced in neurons of the hypothalamic-preoptic area (POA). GnRH1 released from the POA stimulates pituitary release of gonadotropins, which in males causes sperm production and concomitant steroid hormone release from the testes. Kisspeptin, a neuropeptide acting via the kisspeptin receptor (Kiss1r), increases GnRH1 release and is linked to development of the reproductive system in mammals and other vertebrates. In both fish and mammals, kiss1r mRNA levels increase in the brain around the time of puberty but the environmental …

Expression, Localization And Interaction Of Snare Proteins In Arabidopsis Are Selectively Altered By The Dark, Naohiro Kato, Huancan Bai

Faculty Publications

A method to detect binary interactions among SNAREs, membrane proteins mediating vesicle fusion, in Arabidopsis cells was established. In this method, a pair of recombinant SNAREs is first expressed within Arabidopsis protoplasts at levels similar to their endogenous proteins in 96-well plates. Changes of the interaction are then detected by luminescence. Here, we report that the interaction of SYP122 and VAMP721, a SNARE pair mediating exocytosis, is enhanced when Arabidopsis protoplasts are incubated in the dark. Microscopic observation of plants expressing GFPSYP122 by the syp122 promoter suggests SYP122 is expressed in the root tip when the seedlings are grown in …

Gumbo Yearbook, Class Of 2010, Louisiana State University And Agricultural And Mechanical College

Gumbo Yearbook

The Gumbo yearbook chronicles the entire academic year at LSU. In words and especially photos, the Gumbo shows the people, places, and events that make each year unique. In addition to formal portraits of schools and departments, the book contains hundreds of snapshots of students with their friends and dozens of pages showcasing organizations.

The 2010 Gumbo was published with a DVD containing a video yearbook, as well as a PDF. Those files are linked below.

Syntheses Of Protoporphyrin-Ix Derivatives Bearing Extended Propionate Side-Chains, Robert T. Holmes, Jianming Lu, Celinah Mwakwari, Kevin M. Smith

Faculty Publications

In order to investigate the relationship between depth within membranes of singlet oxygen generation and effectiveness of photodynamic therapy of tumors, analogs of protoporphyrin-IX 1 bearing five 4 and seven 5 carbon atoms (in place of the 3-carbon atom chain in 1) were synthesized from monopyrrole precursors.

Improved Peak Capacity For Ce Separations Of Enzyme Inhibitors With Activity-Based Detection Using Magnetic Bead Microreactors, Xiaoyan Yan, S. Douglass Gilman

Faculty Publications

A technique for separating and detecting enzyme inhibitors was developed using CE with an enzyme microreactor. The on-column enzyme microreactor was constructed using NdFeB magnet(s) to immobilize alkaline phosphatase-coated superparamagnetic beads (2.8 mm diameter) inside a capillary before the detection window. Enzyme inhibition assays were performed by injecting a plug of inhibitor into a capillary filled with the substrate, AttoPhos. Product generated in the enzyme microreactor was detected by LIF. Inhibitor zones electrophoresed through the capillary, passed through the enzyme microreactor, and were observed as negative peaks due to decreased product formation. The goal of this study was to improve …

Engaging With The Politics Of Determinist Environmental Thinking, Andrew Sluyter

Faculty Publications

No abstract provided.

Renegotiating Barbuda's Commons: Recent Changes In Barbudan Open-Range Cattle Herding, Andrew Sluyter, Amy E. Potter

Faculty Publications

Barbuda remains little developed and sparsely populated relative to its neighbors in the Leeward Lesser Antilles, a rather extraordinary and relatively unknown Caribbean place. Much of its distinctiveness derives from the communal land-tenure system, itself rooted in three centuries of open-range cattle herding. Yet, as revealed through interviews, newspaper archives, and landscape observations, openrange cattle herding has declined over the past three decades, with related changes in land tenure. As the new Barbuda Land Act came into effect in 2008, codifying the communal tenure system, the very landscape elements that manifest open-range herding have become obscure. In particular, the rock-walled …

The Hispanic Atlantic's Tasajo Trail, Andrew Sluyter

Faculty Publications

Produced along the Río de la Plata during the nineteenth century, shipped to Havana, and consumed by African slaves, the salt-cured beef known as tasajo affected both of those places and, to some degree, the Atlantic world in general. Initial exploration of the tasajo trail that connected Buenos Aires and Cuba employs primary sources such as nineteenth-century descriptions and shipping records to characterize the landscapes, places, routes, and agents of the largely unexplored research territory of that anomalous commodity: one that, unlike others such as sugar, slaves not only produced but also consumed; one that underpinned more prominent, latitudinal transatlantic …

Brucella Species Survey In Polar Bears (Ursus Maritimus) Of Northern Alaska, Todd M. O'Hara, Darce Holcomb, Philip Elzer, Jessica Estepp, Quinesha Perry, Sue Hagius, Cassandra Kirk

Faculty Publications

We report on the presence of specific antibodies to Brucella spp. and Yersinia enterocolitica in polar bears (Ursus maritimus) from northern Alaska (southern Beaufort Sea) during 2003-2006. Based on numerous known stressors (e.g., climate change and loss of sea ice habitat, contaminants), there is increased concern regarding the status of polar bears. Considering these changes, it is important to assess exposure to potentially pathogenic organisms and to improve understanding of transmission pathways. Brucella or specific antibodies to Brucella spp. has been reported in marine mammals. Various assays were used to elucidate the pathway or source of exposure (e.g., "marine" vs. …