Digital Commons Network^™

Mammalian Retroelements, Prescott L. Deininger, Mark A. Batzer

Faculty Publications

The eukaryotic genome has undergone a series of epidemics of amplification of mobile elements that have resulted in most eukaryotic genomes containing much more of this 'junk' DNA than actual coding DNA. The majority of these elements utilize an RNA intermediate and are termed retroelements. Most of these retroelements appear to amplify in evolutionary waves that insert in the genome and then gradually diverge. In humans, almost half of the genome is recognizably derived from retroelements, with the two elements that are currently actively amplifying, L1 and Alu, making up about 25% of the genome and contributing extensively to disease. …

Identification Of A Streptolysin S-Associated Gene Cluster And Its Role In The Pathogenesis Of Streptococcus Iniae Disease, Jeffrey D. Fuller, Alvin C. Camus, Carla L. Duncan, Victor Nizet, Darrin J. Bast, Ronald L. Thune, Donald E. Low, Joyce C.S. De Azavedo

Faculty Publications

Streptococcus iniae causes meningoencephalitis and death in cultured fish species and soft-tissue infection in humans. We recently reported that S. iniae is responsible for local tissue necrosis and bacteremia in a murine subcutaneous infection model. The ability to cause bacteremia in this model is associated with a genetic profile unique to strains responsible for disease in fish and humans (J. D. Fuller, D. J. Bast, V. Nizet, D. E. Low, and J. C. S. de Azavedo, Infect. Immun. 69:1994-2000, 2001). S. iniae produces a cytolysin that confers a hemolytic phenotype on blood agar media. In this study, we characterized the …

Heca, A Member Of A Class Of Adhesins Produced By Diverse Pathogenic Bacteria, Contributes To The Attachment, Aggregation, Epidermal Cell Killing, And Virulence Phenotypes Of Erwinia Chrysanthemi Ec16 On Nicotiana Clevelandii Seedlings, Clemencia M. Rojas, Jong Hyun Ham, Wen Ling Deng, Jeff J. Doyle, Alan Collmer

Faculty Publications

Erwinia chrysanthemi is representative of a broad class of bacterial pathogens that are capable of inducing necrosis in plants. The E. chrysanthemi EC16 hecA gene predicts a 3,850-aa member of the Bordetella pertussis filamentous hemagglutinin family of adhesins. A hecA::Tn7 mutant was reduced in virulence on Nicotiana clevelandii seedlings after inoculation without wounding. Epifluorescence and confocal laser-scanning microscopy observations of hecA and wild-type cells expressing the green fluorescent protein revealed that the mutant is reduced in its ability to attach and then form aggregates on leaves and to cause an aggregate-associated killing of epidermal cells. Cell killing also depended on …

Strawberry Anthracnose: Histopathology Of Colletotrichum Acutatum And C. Fragariae, Kenneth J. Curry, Maritza Abril, Jana B. Avant, Barbara J. Smith

Faculty Publications

Ontogeny of the invasion process by Colletotrichum acutatum and C. fragariae was studied on petioles and stolons of the strawberry cultivar Chandler using light and electron microscopy. The invasion of host tissue by each fungal species was similar; however, each invasion event occurred more rapidly with C. fragariae than with C. acutatum. Following cuticular penetration via an appressorium, subsequent steps of invasion involved hyphal growth within the cuticle and within the cell walls of epidermal, subepidermal, and subtending cells. Both species of fungi began invasion with a brief biotrophic phase before entering an extended necrotrophic phase. Acervuli formed once …

Bluetooth: An Emerging Technology For Wireless Personal Area Networks, Eric S. Hall, Charles D. Knutson, David K. Vawdrey

Faculty Publications

Look under your desk or behind your computer. See that rat’s nest of wires and cables? Almost every cable or wire that tethers us to our devices (or our devices to one another) is unnecessary. Bluetooth wireless technology promises to reduce the cabling chaos that afflicts us all. Bluetooth is a recently developed technology that uses radio frequency (RF) transceivers to provide point-to-multipoint wireless connectivity within a personal space. Bluetooth was designed for both voice and data communication at low per-unit costs while consuming little power. To achieve the cost and power goals, Bluetooth limits connectivity to a sphere of …

Direct Estimation Of Aboveground Forest Productivity Through Hyperspectral Remote Sensing Of Canopy Nitrogen, Marie-Louise Smith, Scott V. Ollinger, Mary E. Martin, John D. Aber, Richard A. Hallett, Christine L. Goodale

Faculty Publications

The concentration of nitrogen in foliage has been related to rates of net photosynthesis across a wide range of plant species and functional groups and thus represents a simple and biologically meaningful link between terrestrial cycles of carbon and nitrogen. Although foliar N is used by ecosystem models to predict rates of leaf‐level photosynthesis, it has rarely been examined as a direct scalar to stand‐level carbon gain. Establishment of such relationships would greatly simplify the nature of forest C and N linkages, enhancing our ability to derive estimates of forest productivity at landscape to regional scales. Here, we report on …

The Equatorial Thermocline Outcroppin - A Seasonal Control On The Tropical Pacific Ocean-Atmosphere Instability Strength, Eli Galanti, Eli Tziperman, Matthew Harrison, Anthony Rosati, Ralf Giering, Ziv Sirkes

Faculty Publications

One of the major factors determining the strength and extent of ENSO events is the instability state of the equatorial Pacific coupled ocean-atmosphere system and its seasonal variations. This study analyzes the coupled instability in a hybrid coupled model of the Indo-Pacific region, using the adjoint method for sensitivity studies. It is found that the seasonal changes in the ocean-atmosphere instability strength in the model used here are related to the outcropping of the thermocline in the east equatorial Pacific. From July to December, when the thermocline outcrops over a wide area in the east Pacific, there is a strong …

Atpase Activity Of The Msba Lipid Flippase Of Escherichia Coli, William T. Doerrler, Christian R.H. Raetz

Faculty Publications

Escherichia coli MsbA, the proposed inner membrane lipid flippase, is an essential ATP-binding cassette transporter protein with homology to mammalian multidrug resistance proteins. Depletion or loss of function of MsbA results in the accumulation of lipopolysaccharide and phospholipids in the inner membrane of E. coli. MsbA modified with an N-terminal hexahistidine tag was overexpressed, solubilized with a nonionic detergent, and purified by nickel affinity chromatography to ∼95% purity. The ATPase activity of the purified protein was stimulated by phospholipids. When reconstituted into liposomes prepared from E. coli phospholipids, MsbA displayed an apparent Km of 878 μM and a Vmax of …

The Nature Of Interchain Excitations In Conjugated Polymers: Spatially-Varying Interfacial Solvatochromism Of Annealed Meh-Ppv Films Studied By Near-Field Scanning Optical Microscopy (Nsom), Richard D. Schaller, Lynn F. Lee, Justin C. Johnson, Louis H. Haber, Richard J. Saykally, John Vieceli, Ilan Benjamin, Thuc Quyen Nguyen, Benjamin J. Schwartz

Faculty Publications

The nature of interchain excitations in conjugated polymers was discussed. The spatially-varying solvatochromism of annealed poly(2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylene vinylene) (MEH-PPV) films were studied by near-field scanning optical microscopy (NSOM). The solvatochromic spectral shifts of the interfacial luminescence were measured as a function of solvent polarity. The results were analyzed with an interfacial dielectric continuum model to determine the dipole moment of emissive excited states.

Little Qualitative Rna Misexpression In Sterile Male F1 Hybrids Of Drosophila Pseudoobscura And D. Persimilis, Jane Reiland, Mohamed A.F. Noor

Faculty Publications

Background: Although the genetics of hybrid sterility has been the subject of evolutionary studies for over sixty years, no one has shown the reason(s) why alleles that operate normally within species fail to function in another genetic background. Several lines of evidence suggest that failures in normal gene transcription contribute to hybrid dysfunctions, but genome-wide studies of gene expression in pure-species and hybrids have not been undertaken. Here, we study genome-wide patterns of expression in Drosophila pseudoobscura, D. persimilis, and their sterile F1 hybrid males using differential display. Results: Over five thousand amplifications were analyzed, and 3312 were present in …

Comparative Proteome Analysis Of Brucella Melitensis Vaccine Strain Rev 1 And A Virulent Strain, 16m, Michel Eschenbrenner, Mary Ann Wagner, Troy A. Horn, Jo Ann Kraycer, Cesar V. Mujer, Sue Hagius, Philip Elzer, Vito G. Delvecchio

Faculty Publications

The genus Brucella consists of bacterial pathogens that cause brucellosis, a major zoonotic disease characterized by undulant fever and neurological disorders in humans. Among the different Brucella species, Brucella melitensis is considered the most virulent. Despite successful use in animals, the vaccine strains remain infectious for humans. To understand the mechanism of virulence in B. melitensis, the proteome of vaccine strain Rev 1 was analyzed by two-dimensional gel electrophoresis and compared to that of virulent strain 16M. The two strains were grown under identical laboratory conditions. Computer-assisted analysis of the two B. melitensis proteomes revealed proteins expressed in either 16M …

Alteration Of Oriented Deposition Of Cellulose Microfibrils By Mutation Of A Katanin-Like Microtubule-Severing Protein, David H. Burk, Zheng Hua Ye

Faculty Publications

It has long been hypothesized that cortical microtubules (MTs) control the orientation of cellulose microfibril deposition, but no mutants with alterations of MT orientation have been shown to affect this process. We have shown previously that in Arabidopsis, the fra2 mutation causes aberrant cortical MT orientation and reduced cell elongation, and the gene responsible for the fra2 mutation encodes a katanin-like protein. In this study, using field emission scanning electron microscopy, we found that the fra2 mutation altered the normal orientation of cellulose microfibrils in walls of expanding cells. Although cellulose microfibrils in walls of wild-type cells were oriented transversely …

Active Alu Element "A-Tails": Size Does Matter, Astrid M. Roy-Engel, Abdel Halim Salem, Oluwatosin O. Oyeniran, Lisa Deininger, Dale J. Hedges, Gail E. Kilroy, Mark A. Batzer, Prescott L. Deininger

Faculty Publications

Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly understood. The data presented in this paper indicate that the length of Alu "A-tails" is one of the principal factors in determining the retropositional capability of an Alu element. The A stretches of the Alu subfamilies analyzed, both old (Alu S and J) and young (Ya5), had a Poisson distribution …

Inhibition Of Amyloid-Β Aggregation And Caspase-3 Activation By The Ginkgo Biloba Extract Egb761, Yuan Luo, Julie V. Smith, Vijaykumar Paramasivam, Adam Burdick, Kenneth J. Curry, Justin P. Buford, Ikhlas Khan, William J. Netzer, Huaxi Xu, Peter Butko

Faculty Publications

Standardized extract from the leaves of the Ginkgo biloba tree, labeled EGb761, has been used in clinical trials for its beneficial effects on brain functions, particularly in connection with age-related dementias and Alzheimer's disease (AD). Substantial experimental evidence indicates that EGb761 protects against neuronal damage from a variety of insults, but its cellular and molecular mechanisms remain unknown. Using a neuroblastoma cell line stably expressing an AD-associated double mutation, we report that EGb761 inhibits formation of amyloid-β (Aβ) fibrils, which are the diagnostic, and possibly causative, feature of AD. The decreased Aβ fibrillogenesis in the presence of EGb761 was observed …

Integrating Marriage Education Into Perinatal Education, Alan J. Hawkins, Tamara Gilliland, Glenda Christiaens, Jason S. Carroll

Faculty Publications

Couples making the transition to parenthood experience challenges that can threaten the quality and stability of their relationships and the health of family members. Currently, the educational infrastructure to support the delivery of couple-relationship education during the transition to parenthood is limited. Because new-parent couples interact with the health care system at many points during this transition time, an opportunity exists for strengthening couple relationships within the system to improve the well-being of adults and children. in this article, we propose a productive collaboration between marriage/couple educators and health care systems to integrate couple-relationship education into the standard of perinatal …

Evolution And Dynamics Of Tropical River Plumes In The Great Barrier Reef: An Integrated Remote Sensing And In Situ Study, D.M. Burrage, M.L. Heron, J.M. Hacker, T.C. Stieglitz, C.R. Steinberg, A. Prytz

Faculty Publications

[1] The short-lived but intense discharge of freshwater from tropical rivers into the Great Barrier Reef (GBR) Lagoon and the associated salinity reductions are a critical consideration in marine research and management of the ecologically sensitive GBR World Heritage Area. Salinity provides a unique tracer that gives clues to the origin of river-borne contaminants and allows the influences of storm-induced resuspension and river discharge on turbidity to be clearly distinguished. We describe a field investigation of the evolution and dynamics of the Herbert River plume in the central GBR. Its primary goals were to use an airborne salinity mapper and …

Investigating The Mechanism Of Acoustically Activated Uptake Of Drugs From Pluronic Micelles, Ghaleb A. Husseini, Christopher M. Runyan, William G. Pitt

Faculty Publications

Background

This paper examines the mechanism of ultrasonic enhanced drug delivery from Pluronic micelles. In previous publications by our group, fluorescently labeled Pluronic was shown to penetrate HL-60 cells with and without the action of ultrasound, while drug uptake was increased with the application of ultrasound.

Methods

In this study, the amount of uptake of two fluorescent probes, Lysosensor Green (a pH-sensitive probe) and Cell Tracker Orange CMTMR (a pH-independent probe), was measured in HL-60 and HeLa cells.

Results

The results of our experiments show that the increase in drug accumulation in the cells as a result of ultrasonication is …

Metabotropic Glutamate Receptor 5 And Calcium Signaling In Retinal Amacrine Cells, Romina Sosa, Brian Hoffpauir, Michele L. Rankin, Richard C. Bruch, Evanna L. Gleason

Faculty Publications

To begin to understand the modulatory role of glutamate in the inner retina, we examined the mechanisms underlying metabotropic glutamate receptor 5 (mGluR5)-dependent Ca2+ elevations in cultured GABAergic amacrine cells. A partial sequence of chicken retinal mGluR5 encompassing intracellular loops 2 and 3 suggests that it can couple to both Gq and Gs. Selective activation of mGluR5 stimulated Ca2+ elevations that varied in waveform from cell to cell. Experiments using high external K+ revealed that the mGluR5-dependent Ca2+ elevations are distinctive in amplitude and time course from those engendered by depolarization. Experiments with a Ca2+-free external solution demonstrated that the …

Effects Of Prescribed Burning On Vegetation And Fuel Loading In Three East Texas State Parks, S. Rideout, Brian P. Oswald

Faculty Publications

-This study was conducted to evaluate the initial effectiveness of prescribed burning in the ecological restoration of forests within selected parks in east Texas. Twenty-four permanent plots were installed to monitor fuel loads, overstory, sapling, seedling, shrub and herbaceous layers within bum and control units of Mission Tejas, Tyler and Village Creek state parks. Measurements were taken during the summers of 1999 and 2000. Prescribed burning was conducted between these sampling periods in early spring 2ooo. Results indicated that the current applications of prescribed burning do not significantly influence vegetation or fuels. Sustained drought, prior management practices and imposed local …

Element Ratios And Aquatic Food Webs, R. Eugene Turner

Faculty Publications

Organic matter is the result of concentrating a few non-metals that are relatively rare in the earth’s crust. Most of these essential elements are in a rough proportionality within phylogenetic groupings. Life is thus working against a concentration gradient to extract or accumulate these elements, and this metabolic work is accomplished in interrelated and often subtle ways for many other elements. The physiological requirement to sustain these elemental ratios (commonly discussed in terms of the N∶P ratios, but also C∶N, C∶P, and Si∶N ratios) constrains organization at the cellular, organism, and community level. Humans, as geochemical engineers, significantly influence the …

Simple, Compact Source For Low-Temperature Air Plasmas, D. P. Sheehan, J. Lawson, M. Sosa, Richard A. Long

Faculty Publications

A simple, compact source of low-temperature, spatially and temporally uniform air plasma using a Telsa induction coil driver is described. The low-power ionization discharge plasma is localized (2 cm X 0.5 cm X 0.1 cm) and essentially free of arc channels. A Teflon coated rolling cylindrical electrode and dielectric coated ground plate are essential to the source’s operation and allow flat test samples to be readily exposed to the plasma. The plasma is a copious source of ozone and nitrogen oxides. Its effects on various microbes are discussed.

Towards A National Putative Father Registry Database, Mary M. Beck

Faculty Publications

This Article analyzes putative father registries and proposes federal legislation to create a national database that will enhance and connect the state and local registries. Issues and events leading to the development of registries are reviewed in Part I. Putative father registry mechanics and applicable case law are analyzed in Parts II and III.

Manufacturing Defects, David G. Owen

Faculty Publications

No abstract provided.

Comparison Of Algorithms For Estimating Ocean Primary Production From Surface Chlorophyll, Temperature, And Irradiance, Janet Campbell, David Antoine, Robert Armstrong, Kevin Arrigo, William Balch, Richard Barber, Michael Behrenfield, Robert Bidigare, James Bishop, Mary-Elena Carr, Wayne Esaias, Paul Falkowski, Nicolas Hoepffner, Richard Iverson, Dale Kiefer, Steven E. Lohrenz, John Marra, Andre Morel, John Ryan, Vladimir Vedernekov, Kirk Waters, Charles Yentsch, James Yoder

Faculty Publications

[1] Results of a single-blind round-robin comparison of satellite primary productivity algorithms are presented. The goal of the round-robin exercise was to determine the accuracy of the algorithms in predicting depth-integrated primary production from information amenable to remote sensing. Twelve algorithms, developed by 10 teams, were evaluated by comparing their ability to estimate depth-integrated daily production (IP, mg C m(-2)) at 89 stations in geographically diverse provinces. Algorithms were furnished information about the surface chlorophyll concentration, temperature, photosynthetic available radiation, latitude, longitude, and day of the year. Algorithm results were then compared with IP estimates derived from (14)C uptake measurements …

Justice Unconceived: How Posterity Has Rights, Aaron-Andrew P. Bruhl

Faculty Publications

No abstract provided.

The Structure Of Haplotype Blocks In The Human Genome, Stacey B. Gabriel, Stephen F. Schaffner, Huy Nguyen, Jamie M. Moore, Jessica Roy, Brendan Blumenstiel, John Higgins, Matthew Defelice, Amy Lochner, Maura Faggart, Shau Neen Liu-Cordero, Charles Rotimi, Adebowale Adeyemo, Richard Cooper, Ryk Ward, Eric S. Lander, Mark J. Daly, David Altshuler

Faculty Publications

Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia. We show that the human genome can be parsed objectively into haplotype blocks; sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are …

Ecosystem Decay Of Amazonian Forest Fragments: A 22-Year Investigation, William F. Laurance, Thomas E. Lovejoy, Heraldo L. Vasconcelos, Emilio M. Bruna, Raphael K. Didham, Philip C. Stouffer, Claude Gascon, Richard O. Bierregaard, Susan G. Laurance, Erica Sampaio

Faculty Publications

We synthesized key findings from the Biological Dynamics of Forest Fragments Project, the world's largest and longest-running experimental study of habitat fragmentation. Although initially designed to assess the influence of fragment area on Amazonian biotas, the project has yielded insights that go far beyond the original scope of the study. Results suggest that edge effects play a key role in fragment dynamics, that the matrix has a major influence on fragment connectivity and functioning, and that many Amazonian species avoid even small (<100-m-wide) clearings. The effects of fragmentation are highly eclectic, altering species richness and abundances, species invasions, forest dynamics, the trophic structure of communities, and a variety of ecological and ecosystem processes. Moreover, forest fragmentation appears to interact synergistically with ecological changes such as hunting, fires, and logging, collectively posing an even greater threat to the rainforest biota.

Insect Conservation In America: Status And Perspectives, Janice L. Bossart, Christopher E. Carlton

Faculty Publications

No abstract provided.

Quality Attributes Of Dried Milk Products Packaged For Long-Term Storage, Michelle A. Lloyd, J. Zou, H. Farnsworth, Oscar A. Pike

Faculty Publications

There is a market for dehydrated foods, such as nonfat dry milk (NFDM), that are packaged for long-term storage in case of natural disasters or other emergencies. To maintain quality and optimize shelf-life, NFDM must be properly processed from good quality milk, well-packaged (minimizing moisture, light and oxygen), and stored appropriately. Research is needed to determine the variation in quality that exists in dried milk products intended for retail sale. The objective of this research was to evaluate and compare the quality of several types of dried milk products packaged for long-term storage. Ten brands of dried milk products (5 …

N Uptake As A Function Of Concentration In Streams, Walter K. Dodds, Amanda J. Lopez, William B. Bowden, Stan Gregory, Nancy B. Grimm, Stephen K. Hamilton, Anne E. Hershey, Eugenia Marti, William H. Mcdowell, Judy L. Meyer, Donna Morrall, Patrick J. Mulholland, Bruce J. Peterson, Jennifer L. Tank, H. Maurice Valett, Jackson R. Webster, Wilfred M. Wollheim

Faculty Publications

Detailed studies of stream N uptake were conducted in a prairie reach and gallery forest reach of Kings Creek on the Konza Prairie Biological Station. Nutrient uptake rates were measured with multiple short-term enrichments of NO3− and NH4+ at constant addition rates in the spring and summer of 1998. NH4+ uptake was also measured with 15N-NH4+ tracer additions and short-term unlabeled NH4+ additions at 12 stream sites across North America. Concurrent addition of a conservative tracer was used to account for dilution in all experiments. NH4+ uptake rate per unit area (Ut) was positively correlated to nutrient concentration across all …