Digital Commons Network^™

Extreme Primary And Secondary Protein Structure Variability In The Chimeric Male-Transmitted Cytochrome C Oxidase Subunit Ii Protein In Freshwater Mussels: Evidence For An Elevated Amino Acid Substitution Rate In The Face Of Domain-Specific Purifying Selection, Eric G. Chapman, Helen Piontkivska, Jennifer M. Walker, Donald T. Stewart, Jason P. Curole, Walter R. Hoeh

Faculty Publications

Background

Freshwater unionoidean bivalves, and species representing two marine bivalve orders (Mytiloida and Veneroida), exhibit a mode of mtDNA inheritance involving distinct maternal (F) and paternal (M) transmission routes concomitant with highly divergent gender-associated mtDNA genomes. Additionally, male unionoidean bivalves have a ~550 bp 3' coding extension to the cox2 gene (Mcox2e), that is apparently absent from all other metazoan taxa.

Results

Our molecular sequence analyses of MCOX2e indicate that both the primary and secondary structures of the MCOX2e region are evolving much faster than other regions of the F and M COX2-COX1 gene …

Neuroprotection Via Matrix-Trophic Coupling Between Cerebral Endothelial Cells And Neurons, Shuzhen Guo, Woo Jean Kim, Josephine Lok, Sun Ryung Lee, Elaine Besancon, Bing Hao Luo, Monique F. Stins, Xiaoying Wang, Shoukat Dedhar, Eng H. Lo

Faculty Publications

The neurovascular unit is an emerging concept that emphasizes homeostatic interactions between endothelium and cerebral parenchyma. Here, we show that cerebral endothelium are not just inert tubes for delivering blood, but they also secrete trophic factors that can be directly neuroprotective. Conditioned media from cerebral endothelial cells broadly protects neurons against oxygen-glucose deprivation, oxidative damage, endoplasmic reticulum stress, hypoxia, and amyloid neurotoxicity. This phenomenon is largely mediated by endothelial-produced brain-derived neurotrophic factor (BDNF) because filtering endothelial-conditioned media with TrkB-Fc eliminates the neuroprotective effect. Endothelial production of BDNF is sustained by β-1 integrin and integrin-linked kinase (ILK) signaling. Noncytotoxic levels of …

Maximal Exercise Electrocardiography Responses And Coronary Heart Disease Mortality Among Men With Diabetes Mellitus, G. William Lyerly, Xuemei Sui, Timothy S. Church, Carl J. Lavie, Gregory A. Hand, Steven N. Blair

Faculty Publications

Background - An abnormal ECG during maximal exercise testing has been shown to be a powerful predictor of future coronary heart disease (CHD) mortality in asymptomatic men. However, little is known about the relationship between exercise ECG responses and CHD risk in men with diabetes mellitus.

Methods and Results - We examined the association between exercise ECG responses and mortality in 2854 men with documented diabetes mellitus (mean age 49.5 years) who completed a maximal treadmill exercise test during the period from 1974 to 2001 and who were without a previous cardiovascular disease (CVD) event at baseline. Mortality due to …

Genome Analysis Of The Platypus Reveals Unique Signatures Of Evolution, Wesley C. Warren, La Deana W. Hillier, Jennifer A. Marshall Graves, Ewan Birney, Chris P. Ponting, Frank Grützner, Katherine Belov, Webb Miller, Laura Clarke, Asif T. Chinwalla, Shiaw Pyng Yang, Andreas Heger, Devin P. Locke, Pat Miethke, Paul D. Waters, Frédéric Veyrunes, Lucinda Fulton, Bob Fulton, Tina Graves, John Wallis, Xose S. Puente, Carlos López-Otín, Gonzalo R. Ordóñez, Evan E. Eichler, Lin Chen, Ze Cheng, Janine E. Deakin, Amber Alsop, Katherine Thompson, Patrick Kirby, Anthony T. Papenfuss, Matthew J. Wakefield, Tsviya Olender, Doron Lancet

Faculty Publications

We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus …

Climatically Driven Loss Of Calcium In Steppe Soil As A Sink For Atmospheric Carbon, A. G. Lapenis, G. B. Lawrence, S. W. Bailey, B. F. Aparin, Alexander I. Shiklomanov, N. A. Speranskaya, M. S. Torn, M. Calef

Faculty Publications

During the last several thousand years the semi‐arid, cold climate of the Russian steppe formed highly fertile soils rich in organic carbon and calcium (classified as Chernozems in the Russian system). Analysis of archived soil samples collected in Kemannaya Steppe Preserve in 1920, 1947, 1970, and fresh samples collected in 1998 indicated that the native steppe Chernozems, however, lost 17–28 kg m−2 of calcium in the form of carbonates in 1970–1998. Here we demonstrate that the loss of calcium was caused by fundamental shift in the steppe hydrologic balance. Previously unleached soils where precipitation was less than potential evapotranspiration are …

Usability Of Image Generation Platforms To Produce Oblique World Views, Michael T. Curtis, David Schuster, Florian Jentsch, R. Swanson, Michelle Harper-Sciarini

Faculty Publications

The interpretation of oblique aerial views in UAV operations is an important task, yet one that provides unique challenges. The human visual system is mal-adapted to visual perception from the air, especially when oblique views are involved. Hence, UAV operators have to be given training in the interpretation of oblique aerial visual stimuli. A novel way to train operators on how to accurately inspect and perceive oblique aerial images is to administer multiple trials of discrimination tasks for paired oblique images. In discrimination training, trainees view pairs of oblique aerial views and determine whether the images are taken from comparable …

This Bridge Called Imagination: On Reading The Arab Image Foundation And Its Collection, Dore Bowen

Faculty Publications

This essay examines the benefits and disadvantages of using imagination as a method of historical research in the archive. Employing Jean-Paul Sartre's notion of “image-consciousness” in The Psychology of Imagination, imagination is defined and explored as a form of perception based upon temporal absence or suspension. This method is then discussed in relation to the exhibition “Not Given: Talking of and Around Photographs of Arab Women” (2006), curated by the author with artist Isabelle Massu. The installation was assembled with the cooperation of the Arab Image Foundation in Beirut and traveled from Marseille (2005-06) to San Francisco (2007). The author …

Effect Of Epigenetic Modifications Of Donor Somatic Cells On The Subsequent Chromatin Remodeling Of Cloned Bovine Embryos, Angelica M. Giraldo, Darin A. Hylan, Casey B. Ballard, Megan N. Purpera, Todd D. Vaught, John W. Lynn, Robert A. Godke, Kenneth R. Bondioli

Faculty Publications

Evidence indicates that failure of nuclear transfer (NT) embryos to develop normally can be attributed, at least partially, to the use of differentiated cells as the donor karyoplast. Blastocyst production and development to term of cloned embryos has been hypothesized to differ between population doublings of the same cell line as a consequence of changes in the levels of DNA methyltransferase 1 (DNMT1) and methylated DNA during in vitro culture. The objective of this study was to determine embryo production, developmental potential, and gene expression patterns of prehatched and posthatched embryos generated using donor cells with different levels of DNMT1 …

Post-Allergen Challenge Inhibition Of Poly(Adp-Ribose) Polymerase Harbors Therapeutic Potential For Treatment Of Allergic Airway Inflammation, A. S. Naura, C. P. Hans, M. Zerfaoui, D. You, S. A. Cormier, M. Oumouna, A. H. Boulares

Faculty Publications

Background: Identifying therapeutic drugs that block the release or effects of T-helper type 2 (Th2) cytokines after allergen exposure is an important goal for the treatment of allergic inflammatory diseases including asthma. We recently showed, using a murine model of allergic airway inflammation, that poly(ADP-ribose) polymerase (PARP) plays an important role in the pathogenesis of asthma-related lung inflammation. PARP inhibition, by single injection of a novel inhibitor, thieno[2,3-c]isoquinolin-5-one (TIQ-A), before ovalbumin (OVA) challenge, prevented airway eosinophilia in C57BL/6 mice with concomitant suppression of Th2 cytokine production and mucus secretion. Objective: To evaluate the efficacy of the drug when it is …

Culture-Independent Identification Of Gut Bacteria In Fourth-Instar Red Imported Fire Ant, Solenopsis Invicta Buren, Larvae, Albert H. Lee, Claudia Husseneder, Linda Hooper-Bùi

Faculty Publications

Red imported fire ants (RIFA), Solenopsis invicta Buren, are medical, urban, and agricultural pests from South America. They are successful invaders due to their preference for disturbed habitats, high reproductive rates, and the ability to feed on a wide variety of food items (omnivorous). Fourth-instar larvae are used by the colony to digest solid food and then regurgitate it for consumption by workers and queens. Larvae are an ideal source of investigations of endosymbiotic bacteria possibly involved in nutrient distributions. Our study utilized 16S rDNA sequencing to describe the composition of the bacterial community in fourth-instar ant larvae in order …

Chimpanzees Do Not Take Advantage Of Very Low Cost Opportunities To Deliver Food To Unrelated Group Members, Jennifer Vonk, Sarah F. Brosnan, Joan B. Silk, Joseph Heinrich, Amanda S. Richardson, Susan P. Lambeth, Steven J. Schapiro, Daniel J. Povinelli

Faculty Publications

We conducted experiments on two populations of chimpanzees, Pan troglodytes, to determine whether they would take advantage of opportunities to provide food rewards to familiar group members at little cost to themselves. In both of the experiments described here, chimpanzees were able to deliver identical rewards to themselves and to other members of their social groups. We compared the chimpanzees' behaviour when they were paired with another chimpanzee and when they were alone. If chimpanzees are motivated to provide benefits to others, they are expected to consistently deliver rewards to others and to distinguish between the partner-present and partner-absent …

Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Joshua Udall, Lex E. Flagel, Dan Nettleton, Jonathan F. Wendel

Faculty Publications

Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes. Results- We compared homoeolog (genes duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 …

What Every Christian Should Know About Amos And Hosea, Rolf A. Jacobson

Faculty Publications

To overcome the biblical illiteracy of the churches, leaders need to teach parishioners the basic content of the Bible. This essay offers a resource for that important task.

Effects Of Imperfect Dynamic Clamp: Computational And Experimental Results., Bettencourt Jc, Lillis Kp, Stupin Lr, White Ja

Faculty Publications

No abstract provided.

Artificial Synaptic Conductances Reduce Subthreshold Oscillations And Periodic Firing In Stellate Cells Of The Entorhinal Cortex., Fernandez Fr, White Ja

Faculty Publications

No abstract provided.

Seeing Inside The Mountains: Cynthia Rylant's Appalachian Literature And The "Hillbilly" Stereotype, Karen Roggenkamp

Faculty Publications

If Ob, as a West Virginia native, possesses the ability to see The Mysteries where others see only primitivistic whittling or, more pejoratively, tacky wooden trash cluttering the yards of mountain families, then Rylant's Appalachian works likewise depict characters who possess an ability to see beyond external markers and predictable interpretations, and who seek an emotional and spiritual interiority based on family, love, and sense of place. Rylant's words in The Relatives Came, When I Was Young in the Mountains, and Missing May work to restore the integrity of Appalachia as a place of "interior" values, a setting that symbolizes …

Further Characterization Of Vibrio Vulnificus Rugose Variants And Identification Of A Capsular And Rugose Exopolysaccharide Gene Cluster, Brenda L. Grau, Margaret C. Henk, Katherine L. Garrison, Brett J. Olivier, Randall M. Schulz, Kathy L. O'Reilly, Gregg S. Pettis

Faculty Publications

Capsular polysaccharide (CPS) is a major virulence factor in Vibrio vulnificus, and encapsulated strains have an opaque, smooth (OpS) colony morphology, while nonencapsulated strains have a translucent, smooth (TrS) colony morphology. Previously, we showed that OpS and TrS parental strains can yield a third colony type, rugose (R), and that the resulting strains, with the OpR and TrR phenotypes, respectively, form copious biofilms. Here we show that while OpR and TrR strains both produce three-dimensional biofilm structures that are indicative of rugose extracellular polysaccharide (rEPS) production, OpR strains also retain expression of CPS and are virulent in an iron-supplemented mouse …

The Effect Of Diets Varying In Dietary Cation-Anion Difference Fed In Late Gestation And In Lactation On Sow Productivity, M. L. Roux, S. L. Johnston, R. D. Lirette, T. D. Bidner, L. L. Southern, P. W. Jardon

Faculty Publications

© 2008 American Registry of Professional Animal Scientists. Eighty-six primiparous or multiparoussows and their pigs were used to evaluatethe effects of changing DCAD in late gestation and in lactation on sow productivity.Sows were allotted to treatment based on parity and their farrowing date. Experiment 1 was a preliminary experiment conducted to determine the level of DCAD that would reduce urinary pH. Twenty sows were used in Exp. 1, and the dietary treatments consisted of a corn-soybean meal diet with 4 levels of DCAD (140, 103, 80, and 56 mEq/kg). These DCAD were achieved by addition of 4 levels of chloride …

First Report Of Multiple Drug Resistance In Trichostrongyles Affecting Sheep Under Field Conditions In Italy (Parasitology Research (2007) 101, 6, (1713-1716) Doi: 10.1007/S00436-007-0707-4), Donato Traversa, Barbara Paoletti, Domenico Otranto, James Miller

Faculty Publications

No abstract provided.

The Sinorhizobium Meliloti Msba2 Protein Is Essential For The Legume Symbiosis, Sebastian Beck, Victoria L. Marlow, Katy Woodall, William T. Doerrler, Euan K. James, Gail P. Ferguson

Faculty Publications

Sinorhizobium meliloti is a beneficial legume symbiont, closely related to Brucella species, which are chronic mammalian pathogens. We discovered that the S. meliloti MsbA2 protein is essential to ensure the symbiotic interaction with the host plant, alfalfa. S. meliloti invades plant cells via plant-derived structures known as infection threads. However, in the absence of MsbA2, S. meliloti remains trapped within abnormally thickened infection threads and induces a heightened plant defence response, characterized by a substantial thickening of the nodule endodermis layer and the accumulation of polyphenolic compounds. The S. meliloti MsbA2 protein is homologous to the Escherichia coli lipopolysaccharide/phospholipid trafficking …

An Appreciation Of Marc Galanter's Scholarship, John M. Lande

Faculty Publications

This brief essay highlights three of Marc Galanter's works to illustrate qualities that seem especially worth emulating. Galanter's classic article, Why the “Haves” Come Out Ahead: Speculations on the Limits of Legal Change, focuses on how the legal system actually operates in daily life and challenges a conventional wisdom that simply providing have-nots with more lawyers would substantially reduce inequality. The article is particularly relevant to the dispute resolution field, focusing on the vast majority of legally-oriented behavior that occurs outside of court. It distinguishes truly private dispute resolution (such as self-help, withdrawal from relationships, and intra-group processes) from settlement …

Legal Theoretic Inadequacy And Obesity Epidemic Analysis, David Yosifon

Faculty Publications

This Article explores crucial analytic and normative limitations in presently dominant and ascendant approaches to legal theory. The approaches' failure to provide a satisfying framework for analyzing the obesity epidemic presently raging undeterred in American society reveals these limitations. Conventional law and economics scholars writing on the subject have deployed familiar frameworks to reach predictable conclusions that are neither intellectually nor morally justifiable. This Article argues that recent theoretical innovations promulgated within the burgeoning law and behavioralism movement have thus far provided no more reliable a framework for legal analysis of the obesity epidemic than has conventional law and economics. …

Entrepreneurs On Horseback: Reflections On The Organization Of Law, Darian M. Ibrahim, D. Gordon Smith

Faculty Publications

“Law and entrepreneurship” is an emerging field of study. Skeptics might wonder whether law and entrepreneurship is a variant of that old canard, the Law of the Horse. In this Essay, we defend law and entrepreneurship against that charge and urge legal scholars to become even more engaged in the wide-ranging scholarly discourse regarding entrepreneurship. In making our case, we argue that research at the intersection of entrepreneurship and law is distinctive. In some instances, legal rules and practices are tailored to the entrepreneurial context, and in other instances, general rules of law find novel expression in the entrepreneurial context. …

Jacobus Tenbroek, Participatory Justice, And The Un Convention On The Rights Of Persons With Disabilities, Michael Ashley Stein, Janet E. Lord

Faculty Publications

No abstract provided.

The Decalogue Predates Mount Sinai: Indicators From The Book Of Genesis, Jo Ann Davidson

Faculty Publications

No abstract provided.

Neogene Evolution Of The Mixed Carbonate-Siliciclastic System In The Gulf Of Papua, Papua New Guinea, Evgueni N. Tcherepanov, André W. Droxler, Philippe Lapointe, Gerald R. Dickens, Sam J. Bentley, Luc Beaufort, Larry C. Peterson, James Daniell, Bradley N. Opdyke

Faculty Publications

This paper outlines the evolution of the late Cenozoic mixed carbonate-siliciclastic depositional system in the Gulf of Papua (GoP), using seismic, gravity, multibeam bathymetry, well data sets, and Landsat imagery. The deposition of the mixed sedimentary sequences was influenced by dynamic interplay of tectonics, eustasy, in situ carbonate production, and siliciclastic sediment supply. The roles of these major factors are estimated during different periods of the GoP margin evolution. The Cenozoic mixed system in the GoP formed in distinct phases. The first phase (Late Cretaceous-Paleocene) was mostly driven by tectonics. Rifting created grabens and uplifted structural blocks which served later …

Gene Rearrangement Analysis And Ancestral Order Inference From Chloroplast Genomes With Inverted Repeat, Feng Yue, Liying Cui, Claude W. Depamphilis, Bernard M.E. Moret, Jijun Tang

Faculty Publications

Background
Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction.

Results
We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR …

Molecular Dynamics Simulations Of Biotin Carboxylase, Sten O.Nilsson Lili, Jiali Gao, Grover L. Waldrop

Faculty Publications

Biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin and is one component of the multienzyme complex acetyl-CoA carboxylase that catalyzes the first committed step in fatty acid synthesis in all organisms. Biotin carboxylase from Escherichia coli, whose crystal structures with and without ATP bound have been determined, has served as a model system for this component of the acetyl-CoA carboxylase complex. The two crystal structures revealed a large conformational change of one domain relative to the other domains when ATP is bound. Unfortunately, the crystal structure with ATP bound was obtained with an inactive site-directed mutant of the enzyme. As …

The Innate Immune Database (Iidb), Martin Korb, G. R. Aistair, Vesteinn Thorsson, Christophe Battail, Bin Li, Daehee Hwang, Kathleen A. Kennedy, Jared C. Roach, Carrie M. Rosenberger, Mark Gilchrist, Daniel Zak, Carrie Johnson, Bruz Marzolf, Alan Aderem, Ilya Shmulevich, Hamid Bolouri

Faculty Publications

Background: As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site http://www.innateImmunity-systemsbiology.org. Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the …

Double-Stranded Rna-Activated Protein Kinase Pkr Of Fishes And Amphibians: Varying The Number Of Double-Stranded Rna Binding Domains And Lineage-Specific Duplications, Loubna Tazi, Stefan Rothenburg, Nikolaus Deigendesch, Madhusudan Dey, Thomas E. Dever

Faculty Publications

Double-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2alpha leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs). Fish and amphibian PKR genes have not been described so far. Results- Here we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of …