Digital Commons Network^™

Studies On The Subcellular Localization Of The Porphycene Cpo, David Kessel, Mary Conley, M. Graça H. Vicente, John J. Reiners

Faculty Publications

This study was designed to provide more detailed information on the subcellular sites of binding of the porphycene, termed 9-capronyloxytetrakis (methoxyethyl) porphycene (CPO), with a fluorescence resonance energy transfer (FRET) technique. The proximity of CPO to two fluorescent probes was determined: nonyl acridine orange (NAO), a dye with specific affinity for the mitochondrial lipid cardiolipin, and dihexaoxacarbocyanine iodide (DiOC 6), an agent that labels the endoplasmic reticulum (ER). FRET spectra indicated energy transfer between DiOC 6 and CPO but no significant transfer between NAO and CPO. These results confirm data obtained by fluorescence microscopy, suggesting a similar pattern of subcellular …

Under The Genomic Radar: The Stealth Model Of Alu Amplification, Kyudong Han, Jinchuan Xing, Hui Wang, Dale J. Hedges, Randall K. Garber, Richard Cordaux, Mark A. Batzer

Faculty Publications

Alu elements are the most successful SINEs (Short INterspersed Elements) in primate genomes and have reached more than 1,000,000 copies in the human genome. The amplification of most Alu elements is thought to occur through a limited number of hyperactive "master" genes that produce a high number of copies during long evolutionary periods of time. However, the existence of long-lived, low-activity Alu lineages in the human genome suggests a more complex propagation mechanism. Using both computational and wet-bench approaches, we reconstructed the evolutionary history of the AluYb lineage, one of the most active Alu lineages in the human genome. We …

Effects Of Density On Timing Of Emergence And Its Consequences For Survival And Growth In Two Communities Of Annual Plants, Roy Turkington, Deborah E. Goldberg, Linda Olsvig-Whittaker, Andrew R. Dyer

Faculty Publications

We tested whether increasing seed density results in a change in the timing of emergence in two communities of sand dune annual plants in Israel. Specifically we tested (i) if emergence is accelerated or delayed due to high seed density. We also tested two predictions about the consequences of changes in the timing of emergence; (ii) seedlings emerging earlier will have higher survival and growth; (iii) the advantage of earlier emergence increases as seed density increases. We examined these predictions for both monocots and dicots growing under different irrigation regimes and using species from a desert and a semi-arid community …

The Manganese-Stabilizing Protein Is Required For Photosystem Ii Assembly/Stability And Photoautotrophy In Higher Plants, Xiaoping Yi, Myriam Mcchargue, Susan Laborde, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

Interfering RNA was used to suppress the expression of two genes that encode the manganese-stabilizing protein of photosystem II in Arabidopsis thaliana, MSP-1 (encoded by psbO-1, At5g66570), and MSP-2 (encoded by psbO-2, At3g50820). A phenotypic series of transgenic plants was recovered that expressed high, intermediate, and low amounts of these two manganese-stabilizing proteins. Chlorophyll fluorescence induction and decay analyses were performed. Decreasing amounts of expressed protein led to the progressive loss of variable fluorescence and a marked decrease in the fluorescence quantum yield (F v/Fm) in both the absence and the presence of dichloromethylurea. This result indicated that the amount …

The Neural Substrates Of Infant Sleep In Rats, Karl Æ. Karlsson, Andrew J. Gall, Ethan J. Mohns, Adele M. H. Seelke, Mark S. Blumberg

Faculty Publications

Sleep is a poorly understood behavior that predominates during infancy but is studied almost exclusively in adults. One perceived impediment to investigations of sleep early in ontogeny is the absence of state-dependent neocortical activity. Nonetheless, in infant rats, sleep is reliably characterized by the presence of tonic (i.e., muscle atonia) and phasic (i.e., myoclonic twitching) components; the neural circuitry underlying these components, however, is unknown. Recently, we described a medullary inhibitory area (MIA) in week-old rats that is necessary but not sufficient for the normal expression of atonia. Here we report that the infant MIA receives projections from areas containing …

Tb3+-Doped K Pb2Br5: Low-Energy Phonon Mid-Infrared Laser Crystal, U. N. Roy, R. H. Hawrami, Y. Cui, S. Morgan, A. Burger, K. C. Mandal, C. C. Noblitt, S. A. Speakman, K. Rademaker, S. A. Payne

Faculty Publications

No abstract provided.

High-Frequency Phase Variation Of Vibrio Vulnificus 1003: Isolation And Characterization Of A Rugose Phenotypic Variant, Brenda L. Grau, Margaret C. Henk, Gregg S. Pettis

Faculty Publications

The marine bacterium Vibrio vulnificus is a human pathogen that can spontaneously switch between virulent opaque and avirulent translucent phenotypes. Here, we document an additional form, the rugose variant, which produces copious biofilms and which may contribute both to pathogenicity of V. vulnificus and to its survival under adverse environmental conditions. Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Murder, Meth, Mammon & Moral Values: The Political Landscape Of American Sentencing Reform (In Symposium On White Collar Crime), Frank O. Bowman Iii

Faculty Publications

This Article examines the ongoing American experiment in mass incarceration and considers the prospects for meaningful sentencing reform.

Differential Dna Binding And Protection By Dimeric And Dodecameric Forms Of The Ferritin Homolog Dps From Deinococcus Radiodurans, Anne Grove, Steven P. Wilkinson

Faculty Publications

Bacterial iron storage proteins such as ferritin serve as intracellular iron reserves. Members of the DNA protection during starvation (Dps) family of proteins are structurally related to ferritins, and their function is to protect the genome from iron-induced free radical damage. Some members of the Dps family bind DNA and are thought to do so only as fully assembled dodecamers. We present the cloning and characterization of a Dps homolog encoded by the radiation-resistant eubacterium Deinococcus radiodurans and show that DNA binding does not require its assembly into a dodecamer. D. radiodurans Dps-1, the product of gene DR2263, adopts a …

Regionally Isolated Populations Of An Imperiled Caribbean Coral, Acropora Palmata, Iliana B. Baums, Margaret W. Miller, Michael E. Hellberg

Faculty Publications

The movements of larvae between marine populations are difficult to follow directly and have been the subject of much controversy, especially in the Caribbean. The debate centres on the degree to which populations are demographically open, such that depleted populations can be replenished by recruitment from distant healthy populations, or demographically closed and thus in need of local management. Given the depressed state of many tropical reef populations, the understanding of these movements now bears critically on the number, placement, and size of marine reserves. Most genetic analyses assume that dispersal patterns have been stable for thousands of generations, thus …

Egf-Stimulation Activates The Nuclear Localization Signal Of Shp-1, Dandan He, Xi Song, Lijun Liu, David H. Burk, G. Wayne Zhou

Faculty Publications

Protein tyrosine phosphatase SHP-1 plays a critical role in the regulation of a variety of intracellular signaling pathways. SHP-1 is predominantly expressed in the cells of hematopoietic origin, and is recognized as a negative regulator of lymphocyte development and activation. SHP-1 consists of two Src homology 2 (SH2) domains and one protein tyrosine phosphatase (PTP) domain followed by a highly basic C-terminal tail containing tyrosyl phosphorylation sites. It is unclear how the C-terminal tail regulates SHP-1 function. We report the examination of the subcellular localization of a variety of truncated or mutated SHP-1 proteins fused with enhanced green fluorescent protein …

Should Liability Play A Role In The Social Control Of Biobanks?, Larry I. Palmer

Faculty Publications

No abstract provided.

Hibernation Is Recorded In Lower Incisors Of Recent And Fossil Ground Ssquirrels (Spermophilus), Tom Goodwin, Gail R. Michener, Daniel Gonzalez, Caroline E. Rinaldi

Faculty Publications

Incremental dentin and associated enamel, features visible on the surface of lower incisors, were characterized for 3 species of ground squirrels (Spermophilus): Pleistocene and Recent S. elegans, Recent S. richardsonii, and Recent S. parryii. A hibernation mark was evident in incisor dentin and enamel, most characteristically as a sleeve of enamel terminating basally adjacent to medially depressed dentin with indistinct and often very fine increments. This mark was absent in juveniles but present in older animals of both sexes for at least 6 weeks after hibernation, eventually being lost through growth and wear of the incisor. Temporal association with hibernation …

Semiclassical Nonadiabatic Dynamics With Quantum Trajectories, Vitaly A. Rassolov, Sophya V. Garashchuk

Faculty Publications

Dynamics based on quantum trajectories with approximate quantum potential is generalized to nonadiabatic systems and its semiclassical properties are discussed. The formulation uses the mixed polar-coordinate space representation of a wave function. The polar part describes the overall time evolution of the wave-function components semiclassically using the single-surface approximate quantum potential. The coordinate part represents a complex“population” amplitude, which in case of localized coupling can be solved for quantum mechanically in an efficient manner. In the high-energy regime this is accomplished by using a small basis determined by the coupling between surfaces. An illustration is given for a typical curve-crossing …

Mendelian Microsatellite Loci For The Caribbean Coral Acropora Palmata, Iliana B. Baums, Colin R. Hughes, Michael E. Hellberg

Faculty Publications

The genus Acropora constitutes the most species-rich clade of hermatypic corals, and its members are important reef builders throughout their broad tropical range. In the Caribbean, acroporid populations have declined over the last 2 decades due to disease, hurricanes, predation, and bleaching episodes, and some are now subjects of conservation efforts. Genetic estimates of population connectivity and clonal structure should be part of these efforts, but such studies have been hampered by low levels of mitochondrial DNA variation in corals, and an apparent dearth of variable single-copy nuclear markers. Developing microsatellite markers in Acropora has proven especially difficult. We used …

Disrupting Integrin Transmembrane Domain Heterodimerization Increases Ligand Binding Affinity, Not Valency Or Clustering, Bing Hao Luo, Christopher V. Carman, Junichi Takagi, Timothy A. Springer

Faculty Publications

Residues important in the interaction between the 23-residue transmembrane (TM) domains of the integrin αIIb- and β3- subunits were identified by mutating each non-Leu residue to Leu. Leu substitutions of αIIb at G972, G976, and T981, and of β3 at 1693 and G708, increased ligand binding. Substitutions with other amino acids at αIIbG972 and β3G708 could also increase ligand binding. The results are consistent with and extend the helical interface between the integrin α- and β-subunit TM domains previously defined by cysteine scanning and disulfide bond formation. We differentiated between affinity- and valency-based modes of activation by TM domain mutations. …

Haplotypes Produced From Rare Variants In The Promoter And Coding Regions Of Angiotensinogen Contribute To Variation In Angiotensinogen Levels, Xiaofeng Zhu, Laura Fejerman, Amy Luke, Adebowale Adeyemo, Richard S. Cooper

Faculty Publications

The most efficient study design to map genes underlying complex traits will be determined by assumptions about whether the genetic effects are likely to be due to relatively few common variants or multiple rare variants. To examine the possibility that rare variants may influence blood pressure, we sequenced a 6.8 kb region of the angiotensinogen (AGT) gene in 29 male Nigerians with high plasma AGT levels and 28 with low levels. The frequency of haplotypes produced from rare variants in the promoter and coding regions was significantly different between the two groups, and it is unlikely that this difference was …

Christian Environmentalism: Cosmos, Community, And Place, John R. Wood, Janel Curry, Steven C. Bouma-Prediger, Mark Bjelland, Susan P. Bratton

Faculty Publications

No abstract provided.

Neotypification Of Lulworthia Fucicola, Jinx Campbell

Faculty Publications

There are no herbarium specimens or culture material for the type of Lulworthia fucicola G.K. Sutherl. With the absence of original material, and to preserve current usage of the name, a neotype is designated hereby. The neotype chosen for L. fucicola is a specimen from Chile.

Differential Rhizosphere Establishment And Cyanide Production By Alginate-Formulated Weed-Deleterious Rhizobacteria, Horace G. Gurley, Robert E. Zdor

Faculty Publications

The effects of Pseudomonas putida ATH2-1RI/9 and Acidovorax delafieldii ATH2-2RS/1 on rhizosphere colonization, cyanide production, and growth of velvetleaf and corn was examined. When formulated in alginate beads and inoculated onto velvetleaf and corn plants (109 CFU/plant), only P. putida ATH2-1RI/9 consistently reduced velvetleaf growth. Neither isolate inhibited corn growth. Interestingly the levels of P. putida ATH2-1RI/9 in the velvetleaf rhizosphere were 1000-fold higher (7 × 107 CFU/g root) than the A. delafieldii ATH2-2RS/1 populations. Cyanide (53-68 mM/g root) was recovered from the P. putida ATH2-1RI/9-inoculated velvetleaf plants. In contrast both A. delafieldii ATH2-2RS/1 and P. putida ATH2-1RI/9 colonized the …

Reporting Quality Of Randomized Trials In The Diet And Exercise Literature For Weight Loss, Cheryl A. Gibson, Erik P. Kirk, James D. Lecheminant, Bruce W. Bailey Jr, Guoyuan Huang, Joseph E. Donnelly

Faculty Publications

Background

To adequately assess individual studies and synthesize quantitative research on weight loss studies, transparent reporting of data is required. The authors examined the reporting quality of randomized trials in the weight loss literature, focusing exclusively on subject characteristics as they relate to enrollment, allocation, and follow-up.

Methods

An extensive literature review, which included a computerized search of the MEDLINE database, manual searches of bibliographic references, and cross-referencing of 92 review articles was conducted. A checklist, based on CONSORT recommendations, was used to collect information on whether or not authors reported age, gender, co-morbid disease, medication use, race/ethnicity, and postmenopausal …

Analysis Of The Human Alu Ye Lineage, Abdel Halim Salem, David A. Ray, Dale J. Hedges, Jerzy Jurka, Mark A. Batzer

Faculty Publications

Background: Alu elements are short (∼300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and function of primate genomes. Approximately 10 % of the mass of the human genome is comprised of Alu elements, making them the most abundant short interspersed element (SINE) in our genome. The majority of Alu amplification occurred early in primate evolution, and the current rate of Alu retroposition is at least 100 fold slower than the peak of amplification that occurred 30-50 million years ago. Alu elements …

Consequences Of The Historical Demography On The Global Population Structure Of Two Highly Migratory Cosmopolitan Marine Fishes: The Yellowfin Tuna (Thunnus Albacares) And The Skipjack Tuna (Katsuwonus Pelamis), Bert Ely, Jordi Viñas, Jaime R. Alvarado Bremer, Donna Black, Luciano Lucas, Kelly Covello, Alexis V. Labrie, Eric Thelen

Faculty Publications

Background

Yellowfin and skipjack tuna are globally distributed in the world's tropical and sub-tropical oceans. Since little, if any, migration of these fishes occurs between the Atlantic and Indo-Pacific Oceans, one might expect to see genetic differences between sub-populations in these ocean basins. However, yellowfin and skipjack tuna have extremely large population sizes. Thus, the rate of genetic drift should be slower than that observed for other tunas.

Results

Low levels of genetic differentiation were observed between Atlantic and Pacific samples of yellowfin tuna. In contrast, no genetic differentiation was observed between Atlantic and Pacific samples of skipjack tuna.

Conclusion …

A Study Of Wave Effects On Wind Stress Over The Ocean In A Fetch-Limited Case, Jiayi Pan, David W. Wang, Paul A. Hwang

Faculty Publications

A field experiment was conducted for collecting three-dimensional wind, wave, and air-sea environmental data off the coast of Louisiana in the Gulf of Mexico in the mixed sea state of a wind sea limited by fetch and with swell propagating against the wind direction. Two methods, the inertial dissipation (ID) and eddy correlation (EC), are used to calculate wind stress. The results show that under the fetch-limited condition, the EC wind stress is greater than the ID stress. This difference is found to be correlated with the counter-wind swell. The swell-related drag coefficient is computed from the wind stress difference …

Temperature Dependence Of The Double Layer Capacitance For The Restricted Primitive Model Of An Electrolyte Solution From A Density Functional Approach, Douglas Henderson, J. Reszko-Zygmunt, Stefan Sokolowski, Dezso Boda

Faculty Publications

We apply a different version of the density functional theory, given by Pizio, Patrykiejew, and Sokolowski [J. Chem. Phys. 121, 11957 (2004)], for a nonuniform restricted primitive model of an electrolyte solution to evaluate the temperature dependence of the capacitance of an electric double layer. We show that this theory is capable of reproducing the computer simulation data at a quantitative level. In particular, the reversal of the temperature dependence of the capacitance at low temperatures is predicted. This phenomenon has been difficult to predict from theory. Further, this theory also leads to an accurate description of the double layer …

Multiplex Polymerase Chain Reaction For Simultaneous Quantitation Of Human Nuclear, Mitochondrial, And Male Y-Chromosome Dna: Application In Human Identification, Jerilyn A. Walker, Dale J. Hedges, Benjamin P. Perodeau, Kate E. Landry, Nadica Stoilova, Meredith E. Laborde, Jaiprakash Shewale, Sudhir K. Sinha, Mark A. Batzer

Faculty Publications

Human forensic casework requires sensitive quantitation of human nuclear (nDNA), mitochondrial (mtDNA), and male Y-chromosome DNA from complex biomaterials. Although many such systems are commercially available, no system is capable of simultaneously quantifying all three targets in a single reaction. Most available methods either are not multiplex compatible or lack human specificity. Here, we report the development of a comprehensive set of human-specific, target-specific multiplex polymerase chain reaction (PCR) assays for DNA quantitation. Using TaqMan-MGB probes, our duplex qPCR for nDNA/mtDNA had a linear quantitation range of 100 ng to 1 pg, and our triplex qPCR assay for nDNA/mtDNA/male Y …

Meiotic Recombination In Drosophila Females Depends On Chromosome Continuity Between Genetically Defined Boundaries, Dalia Sherizen, Janet K. Jang, Rajal Bhagat, Naohiro Kato, Kim S. Mckim

Faculty Publications

In the pairing-site model, specialized regions on each chromosome function to establish meiotic homolog pairing. Analysis of these sites could provide insights into the mechanism used by Drosophila females to form a synaptonemal complex (SC) in the absence of meiotic recombination. These specialized sites were first established on the X chromosome by noting that there were barriers to crossover suppression caused by translocation heterozygotes. These sites were genetically mapped and proposed to be pairing sites. By comparing the cytological breakpoints of third chromosome translocations to their patterns of crossover suppression, we have mapped two sites on chromosome 3R. We have …

Association Between Dietary Carbohydrates And Body Weight, Yunsheng Ma, Barbara Olendzki, David Chiriboga, James R. Hébert, Youfu Li, Wenjun Li, Mary Jane Campbell, Katherine Gendreau, Ira S. Ockene

Faculty Publications

The role of dietary carbohydrates in weight loss has received considerable attention in light of the current obesity epidemic. The authors investigated the association of body mass index (weight (kg)/height (m)²) with dietary intake of carbohydrates and with measures of the induced glycemic response, using data from an observational study of 572 healthy adults in central Massachusetts. Anthropometric measurements, 7-day dietary recalls, and physical activity recalls were collected quarterly from each subject throughout a 1-year study period. Data were collected between 1994 and 1998. Longitudinal analyses were conducted, and results were adjusted for other factors related to body …

Fine Root Dynamics And Trace Gas Fluxes In Two Lowland Tropical Forest Soils, Whendee L. Silver, Andrew W. Thompson, Megan E. Mcgroddy, Ruth K. Varner, Jadson D. Dias, Hudson Silva, Patrick M. Crill, Michael Keller

Faculty Publications

Fine root dynamics have the potential to contribute significantly to ecosystem-scale biogeochemical cycling, including the production and emission of greenhouse gases. This is particularly true in tropical forests which are often characterized as having large fine root biomass and rapid rates of root production and decomposition. We examined patterns in fine root dynamics on two soil types in a lowland moist Amazonian forest, and determined the effect of root decay on rates of C and N trace gas fluxes. Root production averaged 229 ( 35) and 153 ( 27) gm 2 yr 1 for years 1 and 2 of the …

Predicting Numbers Of Hauled-Out Harbour Seals: A Mathematical Model, James L. Hayward, Shandelle M. Henson, Clara J. Logan, Catherine R. Parris, Matthew W. Meyer, Brian Dennis

Faculty Publications

1. It was once assumed that commercially important fish make up significant portions of seal diets. As a consequence, prior to the 1970s many seal populations were dramatically reduced by rampant slaughtering. Today, seals and other marine mammals are valued components of marine ecosystems and their numbers are carefully managed. To facilitate management, government statutes mandate the systematic monitoring of seal populations. Population estimates are based on counts of hauled-out seals obtained by aerial survey and radio and satellite telemetry; hence, considerable effort has been devoted to finding optimal times for such counts. We have developed a predictive mathematical model …