Digital Commons Network^™

Increased Rates Of Molecular Evolution In An Equatorial Plant Clade: An Effect Of Environment Or Phylogenetic Nonindependence?, Jeremy M. Brown, Gregory B. Pauly

Faculty Publications

A recent study of environmental effects on rates of molecular evolution in the plant subgenus Mearnsia shows that species occurring in more equatorial latitudes have higher rates of substitution in rDNA sequences as compared to their more southerly congeners (Wright et al. 2003). However, we believe that the statistical approach employed by Wright et al. (2003) insufficiently accounts for the phylogenetic nonindependence of the species examined, given that all six equatorial species of Mearnsia form a clade. To distinguish between the effect of latitude and that of phylogenetic nonindependence, we have employed a variety of comparative approaches that use independent …

Future Of Avian Genetic Resources Collections: Archives Of Evolutionary And Environmental History, Scott V. Edwards, Sharon Birks, Robb T. Brumfield, Robert Hanner

Faculty Publications

No abstract provided.

Mitochondrial Variation In Bolivian Populations Of The Variable Antshrike (Thamnophilus Caerulescens), Robb T. Brumfield

Faculty Publications

The Variable Antshrike (Thamnophilus caerulescens) is arguably the most polytypic thamnophilid, with males ranging from almost entirely jet black to nearly white. The four subspecies that occur in Bolivia are strikingly divergent in male plumage: T. c. aspersiventer (black with white-barred belly), T. c. connectens (black back and bib with white belly), T. c. dinellii (gray throat and back with rufous belly), and T. c. paraguayensis (light gray with white belly). To assess the genetic structure of those taxa in Bolivia, sequence variation at the mitochondrial cytochrome-b gene was screened in 126 individuals collected across transects spanning the plumage and …

Norleucine, A Natural Occurrence In A Novel Ergot Alkaloid Γ-Ergokryptinine, L. Cvak, A. Jegorov, P. Sedmera, I. Císařová, J. Čejka, B. Kratochvíl, S. Pakhomova

Faculty Publications

A novel natural peptide ergot alkaloid γ-ergokryptinine containing norleucine has been isolated from ergot sclerotia of the field-growing parasitic fungus Claviceps purpurea CCM 8059. Its structure was deduced from the NMR and mass spectral data. The final structural proof was provided by the crystal structure determination, which is the first X-ray structure of a natural Nle-containing secondary metabolite. The conformations of three ergopeptinines: γ-ergokryptinine, ergoladinine, and α-ergokryptinine were compared. © Springer-Verlag 2005.

Marine Radiations At Small Geographic Scales: Speciation In Neotropical Reef Gobies (Elacatinus), Michael S. Taylor, Michael E. Hellberg

Faculty Publications

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation <1000 >km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of …

The Structures Of The Unique Sulfotransferase Retinol Dehydratase With Product And Inhibitors Provide Insight Into Enzyme Mechanism And Inhibition, Svetlana Pakhomova, Jochen Buck, Marcia E. Newcomer

Faculty Publications

The structure of retinol dehydratase (DHR) from Spodoptera frugiperda, a member of the sulfotransferase superfamily, in complexes with the inactive form of the cofactor PAP 3′-phosphoadenosine 5′-phosphate (PAP) and (1) the product of the reaction with retinol anhydroretinol (AR), (2) the retinoid inhibitor all-frans-4-oxoretinol (OR), and (3) the potent steroid inhibitor androsterone (AND) have been determined and compared to the enzyme complex with PAP and retinol. The structures show that the geometry of the active-site amino acids is largely preserved in the various complexes. However, the β-ionone rings of the retinoids are oriented differently with respect to side chains that …

Formosan Subterranean Termite (Isoptera: Rhinotermitidae) Soldiers Regulate Juvenile Hormone Levels And Caste Differentiation In Workers, Lixin Mao, Gregg Henderson, Yuxiu Liu, Roger A. Laine

Faculty Publications

A caste structure is maintained in termite societies and juvenile hormone (JH) is generally regarded as the most important regulator in these termite colonies. Here, we demonstrate that the soldier caste regulates JH in workers of Coptotermes formosanus Shiraki. Worker termites (80-100 individuals) were placed in petri dishes with 0, 5, 10, or 20% soldiers. JH III titers of groups of these workers were monitored at 14, 28, 42, and 56 d. Any changes in soldier caste proportions also were noted at each sample date. On the first sample date, the JH levels in workers were similar among treatments with …

Snp Haplotypes In The Angiotensin I-Converting Enzyme (Ace) Gene: Analysis Of Nigerian Family Data Using Gamete Competition Models, Colin A. Mckenzie, J. S. Sinsheimer, A. A. Adeyemo, R. D. Cox, L. Southam, A. Hugill, N. Bouzekri, M. Lathrop, T. E. Forrester, R. S. Cooper, R. Ward

Faculty Publications

Gamete competition models were used to explore the relationships between 13 ACE gene polymorphisms and plasma ACE concentration in a set of Nigerian families. Several markers in the 5′ and 3′ regions of the gene were significantly associated with ACE concentration (P < 10-4). Multi-locus genotypes comprising different combinations of markers from the 5′ UTR and the 3′ region of the gene were also analysed; in addition to G2350A, in the 3′ region, two markers from the 5′ UTR (A-5466C and A-240T) were found to be associated with ACE concentration. These results are consistent with reports that have suggested the presence of at least two ACE-linked QTLs, and demonstrate the utility of gamete competition models in the exploratory investigation of the relationship between a quantitative trait and multiple variants in a small genomic region. © University College London 2005.

Ethnicity And Human Genetic Linkage Maps, Eric Jorgenson, Hua Tang, Maya Gadde, Mike Province, Mark Leppert, Sharon Kardia, Nicholas Schork, Richard Cooper, D. C. Rao, Eric Boerwinkle, Neil Risch

Faculty Publications

Human genetic linkage maps are based on rates of recombination across the genome. These rates in humans vary by the sex of the parent from whom alleles are inherited, by chromosomal position, and by genomic features, such as GC content and repeat density. We have examined-for the first time, to our knowledge-racial/ethnic differences in genetic maps of humans. We constructed genetic maps based on 353 microsatellite markers in four racial/ethnic groups: whites, African Americans, Mexican Americans, and East Asians (Chinese and Japanese). These maps were generated using 9,291 subjects from 2,900 nuclear families who participated in the National Heart, Lung, …

Colony Social Organization And Population Genetic Structure Of An Introduced Population Of Formosan Subterranean Termite From New Orleans, Louisiana, Claudia Husseneder, Matthew T. Messenger, Nan Yao Su, J. Kenneth Grace, Edward L. Vargo

Faculty Publications

The Formosan subterranean termite, Coptotermes formosanus Shiraki, is an invasive species in many parts of the world, including the U.S. mainland. The reasons for its invasive success may have to do with the flexible social and spatial organization of colonies. We investigated the population and breeding structure of 14 C. formosanus colonies in Louis Armstrong Park, New Orleans, LA. This population has been the focus of extensive study for many years, providing the opportunity to relate aspects of colony breeding structure to previous findings on colony characteristics such as body weight and number of workers, wood consumption, and intercolony aggression. …

Reduced Susceptibility To Tebufenozide In Populations Of The Sugarcane Borer (Lepidoptera: Crambidae) In Louisiana, F. P.F. Reay-Jones, W. Akbar, C. D. Mcallister, T. E. Reagan, J. A. Ottea

Faculty Publications

Susceptibility of the sugarcane borer, Diatraea saccharalis (F.), to tebufenozide was measured using a feeding bioassay, and values obtained were compared with baselines generated before the use of this insecticide in Louisiana sugarcane, Saccharum spp. Results from our study suggest that susceptibility to tebufenozide is decreasing in field-collected sugarcane borers. Inflections in the log dosage-probit lines were detected for many of the field collections, indicating increased heterogeneity within these populations in response to tebufenozide. Where appropriate, probit transformation was used to estimate susceptibility, and significant differences (1.6-2.7-fold) were measured in LC50 values between some field-collected cohorts and the previously measured …

Optimal Random Libraries For The Isolation Of Catalytic Rna, Tricia M. Coleman, Faqing Huang

Faculty Publications

The relationship between ribozyme size and catalytic activity is of fundamental importance for RNA catalysis and molecular evolution in the RNA world. We have performed a series of competitive in vitro selection experiments to probe the relationship using RNA libraries containing size-heterogeneous random regions. Our experiments have established an inverse correlation between RNA replication efficiency (the combined efficiency of PCR amplification, transcription, and reverse transcription) and RNA size. A number of ribozyme sequences have been isolated from different RNA size groups under competitive selection conditions. Comprehensive kinetic analysis on isolated ribozymes has revealed that large ribozymes do not confer a …

Alu Insertion Loci And Platyrrhine Primate Phylogeny, David A. Ray, Jinchuan Xing, Dale J. Hedges, Michael A. Hall, Meredith E. Laborde, Bridget A. Anders, Brittany R. White, Nadica Stoilova, Justin D. Fowlkes, Kate E. Landry, Leona G. Chemnick, Oliver A. Ryder, Mark A. Batzer

Faculty Publications

Short INterspersed Elements (SINEs) make very useful phylogenetic markers because the integration of a particular element at a location in the genome is irreversible and of known polarity. These attributes make analysis of SINEs as phylogenetic characters an essentially homoplasy-free affair. Alu elements are primate-specific SINEs that make up a large portion of the human genome and are also widespread in other primates. Using a combination wet-bench and computational approach we recovered 190 Alu insertions, 183 of which are specific to the genomes of nine New World primates. We used these loci to investigate branching order and have produced a …

Modeling The Amplification Dynamics Of Human Alu Retrotransposons, Dale J. Hedges, Richard Cordaux, Jinchuan Xing, David J. Witherspoon, Alan R. Rogers, Lynn B. Jorde, Mark A. Batzer

Faculty Publications

Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed …

Home-Range Size, Response To Fire, And Habitat Preferences Of Wintering Henslow's Sparrows, Catherine L. Bechtoldt, Philip C. Stouffer

Faculty Publications

Henslow's Sparrow (Ammodramus henslowii) is a declining, disturbance-dependent grassland bird that winters in the longleaf pine (Pinus palustris) ecosystem of the southeastern United States. During two winters (2001, 2002), we estimated the relative abundances, movement patterns, and habitat associations of Henslow's Sparrows wintering in habitat patches differing in time since last burn (burn treatment). We conducted our study in southeastern Louisiana in Andropogon spp.-dominated longleaf pine savanna habitat. Henslow's Sparrows were most abundant in savannas burned the previous growing season, with a mean relative abundance of 2.6 individuals/ha. The most dramatic decline occurred between burn year 0 and year 1 …

Role Of The Posterior Vacuole In Spraguea Lophii (Microsporidia) Spore Hatching, Ann M. Findley, Earl H. Weidner, Kevin R. Carman, Zhimin Xu, J. Samuel Godbar

Faculty Publications

Microsporidia constitute a large group of obligate intracellular protozoan parasites that inject themselves into host cells via the extrusion apparatus of the infective spore stage. Although the injection process is poorly understood, its energy source is thought to reside in the posterior vacuole that swells significantly during spore firing. Here we report the presence and localisation of the key peroxisomal enzymes catalase and acyl-CoA oxidase (ACOX) within the posterior vacuole of Spraguea lophii (Doflein, 1898) spores. Western blot analyses show that these enzymes discharge out of the spore and end up in the medium external to the extruded sporoplasms. The …

Storage Stability Of Lutein During Ripening Of Cheddar Cheese, S. T. Jones, K. J. Aryana, J. N. Losso

Faculty Publications

Lutein (3,3′-dihydroxy-α-carotene) has been identified as a dietary factor that can delay the onset of age-related macular degeneration (AMD). However, available food sources of lutein contain only modest amounts of the carotenoid. Food fortification with lutein extract has been identified as a low-budget approach to prevent the onset or progression of AMD. The objectives of this study were to 1) incorporate various amounts of lutein into Cheddar cheese; 2) examine the color, pH, microbiological, and sensory characteristics of the Cheddar cheese during storage; and 3) analyze the stability of lutein during the cheese maturation process. Lutein extracted from corn was …

Laser Induced Fluorescence Photobleaching Anemometer For Microfluidic Devices, Guiren Wang

Faculty Publications

We have developed a novel, non-intrusive fluid velocity measurement method based on photobleaching of a fluorescent dye for microfluidic devices. The residence time of thefluorescent dye in a laser beam depends on the flow velocity and approximately corresponds to the decaying time of the photobleaching of the dye in the laser beam. The residence time is inversely proportional to the flow velocity. The fluorescence intensity increases with the flow velocity due to the decrease of the residence time. A calibration curve between fluorescence intensity and known flow velocity should be obtained first. The calibration relationship is then used to calculate …

Navigating Dangerous Constitutional Straits: A Prolegomenon On The Federal Marriage Amendment And The Disenfrachisement Of Sexual Minorities, E. Gary Spitko, Ronald J. Krotoszynski Jr.

Faculty Publications

Navigating Dangerous Constitutional Straits: A Prolegomenon on the Federal Marriage Amendment and the Disenfranchisement of Sexual Minorities considers the nature of the constitutional amendment process and the Supreme Court's historical approach to incorporating new amendments into the existing constitutional text. Professors Krotoszynski and Spitko argue that, given the Supreme Court's consistent narrow reading of new amendments to preserve pre-existing constitutional rights, the Federal Marriage Amendment must be broadly written to override expressly due process and equal protection guarantees against not only sexual orientation discrimination, but also gender discrimination. In our view, however, if a proposed Federal Marriage Amendment were sufficiently …

The Persistence Of White Privilege, Stephanie M. Wildman

Faculty Publications

Most discussions of white privilege emphasize the individual benefit to the holder of privilege. Yet dynamics beyond the individual combine to reinforce and reinvent white privilege. Socio-cultural factors operate in conjunction with material forces, enabling whites to self-perpetuate as a dominant racialized identity. Material forces such as the distribution of societal goods and resources, the division of labor, and immigration policies, create a world that privileges whiteness. Socio-cultural factors, including discursive practices, patterns of behavior, and the thinking patterns that language creates, further strengthen white privilege, contributing to its endurance.

This article focuses on four socio-cultural factors that reinforce white …

When The Truth Is Not Enough: Tissue Donation, Altruism, And The Market, Michelle Oberman

Faculty Publications

No abstract provided.

The Pathogenic Copepod Phrixocephalus Cincinnatus (Copepoda: Pennellidae) In The Eye Of Arrowtooth Flounder, Atherestes Stomias, And Rex Sole, Glyptocephalus Zachirus, From British Columbia, Reginald B. Blaylock, Robin M. Overstreet, A. Morton

Faculty Publications

We report Phrixocephalus cincinnatus, a pennellid copepod infecting the eyes of flatfishes, from a single specimen of rex sole, Glyptocephalus zachirus, for the first time. In the typical host, the arrowtooth flounder, Atherestes stomias, the parasite occurred commonly in sampled populations from the Broughton Archipelago in British. Columbia, infected primarily the right eye of the flounder, and on only one occasion presented more than two parasites per eye. The copepod attached to the choroid layer and ramified throughout the posterior compartment of the eye, resulting in the disruption of the retina and probably impairing host vision. Inflammation and hyperplasia progressed …

Medicare Should, But Cannot, Consider Cost: Legal Impediments To Sound Policy, Jacqueline R. Fox

Faculty Publications

No abstract provided.

Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara

Faculty Publications

Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy …

Research Directions For Service-Oriented Multiagent Systems, Michael N. Huhns, Munindar P. Singh, Mark Burstein, Keith Decker, Edmund Durfee, Tim Finin, Les Gasser, Hrishikesh Goradia, Nick Jennings, Kiran Lakkaraju, Hideyuki Nakashima, H. Van Dyke Parunak, Jeffrey S. Rosenschein, Alicia Ruvinsky, Gita Sukthankar, Samarth Swarup, Katia Sycara, Milind Tambe, Tom Wagner, Laura Zavala, Mas Research Roadmap Project

Faculty Publications

Today's service-oriented systems realize many ideas from the research conducted a decade or so ago in multiagent systems. Because these two fields are so deeply connected, further advances in multiagent systems could feed into tomorrow's successful service-oriented computing approaches. This article describes a 15-year roadmap for service-oriented multiagent system research.

Monsoon-Driven Biogeochemical Processes In The Arabian Sea, Jerry D. Wiggert, Raleigh Hood, Karl Banse, John Kindle

Faculty Publications

Although it is nominally a tropical locale, the semiannual wind reversals associated with the Monsoon system of the Arabian Sea result annually in two distinct periods of elevated biological activity. While in both cases monsoonal forcing drives surface layer nutrient enrichment that supports increased rates of primary productivity, fundamentally different entrainment mechanisms are operating in summer (Southwest) and winter (Northeast) Monsoons. Moreover, the intervening intermonsoon periods, during which the region relaxes toward oligotrophic conditions more typical of tropical environments, provide a stark contrast to the dynamic biogeochemical activity of the monsoons. The resulting spatial and temporal variability is great and …

Novel Cyanine-Amp Conjugates For Efficient 5' Rna Fluorescent Labeling By One-Step Transcription And Replacement Of [γ-32P] Atp In Rna Structural Investigation, Na Li, Changjun Yu, Faqing Huang

Faculty Publications

Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 φ2.5 promoter. Efficient fluorophore labeling of 5′ RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current work makes fluorescently labeled RNA readily available for broad applications in biochemistry, molecular biology, structural biology and biomedicine. In particular, site-specifically fluorophore-labeled large RNAs prepared by the current method may be used to investigate RNA structure, folding and mechanism by various fluorescence techniques. In addition, F550/570 and F650/670 may replace [γ-³²P]ATP to prepare …

Myths And Realities In The Sameness/Difference Debate, Rosemary C. Salomone

Faculty Publications

(Excerpt)

Remarks made by Lawrence H. Summers, the President of Harvard University, suggesting by his "best guess" that "intrinsic aptitude" primarily accounts for the paucity of women holding senior academic positions in math, physics, engineering, and technology' have touched off a new round in a timeless debate over gender sameness and difference. This seeming bow to biology, emanating from the head of the nation's most prestigious academic institution, conjures up memories of yet another Harvard figure almost a century and a half ago. At that time, Dr. Edward Clarke, a member of Harvard's Board of Overseers and a former member …

On Discovering Doctrine: "Justice" In Contract Agreement, Peter A. Alces

Faculty Publications

No abstract provided.

The Discourse Beneath: Emotional Epistemology In Legal Deliberation And Negotiation, Erin Ryan

Faculty Publications

No abstract provided.