Digital Commons Network^™

The Extrinsic Proteins Of Photosystem Ii, Johnna L. Roose, Kimberly M. Wegener, Himadri B. Pakrasi

Faculty Publications

Years of genetic, biochemical, and structural work have provided a number of insights into the oxygen evolving complex (OEC) of Photosystem II (PSII) for a variety of photosynthetic organisms. However, questions still remain about the functions and interactions among the various subunits that make up the OEC. After a brief introduction to the individual subunits Psb27, PsbP, PsbQ, PsbR, PsbU, and PsbV, a current picture of the OEC as a whole in cyanobacteria, red algae, green algae, and higher plants will be presented. Additionally, the role that these proteins play in the dynamic life cycle of PSII will be discussed. …

Low Incidence Of Candidatus Liberibacter Asiaticus In Diaphorina Citri (Hemiptera: Psyllidae) Populations Between Nov 2005 And Jan 2006: Relevance To Management Of Citrus Greening Disease In Florida, Jason M. Meyer, Marjorie A. Hoy, Raghuwinder Singh

Faculty Publications

Populations of D. citri in Florida citrus were surveyed between Sep 2005 and Jan 2006 for Ca. L. asiaticus, the causal agent of HLB. No field-collected adults or immatures of the 1,972 D. citri tested were positive for the HLB pathogen in these samples, indicating that the proportion of D. citri populations hosting Ca. L. asiaticus in the regions sampled was very low (<0.05%) during this survey. More extensive surveys for Ca. L. asiaticus in D. citri are recommended to learn more about the epidemiology of disease transmission in Florida.

Citrus Leafminer, Phyllocnistis Citrella (Lepidoptera: Gracillariidae), And Natural Enemy Dynamics In Central Florida During 2005, Marjorie A. Hoy, Raghuwinder Singh, Michael E. Rogers

Faculty Publications

After the citrus leafminer (CLM), Phyllocnistis citrella Stainton (Lepidoptera: Gracillariidae), invaded Florida in 1993, the endoparasitoid Ageniaspis citricola Logvinovskaya (Hymenoptera: Encyrtidae) was introduced in 1994 in a classical biological control program. Subsequent to its establishment, only limited information has been obtained regarding the seasonal abundance of A. citricola and its host in central Florida citrus groves. During 2005, we monitored replicated plots treated with oil or imidacloprid once on 23 Jun 2005, along with untreated control trees, in a Polk County commercial Valencia orange grove on a weekly basis when tender new growth (= flush) was available. As expected, CLM …

Applications Of Chitosan For Improvement Of Quality And Shelf Life Of Foods: A Review, H. K. No, S. P. Meyers, W. Prinyawiwatkul, Z. Xu

Faculty Publications

Chitosan is a modified, natural biopolymer derived by deacetylation of chitin, a major component of the shells of crustacean. Recently, chitosan has received increased attention for its commercial applications in the biomedical, food, and chemical industries. Use of chitosan in food industry is readily seen due to its several distinctive biological activities and functional properties. The antimicrobial activity and film-forming property of chitosan make it a potential source of food preservative or coating material of natural origin. This review focuses on the applications of chitosan for improvement of quality and shelf life of various foods from agriculture, poultry, and seafood …

Modeling And Prediction Of Marine Microbial Populations In The Genomic Era, Raleigh R. Hood, Edward A. Laws, Michael J. Follows, David A. Siegel

Faculty Publications

No abstract provided.

Rnai Knockdown Of Nopp140 Induces Minute-Like Phenotypes In Drosophila, Zhengfang Cui, Patrick J. Dimario

Faculty Publications

Nopp140 associates with small nucleolar RNPs to chaperone pre-rRNA processing and ribosome assembly. Alternative splicing yields two isoforms in Drosophila: Nopp140-True is homologous to vertebrate Nopp140 particularly in its carboxy terminus, whereas Nopp140-RGG contains a glycine and arginine-rich (RGG) carboxy terminus typically found in vertebrate nucleolin. Loss of ribosome function or production at critical points in development leads to Minute phenotypes in Drosophila or the Treacher Collins syndrome (TCS) in humans. To ascertain the functional significance of Nopp140 in Drosophila development, we expressed interfering RNA using the GAL4/UAS system. Reverse transcription-PCR showed variable losses of Nopp140 mRNA in larvae from …

Brainstem Cholinergic Modulation Of Muscle Tone In Infant Rats, Andrew J. Gall, Amy Poremba, Mark S. Blumberg

Faculty Publications

In week-old rats, lesions of the dorsolateral pontine tegmentum (DLPT) and nucleus pontis oralis (PnO) have opposing effects on nuchal muscle tone. Specifically, pups with DLPT lesions exhibit prolonged bouts of nuchal muscle atonia (indicative of sleep) and pups with PnO lesions exhibit prolonged bouts of high nuchal muscle tone (indicative of wakefulness). Here we test the hypothesis that nuchal muscle tone is modulated, at least in part, by cholinergically mediated interactions between these two regions. First, in unanesthetized pups, we found that chemical infusion of the cholinergic agonist carbachol (22 mM, 0.1 µL) within the DLPT produced high muscle …

Structural Analysis Of Csos1a And The Protein Shell Of The Halothiobacillus Neapolitanus Carboxysome, Yingssu Tsai, Michael R. Sawaya, Gordon C. Cannon, Fei Cai, Eric B. Williams, Sabine Heinhorst, Cheryl A. Kerfeld, Todd O. Yeates

Faculty Publications

The carboxysome is a bacterial organelle that functions to enhance the efficiency of CO2 fixation by encapsulating the enzymes ribulose bisphosphate carboxylase/ oxygenase (RuBisCO) and carbonic anhydrase. The outer shell of the carboxysome is reminiscent of a viral capsid, being constructed from many copies of a few small proteins. Here we describe the structure of the shell protein CsoS1A from the chemoautotrophic bacterium Halothiobacillus neapolitanus. The CsoS1A protein forms hexameric units that pack tightly together to form a molecular layer, which is perforated by narrow pores. Sulfate ions, soaked into crystals of CsoS1A, are observed in the pores of the …

Assessment Of Labview And Multisim In The Delivery Of Electronics Laboratory Content, Julio Garcia, Patricia Backer

Faculty Publications

The goal of this study, funded by the National Science Foundation, was to adapt the work of other researchers to improve the delivery of electronics lecture and laboratory content in the Electronics & Computer Technology (ECT) area. From the extensive research on ethnic and gender differences in learning styles, the evidence suggests that ethnic minorities and women work best when the material is organized so that students work in teams and have a high level of hands-on experimentation and problem-solving. We developed our materials to maximize these aspects since in our institution the “minority” constitutes the majority of our student …

Distinguishing Importation From Diversification Of Quinolone-Resistant Neisseria Gonorrhoeae By Molecular Evolutionary Analysis, Keith A. Crandall, Marcos Perez-Losada, Margaret C. Bash, Michael Dan, Jonathan Zenilman, Raphael P. Viscidi

Faculty Publications

Distinguishing the recent introduction of quinolone resistant gonococci into a population from diversification of resistant strains already in the population is important for planning effective infection control strategies. We applied molecular evolutionary analyses to DNA sequences from 9 housekeeping genes and gyrA, parC and porB of 24 quinolone resistant N. gonorrhoeae (QRNG) and 24 quinolone sensitive isolates collected in Israel during 2000-2001. Results- Phylogenetic and eBURST analyses and estimates of divergence time indicated QRNG were introduced on 3 separate occasions and underwent limited diversification by mutation, deletion and horizontal gene transfer. Reconstruction of N. gonorrhoeae demography showed a slowly declining …

Impacts Of Hurricanes Katrina And Rita On The Microbial Landscape Of The New Orleans Area, C. D. Sinigalliano, M. L. Gidley, T. Shibata, D. Whitman, T. H. Dixon, E. Laws, A. Hou, D. Bachoon, L. Brand, L. Amaral-Zettler, R. J. Gast, G. F. Steward, O. D. Nigro, R. Fujioka, W. Q. Betancourf, G. Vithanage, J. Mathews, L. E. Fleming, H. M. Solo-Gabriele

Faculty Publications

Floodwaters in New Orleans from Hurricanes Katrina and Rita were observed to contain high levels of fecal indicator bacteria and microbial pathogens, generating concern about long-term impacts of these floodwaters on the sediment and water quality of the New Orleans area and Lake Pontchartrain. We show here that fecal indicator microbe concentrations in offshore waters from Lake Pontchartrain returned to prehurricane concentrations within 2 months of the flooding induced by these hurricanes. Vibrio and Legionella species within the lake were more abundant in samples collected shortly after the floodwaters had receded compared with samples taken within the subsequent 3 months; …

'There It Is: Take It' Endangered Species And Water Management In The San Francisco Bay Delta, W. David Ball

Faculty Publications

This paper explores endangered species and water management in the San Francisco Bay Delta. Two endangered species, the Delta Smelt and the Winter-run Chinook Salmon, use the Bay Delta for crucial portions of their life cycle. At the same time, California's agricultural industry, as well as population centers to the South, require substantial outflows of Bay-Delta water. The paper explores the multi-jurisdictional regulation of the Bay-Delta's water, takes a hard look at the purported success of the Environmental Water Account (EWA) program, and reports on the tensions between scientists at regulatory agencies and the political appointees who oversee them. We …

Sea Surface Pco2‐Sst Relationships Across A Cold‐Core Cyclonic Eddy: Implications For Understanding Regional Variability And Air‐Sea Gas Exchange, Feizhou Chen, Wei‐Jun Cai, Claudia R. Benitez-Nelson, Yongchen Wang

Faculty Publications

[1] This study is designed to improve the understanding of how biologically productive, cold‐core cyclonic eddies affect sea surface pCO2 in the lee of the main Hawaiian Islands in the subtropical North Pacific Gyre. We identified three unique relationships between pCO2 and sea surface temperature (SST). A positive correlation between pCO2 and SST was observed in the waters surrounding the eddy suggesting surface CO2 is controlled primarily by thermodynamics. In contrast, a negative relationship was observed within the eddy core as a result of the upwelling of CO2‐enriched subsurface waters. A third relationship existed throughout the rest …

Variability In The Bulk Composition And Abundance Of Dissolved Organic Matter In The Lower Mississippi And Pearl Rivers, Shuiwang Duan, Thomas S. Bianchi, Alan M. Shiller, Karl Dria, Patrick G. Hatcher, Kevin R. Carman

Faculty Publications

[1] In this study, we examined the temporal and spatial variability of dissolved organic matter (DOM) abundance and composition in the lower Mississippi and Pearl rivers and effects of human and natural influences. In particular, we looked at bulk C/N ratio, stable isotopes (delta N-15 and delta C-13) and C-13 nuclear magnetic resonance (NMR) spectrometry of high molecular weight (HMW; 0.2 mu m to 1 kDa) DOM. Monthly water samples were collected at one station in each river from August 2001 to 2003. Surveys of spatial variability of total dissolved organic carbon (DOC) and nitrogen ( DON) were also conducted …

Low Temperature Induces Two Growth-Arrested Stages And Change Of Secondary Metabolites In Bursaphelenchus Xylophilus, L. L. Zhao, W. Wei, David L. Kulhavy, Xing Yao Zhang, Jiang Hua Sun

Faculty Publications

The third-stage dispersal juvenile (JIII) is the stage for survival and dispersal in the winter of the pine wood nematode,

Bursaphelenchus xylophilus. Through investigations at different temperatures, we found two kinds of growth-arrested development, including the adult longevity extension and JIII formation induced by low temperature. They showed similar characters: densely packed lipid droplets and extended longevity. We considered that there were four stages in the formation of growth-arrested stages: induction, growth-arrested pathway, growth-arrested development and cold-tolerance duration. Moreover, at 4◦C there were significant changes in secondary metabolites, which may be related to signal communication and metabolism associated with …

A Potential Pollen Proxy For Enso Derived From The Sajama Ice Core, Kam-Biu Liu, Carl A. Reese, Lonnie G. Thompson

Faculty Publications

An annually resolved pollen record spanning a 39-year period ( 1958 - 1996) from the Sajama Ice Cap, located on the western Bolivian Altiplano, reveals significant interannual variations in both pollen concentration and composition. The pollen assemblages within the annual layers are dominated by typical Altiplano taxa, especially Poaceae and Asteraceae. On an annual basis the pollen concentrations are strongly negatively correlated (Pearson's r = - 0.716) with the Southern Oscillation Index (SOI). Studies from Sajama and other tropical ice caps have shown that during El Nino years, the weather on the Altiplano is decidedly warmer and drier, which enhances …

Genome Of The Marsupial Monodelphis Domestica Reveals Innovation In Non-Coding Sequences, Tarjei S. Mikkelsen, Matthew J. Wakefield, Bronwen Aken, Chris T. Amemiya, Jean L. Chang, Shannon Duke, Manuel Garber, Andrew J. Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen M.J. Searle, Ted Sharpe, Michelle L. Baker, Mark A. Batzer, Panayiotis V. Benos, Katherine Belov, Michele Clamp, April Cook, James Cuff, Radhika Das, Lance Davidow, Janine E. Deakin, Melissa J. Fazzari, Jacob L. Glass, Manfred Grabherr, John M. Greally, Wanjun Gu, Timothy A. Hore, Gavin A. Huttley, Michael Kleber, Randy L. Jirtle

Faculty Publications

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in …

A Direct Role Of Jh In The Control Of Imaginal Disc Formation And Growth In Manduca, J. W. Truman, K. Hiruma, J. P. Allee, S.G.B. Macwhinnie, David Champlin Ph.D., L. M. Riddiford

Faculty Publications

No abstract provided.

Retroposition And Evolution Of The Dna-Binding Motifs Of Yy1, Yy2 And Rex1, Jeong Do Kim, Christopher Faulk, Joomyeong Kim

Faculty Publications

YY1 is a DNA-binding transcription factor found in both vertebrates and invertebrates. Database searches identified 62 YY1 related sequences from all the available genome sequences ranging from flying insects to human. These sequences are characterized by high levels of sequence conservation, ranging from 66% to 100% similarity, in the zinc finger DNA-binding domain of the predicted proteins. Phylogenetic analyses uncovered duplication events of YY1 in several different lineages, including flies, fish and mammals. Retroposition is responsible for generating one duplicate in flies, PHOL from PHO, and two duplicates in placental mammals, YY2 and Reduced Expression 1 (REX1) from YY1. DNA-binding …

Caspase Activity During Cell Stasis: Avoidance Of Apoptosis In An Invertebrate Extremophile, Artemia Franciscana, Michael A. Menze, Steven C. Hand

Faculty Publications

Evaluation of apoptotic processes downstream of the mitochondrion reveals caspase-9- and low levels of caspase-3-like activities in partly purified extracts of Artemia franciscana embryos. However, in contrast to experiments with extracts of human hepatoma cells, cytochrome c fails to activate caspase-3 or -9 in extracts from A. franciscana. Furthermore, caspase-9 activity is sensitive to exogenous calcium. The addition of 5 mM calcium leads to a 4.86 ± 0.19 fold (SD) (n = 3) increase in activity, which is fully prevented with 150 mM KCl. As with mammalian systems, high ATP (>1.25 mM) suppresses caspase activity in A. franciscana extracts. …

Relationships Among Ecologically Important Dimensions Of Plant Trait Variation In Seven Neotropical Forests, Ian J. Wright, David D. Ackerly, Frans Bongers, Kyle E. Harms, Guillermo Ibarra-Manriquez, Miguel Martinez-Ramos, Susan J. Mazer, Helene C. Muller-Landau, Horacio Paz, Nigel C.A. Pitman, Lourens Poorter, Miles R. Silman, Corine F. Vriesendorp, Cam O. Webb, Mark Westoby, S. Joseph Wright

Faculty Publications

• Background and Aims: When ecologically important plant traits are correlated they may be said to constitute an ecological 'strategy' dimension. Through identifying these dimensions and understanding their inter-relationships we gain insight into why particular trait combinations are favoured over others and into the implications of trait differences among species. Here we investigated relationships among several traits, and thus the strategy dimensions they represented, across 2134 woody species from seven Neotropical forests. • Methods: Six traits were studied: specific leaf area (SLA), the average size of leaves, seed and fruit, typical maximum plant height, and wood density (WD). Trait relationships …

Prediction Of Functional Sites Based On The Fuzzy Oil Drop Model, Michał Bryliński, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochańczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman

Faculty Publications

A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, …

A Genome-Wide Scan Of Loci Linked To Serum Adiponectin In Two Populations Of African Descent, Chindo Hicks, Xiaofeng Zhu, Amy Luke, Donghui Kan, Adebowale Adeyemo, Xiaodong Wu, Richard S. Cooper

Faculty Publications

Objective: The objectives were to identify quantitative trait loci linked to serum adiponectin concentration and to estimate heritability in two populations of African descent. Research Methods and Procedures: We conducted a genome scan for serum adiponectin concentration in two populations of African descent. Genome-wide microsatelitte markers were typed in an African-American population consisting of 203 families from the Chicago area and in a Nigerian Yoruba population consisting of 146 families. Linkage analysis was performed to identify loci. Variance component model was used to estimate heritability. Results: Estimates of heritability adjusted for age, gender, and BMI were 0.45 and 0.70 for …

Association Studies Of Bmi And Type 2 Diabetes In The Neuropeptide Y Pathway: A Possible Role For Npy2r As A Candidate Gene For Type 2 Diabetes In Men, Catarina D. Campbell, Helen N. Lyon, James Nemesh, Jared A. Drake, Tiinamaija Tuomi, Daniel Gaudet, Xiaofeng Zhu, Richard S. Cooper, Kristin G. Ardlie, Leif C. Groop, Joel N. Hirschhorn

Faculty Publications

The neuropeptide Y (NPY) family of peptides and receptors regulate food intake. Inherited variation in this pathway could influence susceptibility to obesity and its complications, including type 2 diabetes. We genotyped a set of 71 single nucleotide polymorphisms (SNPs) that capture the most common variation in NPY, PPY, PYY, NPY1R, NPY2R, and NPY5R in 2,800 individuals of recent European ancestry drawn from the near extremes of BMI distribution. Five SNPs located upstream of NPY2R were nominally associated with BMI in men (P values = 0.001-0.009, odds ratios [ORs] 1.27-1.34). No association with BMI was observed in women, and no consistent …

Genetic Similarities Within And Between Human Populations, D. J. Witherspoon, S. Wooding, A. R. Rogers, E. E. Marchani, W. S. Watkins, M. A. Batzer, L. B. Jorde

Faculty Publications

The proportion of human genetic variation due to differences between populations is modest, and individuals from different populations can be genetically more similar than individuals from the same population. Yet sufficient genetic data can permit accurate classification of individuals into populations. Both findings can be obtained from the same data set, using the same number of polymorphic loci. This article explains why. Our analysis focuses on the frequency, ω, with which a pair of random individuals from two different populations is genetically more similar than a pair of individuals randomly selected from any single population. We compare ω to the …

Revision Of The Nonequilibrium Thermal Dissociation And Stringent Washing Approaches For Identification Of Mixed Nucleic Acid Targets By Microarrays, Alex E. Pozhitkov, Robert D. Stedtfeld, Syed A. Hashsham, Peter A. Noble

Faculty Publications

Microarray experiments typically involve washing steps that remove hybridized nonspecific targets with the purpose of improving the signal- to- noise ratio. The quality of washing ultimately affects downstream analysis of the microarray and interpretation. The paucity of fundamental studies directed towards understanding the dissociation of mixed targets from microarrays makes the development of meaningful washing/ dissociation protocols difficult. To fill the void, we examined activation energies and preexponential coefficients of 47 perfect match ( PM) and double- mismatch ( MM) duplex pairs to discover that there was no statistical difference between the kinetics of the PM and MM duplexes. Based …

Dutch Women's Perceptions Of Childbirth In The Netherlands, Taralyn R. Johnson, Lynn Clark Callister, Donna S. Freeborn, Renea L. Beckstrand, Katinka Huender

Faculty Publications

Purpose: To explore the lived experience of childbirth in Dutch women who had given birth at home in the Netherlands.

Methods: Qualitative study using audiotaped interviews with 14 women.

Results: Themes included the advantages of giving birth in the home, where the women felt more in control of their environment; the difficulty and normalcy of the pain associated with giving birth; the feelings of fulfillment and empowerment that come with childbirth and motherhood; and the importance of the supportive role of the midwife–caregiver.

Nursing Implications: Women in a culture different from that of the United States who gave birth at …

Tests Of The Extension And Deadbolt Models Of Integrin Activation, Jieqing Zhu, Brian Boylan, Bing Hao Luo, Peter J. Newman, Timothy A. Springer

Faculty Publications

Despite extensive evidence that integrin conformational changes between bent and extended conformations regulate affinity for ligands, an alternative hypothesis has been proposed in which a "deadbolt" can regulate affinity for ligand in the absence of extension. Here, we tested both the deadbolt and the extension models. According to the deadbolt model, a hairpin loop in the β3 tail domain could act as a deadbolt to restrain the displacement of the β3 I domain β6-α7 loop and maintain integrin in the low affinity state. We found that mutating or deleting the β3 tail domain loop has no effect on ligand binding …

The N-Terminal Extensions Of Deinococcus Radiodurans Dps-1 Mediate Dna Major Groove Interactions As Well As Assembly Of The Dodecamer, Gargi Bhattacharyya, Anne Grove

Faculty Publications

Dps (DNA protection during starvation) proteins play an important role in the protection of prokaryotic macromolecules from damage by reactive oxygen species. Previous studies have suggested that the lysine-rich N-terminal tail of Dps proteins participates in DNA binding. In comparison with other Dps proteins, Dps-1 from Deinococcus radiodurans has an extended N terminus comprising 55 amino acids preceding the first helix of the 4-helix bundle monomer. In the crystal structure of Dps-1, the first ∼30 N-terminal residues are invisible, and the remaining 25 residues form a loop that harbors a novel metal-binding site. We show here that deletion of the …

Upper-Ocean Response To Hurricane Ivan In A 1/25 Degrees Nested Gulf Of Mexico Hycom, T. G. Prasad, Patrick J. Hogan

Faculty Publications

[ 1] A 20-layer, 1/25 degrees nested Gulf of Mexico (GoM) Hybrid Coordinate Ocean Model (HYCOM) has been employed to examine the evolving three-dimensional ocean response to Hurricane Ivan during 14 - 16 September 2004. Results from several combinations of numerical experiments with and without assimilation of satellite-altimetry sea-surface height (SSH) are being analyzed and compared for the September 2004 hurricane period. A comparison of simulated zonal and meridional velocities using data assimilation shows improved agreement with profiler observations. The amplitude of the cold wake ( similar to 6 degrees C) produced by these simulations compared reasonably well with the …