Digital Commons Network^™

Structure Of A Calcium-Dependent 11r-Lipoxygenase Suggests A Mechanism For Ca2+ Regulation, Priit Eek, Reet Järving, Ivar Järving, Nathaniel C. Gilbert, Marcia E. Newcomer, Nigulas Samel

Faculty Publications

Lipoxygenases (LOXs) are a key part of several signaling pathways that lead to inflammation and cancer. Yet, the mechanisms of substrate binding and allosteric regulation by the various LOX isoforms remain speculative. Here we report the 2.47-Å resolution crystal structure of the arachidonate 11R-LOX from Gersemia fruticosa, which sheds new light on the mechanism of LOXcatalysis. Our crystallographic and mutational studies suggest that the aliphatic tail of the fatty acid is bound in a hydrophobic pocket with two potential entrances. We speculate that LOXs share a common T-shaped substrate channel architecture that gives rise to the varying positional specificities. A …

Potential Role Of Inorganic Polyphosphate In The Cycling Of Phosphorus Within The Hypoxic Water Column Of Effingham Inlet, British Columbia, Julia M. Diaz, Ellery D. Ingall, Samuel D. Snow, Claudia R. Benitez-Nelson, Martial Taillefert, Jay A. Brandes

Faculty Publications

[1] The upper basin of Effingham Inlet possesses permanently anoxic bottom waters, with a water column redox transition zone typically occurring at least 40 m above the sediment‐water interface. During our sampling campaign in April and July 2007, this redox transition zone was associated with sharp peaks in a variety of parameters, including soluble reactive phosphorus (SRP) and total particulate phosphorus (TPP). Based on sequential extraction results, TPP maxima exhibited preferential accumulation of an operationally defined class of loosely adsorbed organic phosphorus (P), which may contain a substantial fraction of polyphosphate (poly‐P). This poly‐P may furthermore be involved in the …

Multiple Molecule Effects On The Cooperativity Of Protein Folding Transitions In Simulations, Jacob I. Lewis, Devin J. Moss, Thomas A. Knotts Iv

Faculty Publications

Though molecular simulation of proteins has made notable contributions to the study of protein folding and kinetics, disagreement between simulation and experiment still exists. One of the criticisms levied against simulation is its failure to reproduce cooperative protein folding transitions. This weakness has been attributed to many factors such as a lack of polarizability and adequate capturing of solvent effects. This work, however, investigates how increasing the number of proteins simulated simultaneously can affect the cooperativity of folding transitions — a topic that has received little attention previously. Two proteins are studied in this work: phage T4 lysozyme (Protein Data …

A Novel Ascaroside Controls The Parasitic Life Cycle Of The Entomopathogenic Nematode Heterorhabditis Bacteriophora, Jaime H. Noguez, Elizabeth S. Conner, Yue Zhou, Todd A. Ciche, Justin R. Ragains, Rebecca A. Butcher

Faculty Publications

Entomopathogenic nematodes survive in the soil as stress-resistant infective juveniles that seek out and infect insect hosts. Upon sensing internal host cues, the infective juveniles regurgitate bacterial pathogens from their gut that ultimately kill the host. Inside the host, the nematode develops into a reproductive adult and multiplies until unknown cues trigger the accumulation of infective juveniles. Here, we show that the entomopathogenic nematode Heterorhabditis bacteriophora uses a small-molecule pheromone to control infective juvenile development. The pheromone is structurally related to the dauer pheromone ascarosides that the free-living nematode Caenorhabditis elegans uses to control its development. However, none of the …

Further Evidence For The Likely Completeness Of The Library Of Solved Single Domain Protein Structures, Jeffrey Skolnick, Hongyi Zhou, Michal Brylinski

Faculty Publications

Recent studies questioned whether the Protein Data Bank (PDB) contains all compact, single domain protein structures. Here, we show that all quasi-spherical, QS, random protein structures devoid of secondary structure are in the PDB and are excellent templates for all native PDB proteins up to 250 residues. Because QS templates have a similar global contour as native, TASSER can refine 98% (90%) of those whose TM-score is 0.4 (0.35) to structures greater than or equal to the 0.5 TM-score threshold (0.74 (0.64) mean TM-score) for CATH/SCOP assignment. On the basis of this and the fact that, at a TM-score of …

Correlates Of Poor Health Among Orphans And Abandoned Children In Less Wealthy Countries: The Importance Of Caregiver Health, Nathan Thielman, Jan Ostermann, Kathryn Whetten, Rachel Whetten, Karen O’Donnell, Positive Outcomes For Orphans (Pofo) Research Team

Faculty Publications

Background: More than 153 million children worldwide have been orphaned by the loss of one or both parents, and millions more have been abandoned. We investigated relationships between the health of orphaned and abandoned children (OAC) and child, caregiver, and household characteristics among randomly selected OAC in five countries.

Methodology: Using a two-stage random sampling strategy in 6 study areas in Cambodia, Ethiopia, India, Kenya, and Tanzania, the Positive Outcomes for Orphans (POFO) study identified 1,480 community-living OAC ages 6 to 12. Detailed interviews were conducted with 1,305 primary caregivers at baseline and after 6 and 12 months. Multivariable logistic …

Amphibious Entrepreneurs And The Emergence Of Organizational Forms, Walter W. Powell, Kurt Sandholtz

Faculty Publications

We study the emergence of organizational forms, focusing on two mechanisms—reconfiguration and transposition—that distinguish the founding models of the first 26 biotechnology companies, all created in the industry's first decade, from 1972 to 1981. We analyze rich archival data using hierarchical cluster analysis, revealing four organizational variants of the dedicated biotech firm (DBF). Three were products of reconfiguration, as executives from Big Pharma used past practices to incorporate new science. One DBF variant resulted from 'amphibious' scientists who imported organizing ideas from the academy into their VC-funded start-ups. We argue that such transpositions are fragile, yet charged with generative possibilities. …

Effect Of Low Temperature Thermal Treatment On Soils Contaminated With Pentachlorophenol And Environmentally Persistent Free Radicals, Albert Leo N.Dela Cruz, Robert L. Cook, Slawomir M. Lomnicki, Barry Dellinger

Faculty Publications

The effect of low temperature thermal treatment on soils from a former Superfund wood-treating site contaminated with pentachlorophenol (PCP) and the environmentally persistent free radical (EPFR), pentachlorophenoxyl, was determined. The pentachlorophenoxyl EPFRs' and the PCP molecules' chemical behavior were simultaneously monitored at temperatures ranging from 25 to 300 °C via electron paramagnetic resonance (EPR) spectroscopy and GC-MS analysis, respectively. Two types of thermal treatment were employed: a closed heating (oxygen-starved condition) where the soil was heated under vacuum and an open heating system (oxygen-rich conditions), where the soil was heated in ambient air. EPR analyses for closed heating indicated the …

Voldemort Tyrannos: Plato’S Tyrant In The Republic And The Wizarding World, Anne Collins Smith, Owen M. Smith

Faculty Publications

In the Harry Potter novel series, by J. K. Rowling, the character of Lord Voldemort is the dictatorial ruler of the Death Eaters and aspiring despot of the entire wizarding community. As such, he serves as an apt subject for the application of Plato’s portrait of the tyrant in Republic IX. The process of applying Plato to Voldemort, however, leads to an apparent anomaly, the resolution of which requires that we move beyond the Republic to the account of beauty presented by Plato in the Symposium. In doing so, we shall find that while Plato can help us to understand …

Tools For The Identification Of Bioactives Impacting The Metabolic Syndrome: Screening Of A Botanical Extract Library Using Subcutaneous And Visceral Human Adipose-Derived Stem Cell-Based Assays, Benjamin M. Buehrer, David J. Duffin, Y. Renee Lea-Currie, David Ribnicky, Ilya Raskin, Jacqueline M. Stephens, William T. Cefalu, Jeffrey M. Gimble

Faculty Publications

Plant extracts continue to represent an untapped source of renewable therapeutic compounds for the treatment and prevention of illnesses including chronic metabolic disorders. With the increase in worldwide obesity and its related morbidities, the need for identifying safe and effective treatments is also rising. As such, use of primary human adipose-derived stem cells represents a physiologically relevant cell system to screen for bioactive agents in the prevention and treatment of obesity and its related complications. By using these cells in a primary screen, the risk and cost of identifying artifacts due to interspecies variation and immortalized cell lines is eliminated. …

Vitronectin Inhibits Neutrophil Apoptosis Through Activation Of Integrin-Associated Signaling Pathways, Hong Beom Bae, Jaroslaw W. Zmijewski, Jessy S. Deshane, Degui Zhi, Lawrence C. Thompson, Cynthia B. Peterson, David D. Chaplin, Edward Abraham

Faculty Publications

Vitronectin is present in large concentrations in serum and the extracellular matrix. Although vitronectin is known to modulate neutrophil adhesion and chemotaxis, and to contribute to neutrophil-associated proinflammatory processes, a role in apoptosis has not been demonstrated. In thepresent studies,wefound that neutrophils demonstrated more rapid progression to spontaneous or TNF-related apoptosisinducing ligand-induced apoptosis when incubated under vitronectinfree conditions thanwhen vitronectinwas present. The ability of native vitronectin to delay neutrophil apoptosis was not recapitulated by the vitronectin somatomedin B domain. In contrast, inclusion of the cyclo[Arg-Gly-Asp-D-Phe-Val] peptide in cultures containing vitronectin resulted in enhanced neutrophil apoptosis, showing that the vitronectin RGD …

Imprinting Control Region (Icr) Of The Peg3 Domain, Joomyeong Kim, Muhammad B. Ekram, Hana Kim, Mohammad Faisal, Wesley D. Frey, Jennifer M. Huang, Kim Ngoc Tran, Michelle M. Kim, Sungryul Yu

Faculty Publications

The imprinting and transcription of the 500 kb genomic region surrounding the mouse Peg3 is predicted to be regulated by the Peg3-differentially methylated region (DMR). In the current study, this prediction was tested using a mutant mouse line lacking this potential imprinting control region (ICR). At the organismal level, paternal and maternal transmission of this knockout (KO) allele caused either reduced or increased growth rates in the mouse, respectively. In terms of the imprinting control, the paternal transmission of the KO allele resulted in bi-allelic expression of the normally maternally expressed Zim2, whereas the maternal transmission switched the transcriptionally dominant …

Food Deprivation Explains Effects Of Mouthbrooding On Ovaries And Steroid Hormones, But Not Brain Neuropeptide And Receptor Mrnas, In An African Cichlid Fish, Brian P. Grone, Russ E. Carpenter, Malinda Lee, Karen P. Maruska, Russell D. Fernald

Faculty Publications

Feeding behavior and reproduction are coordinately regulated by the brain via neurotransmitters, circulating hormones, and neuropeptides. Reduced feeding allows animals to engage in other behaviors important for fitness, including mating and parental care. Some fishes cease feeding for weeks at a time in order to provide care to their young by brooding them inside the male or female parent's mouth. Maternal mouthbrooding is known to impact circulating hormones and subsequent reproductive cycles, but neither the full effects of food deprivation nor the neural mechanisms are known. Here we ask what effects mouthbrooding has on several physiological processes including gonad and …

The Evolution Of Reproductive Structures In Seed Plants: A Re-Examination Based On Insights From Developmental Genetics, Sarah Mathews, Elena M. Kramer

Faculty Publications

The study of developmental genetics is providing insights into how plant morphology can and does evolve, and into the fundamental nature of specific organs. This new understanding has the potential to revise significantly the way we think about seed plant evolution, especially with regard to reproductive structures. Here, we have sought to take a step in bridging the divide between genetic data and critical fields such as paleobotany and systematics. We discuss the evidence for several evolutionarily important interpretations, including the possibility that ovules represent meristematic axes with their own type of lateral determinate organs (integuments) and a model that …

The Tegula Tango: A Coevolutionary Dance Of Interacting, Positively Selected Sperm And Egg Proteins, Michael E. Hellberg, Alice B. Dennis, Patricia Arbour-Reily, Jan E. Aagaard, Willie J. Swanson

Faculty Publications

Reproductive proteins commonly show signs of rapid divergence driven by positive selection. The mechanisms driving these changes have remained ambiguous in part because interacting male and female proteins have rarely been examined. We isolate an egg protein the vitelline envelope receptor for lysin (VERL) from Tegula, a genus of free-spawning marine snails. Like VERL from abalone, Tegula VERL is a major component of the VE surrounding the egg, includes a conserved zona pellucida (ZP) domain at its C-terminus, and possesses a unique, negatively charged domain of about 150 amino acids implicated in interactions with the positively charged lysin. Unlike for …

Ecology And Management Of Bark Beetles (Coleoptera: Curculionidae: Scolytinae) In Southern Pine Forests, T. D. Schowalter

Faculty Publications

Bark beetles (Coleoptera: Curculionidae: Scolytinae) have been an important historic and current factor affecting pine forest production in the southern United States. Although tree mortality to bark beetles often detracts from forest management goals, the natural role of bark beetles is canopy opening, thinning, and diversification of stand structure and composition, effects that contribute to some ecosystem services in forests managed for multiple uses. Strategies to prevent bark beetle outbreaks exploit their sensitivity to host tree spacing and reliance on pheromones to attract sufficient numbers to overwhelm tree defenses. Tree species selection at planting or through selective thinning can favor …

The Bayou Lafourche Oral History Project: Understanding Environmental Change And Religious Identity In Louisiana, Michael Pasquier, Jennifer Cramer

Faculty Publications

The article discusses the Bayou Lafourche Oral History Project, which studied the relation between environmental changes and religion in Bayou Lafourche, a river in South Louisiana. Topics include the role of oral history in community history, the work of Louisiana State University (LSU) students in the project, and the use of audiorecording devices. Also discussed are the role of Roman Catholic devotion to Our Lady of Prompt Succor in the community, the 1965 experience of Hurricane Betsy, and the indexing of interviews from the project.

Oil Impacts On Coastal Wetlands: Implications For The Mississippi River Delta Ecosystem After The Deepwater Horizon Oil Spill, Irving A. Mendelssohn, Gary L. Andersen, Donald M. Baltz, Rex H. Caffey, Kevin R. Carman, John W. Fleeger, Samantha B. Joye, Qianxin Lin, Edward Maltby, Edward B. Overton, Lawrence P. Rozas

Faculty Publications

On 20 April 2010, the Deepwater Horizon explosion, which released a US governmentestimated 4.9 million barrels of crude oil into the Gulf of Mexico, was responsible for the death of 11 oil workers and, possibly, for an environmental disaster unparalleled in US history. For 87 consecutive days, the Macondo well continuously released crude oil into the Gulf of Mexico. Many kilometers of shoreline in the northern Gulf of Mexico were affected, including the fragile and ecologically important wetlands of Louisiana's Mississippi River Delta ecosystem. These wetlands are responsible for a third of the nation's fish production and, ironically, help to …

Concurrent Effects Of Resource Pulse Amount, Type, And Frequency On Community And Population Properties Of Consumers In Detritus-Based Systems, Donald A. Yee, Steven A. Juliano

Faculty Publications

Episodic resource inputs (i.e., pulses) can affect food web properties and community dynamics, but detailed mechanistic understanding of such effects remain elusive. Natural aquatic microsystems (e.g., tree holes, human-made containers) are colonized by invertebrates that form complex food webs dependent on episodic and sometimes sizeable inputs of allochthonous detritus from adjacent terrestrial environments. We investigated how variation in pulse frequency, amount, and resource type interacted to affect richness, abundance, composition, and population sizes of colonizing invertebrates in water-filled tires and tree hole analogs in a forest habitat. Different container types were used to assess the generality of effects across two …

Costs And Benefits Of Jasmonic Acid Induced Responses In Soybean, A. K. Accamando, J. T. Cronin

Faculty Publications

In response to herbivory, plants have evolved defense strategies to reduce herbivore preference and performance. A strategy whereby defenses are induced only upon herbivory can mitigate costs of defense when herbivores are scarce. Although costs and benefits of induced responses are generally assumed, empirical evidence for many species is lacking. Soybean (Glycine max L. Merr.) has emerged as a model species with which to address questions about induced responses. To our knowledge, this is the first study to examine the fitness costs and benefits of jasmonic acid-induced responses by soybean in the absence and presence of soybean loopers (Chrysodeix includens …

High-Amylose Resistant Starch Increases Hormones And Improves Structure And Function Of The Gastrointestinal Tract: A Microarray Study, Michael J. Keenan, Roy J. Martin, Anne M. Raggio, Kathleen L. Mccutcheon, Ian L. Brown, Anne Birkett, Susan S. Newman, Jihad Skaf, Maren Hegsted, Richard T. Tulley, Eric Blair, June Zhou

Faculty Publications

Background/Aims: Type 2 resistant starch from high-amylose maize (HAM-RS2) is associated with increased fermentation, increased expression of proglucagon (gene for GLP-1) and peptide YY (PYY) genes in the large intestine, and improved health. To determine what other genes are up- or downregulated with feeding of HAM-RS2, a microarray was performed. Methods: Adult, male Sprague Dawley rats were fed one of the following three diets for a 4-week study period: cornstarch control (CC, 3.74 kcal/g), dietary energy density control (EC, 3.27 kcal/g), and 30% HAM-RS2 (RS, 3.27 kcal/g). Rat microarray with ∼27,000 genes and validation of 94 representative genes with multiple …

Specific Soluble Oligomers Of Amyloid-Β Peptide Undergo Replication And Form Non-Fibrillar Aggregates In Interfacial Environments, Amit Kumar, Lea C. Paslay, Daniel Lyons, Sarah E. Morgan, John J. Correia, Vijayaraghavan Rangachari

Faculty Publications

Aggregates of amyloid-β (Aβ) peptides have been implicated in the etiology of Alzheimer disease. Among the different forms of Aβ aggregates, low molecular weight species ranging between ∼2- and 50-mers, also called “soluble oligomers,” have emerged as the species responsible for early synaptic dysfunction and neuronal loss. Emerging evidence suggests that the neurotoxic oligomers need not be formed along the obligatory nucleation-dependant fibril formation pathway. In our earlier work, we reported the isolation of one such “off-pathway” 12–18-mer species of Aβ42 generated from fatty acids called large fatty acid-derived oligomers (LFAOs) (Kumar, A., Bullard, R. L., Patel, P., Paslay, L. …

A Name I Call Myself: Creativity And Naming, Laura A. Heymann

Faculty Publications

In recent years, various disputes involving the use of creative works have demonstrated how trademark-related concerns lurk at the heart of what are ostensibly copyright-related claims. When recording artists such as Jackson Browne or the members of Heart object to the unauthorized use of their songs in connection with a political campaign, they are most likely not troubled about the loss of revenue resulting from the use; rather, they are likely concerned that the public will wrongly assume that the use of the song indicates that they have endorsed the political candidate. But because it is sometimes easier for them …

A Preliminary Examination Of The Cost Savings And Learning Impacts Of Using Open Textbooks In Middle And High School Science Classes, John Hilton Iii, David Wiley, Shelley Ellington, Tiffany Hall

Faculty Publications

Proponents of open educational resources claim that significant cost savings are possible when open textbooks displace traditional textbooks in the classroom. Over a period of two years, we worked with 20 middle and high school science teachers (collectively teaching approximately 3,900 students) who adopted open textbooks to understand the process and determine the overall cost of such an adoption. The teachers deployed open textbooks in multiple ways. Some of these methods cost more than traditional textbooks; however, we did identify and implement a successful model of open textbook adoption that reduces costs by over 50% compared to the cost of …

Review Of Marianne Gullberg And Kees De Bot (Eds): Gestures In Language Development., Gale Stam

Faculty Publications

No abstract provided.

Exploring Post-Translational Arginine Modification Using Chemically Synthesized Methylglyoxal Hydroimidazolones, Tina Wang, Rendy Kartika, David A. Spiegel

Faculty Publications

The methylglyoxal-derived hydroimidazolones (MG-Hs) comprise the most prevalent class of non-enzymatic, post-translational modifications of protein arginine residues found in nature. These adducts form spontaneously in the human body, and are also present at high levels in the human diet. Despite numerous lines of evidence suggesting that MG-H-arginine adducts play critical roles in both healthy and disease physiology in humans, detailed studies of these molecules have been hindered by a lack of general synthetic strategies for their preparation in chemically homogeneous form, and on scales sufficient to enable detailed biochemical and cellular investigations. To address this limitation, we have developed efficient, …

Visualizing Evolution In Real-Time Method For Strain Engineering, Luis Reyes, James Winkler, Katy Kao

Faculty Publications

The adaptive landscape for an industrially relevant phenotype is determined by the effects of the genetic determinants on the fitness of the microbial system. Identifying the underlying adaptive landscape for a particular phenotype of interest will greatly enhance our abilities to engineer more robust microbial strains. Visualizing evolution in real-time (VERT) is a recently developed method based on in vitro adaptive evolution that facilitates the identification of fitter mutants throughout the course of evolution. Combined with high-throughput genomic tools, VERT can greatly enhance the mapping of adaptive landscapes of industrially relevant phenotypes in microbial systems, thereby expanding our knowledge on …

Loss Of Mhc And Neutral Variation In Peary Caribou: Genetic Drift Is Not Mitigated By Balancing Selection Or Exacerbated By Mhc Allele Distributions, Sabrina S. Taylor, Deborah A. Jenkins, Peter Arcese

Faculty Publications

Theory and empirical results suggest that the rate of loss of variation at Mhc and neutral microsatellite loci may differ because selection influences Mhc genes, and because a high proportion of rare alleles at Mhc loci may result in high rates of loss via drift. Most published studies compare Mhc and microsatellite variation in various contemporary populations to infer the effects of population size on genetic variation, even though different populations are likely to have different demographic histories that may also affect contemporary genetic variation. We directly compared loss of variation at Mhc and microsatellite loci in Peary caribou by …

Magnitude And Composition Of Sinking Particulate Phosphorus Fluxes In Santa Barbara Basin, California, Emily Sekula‐Wood, Claudia R. Benitez-Nelson, Melissa A. Bennett, Robert Thunell

Faculty Publications

[1] The composition and bioavailability of particulate P influence marine biological community production on both modern and geologic time‐scales, and continental margins play a critical role in the supply, modification, and storage of particulate P. This study examined particulate P cycling in the Santa Barbara Basin (SBB) off the coast of southern California using a ∼520 m deep‐moored sediment trap deployed from 1993–2006 and a sediment core collected in 2005 directly beneath the sediment trap at 590 m. Total particulate P (TPP), particulate inorganic P (PIP), and particulate organic P (POP) were quantified using a 5‐step sequential extraction method (SEDEX) …

The African Cichlid Fish Astatotilapia Burtoni Uses Acoustic Communication For Reproduction: Sound Production, Hearing, And Behavioral Significance, Karen P. Maruska, Uyhun S. Ung, Russell D. Fernald

Faculty Publications

Sexual reproduction in all animals depends on effective communication between signalers and receivers. Many fish species, especially the African cichlids, are well known for their bright coloration and the importance of visual signaling during courtship and mate choice, but little is known about what role acoustic communication plays during mating and how it contributes to sexual selection in this phenotypically diverse group of vertebrates. Here we examined acoustic communication during reproduction in the social cichlid fish, Astatotilapia burtoni. We characterized the sounds and associated behaviors produced by dominant males during courtship, tested for differences in hearing ability associated with female …