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Item STUDIES ON THE GNRH/GTH SYSTEM OF FEMALE STRIPED BASS (Marone saxatilis): EFFECTS OF GNRH AGONJST THERAPY AND COMPARISON OF REPRODUCTIVE ENDOCRINE PARAMETERS BETWEEN WILD AND CAPTIVE FISH(1999) Steven, Colin R.; Zohar, Yonathan; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, MD)In the striped bass (Marone saxatilis), and many other commercially important fish species, captivity results in an inability to complete final oocyte maturation (FOM), ovu lation , and spawning. We hypothesize that this effect is mediated by a disruption of the hypothalamo-pituitary-gonadal (HPG) axis at the level of the gonadotropin -releasing hormones (GnRHs). To confirm this hypothesis research was conducted focused on three objectives: First, to complement the battery of assays previously developed for analysis of the GnRH/GtH system in striped bass, an RNAse protection assay was developed to measure specific expression of the three forms of GnRH in striped bass (salmon GnRH, chicken GnRH-If and seabream GnRH). Secondly, effects of GnRH agonist-induced ovulation on the HPG axis of captive striped bass was examined by comparison of several reproductive endocrine parameters between females sampled at four stages of oocyte development. Finally, differences were examined between the reproductive endocrine status of wild and captive female striped bass. We conclude that sbGnRH is the most important form for the preovulatory release of pituitary GtH-II in striped bass. We suggest that captive females synthesize levels of GnRH mRNA that are comparable to their wild counterparts, however fail to release adequate quantities of bioactive GnRH within the pituitary to stimulate completion of FOM. This data may indicate that regulation of sbGnRH in striped bass occurs via post-transcriptional/ translational mechanisms. Furthermore, the presence of salmon GnRH in the pituitaries of captive fema les may be indicative of a possible role for salmon GnRH in the regulation of FOM.Item Adenyl Cyclase and Its Relationship to Insect Diapause in the European Corn Borer, Ostrinia Nubilalis (Hubner)(1978) Gelman, Dale Berkman; Lockard, J. David; Hayes, Dora K.; Botany and Science Teaching; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)The purpose of this study was to determine if there is a link between adenyl cyclase activity and the diapause condition in the European corn borer, Ostrinia nubilalis. Insects inhabiting those latitudes where cold and warm seasons alternate with one another have evolved mechanisms which allow them to remain dormant (in a state of diapause) during the winter months of the year. Photoperiod, as well as temperature and humidity, has been shown to control the onset, maintenance and termination of insect diapause. In recent years, evidence supporting a role for the cyclic AMP system, including adenyl cyclase, as well as a role for one or more biogenic amines in the pathway between light reception and the neuroendocrine regulation of the insect life cycle and in the multitude of neuroendocrine pathways controlling insect growth and metamorphosis has been accumulating. In light of this evidence, it was decided to investigate the effects of two light regimens, short day (diapausing-inducing) and long day (pupation-inducing), on adenyl cyclase activity of various stages of fifth instar European corn borer larval heads, and to determine the effects of the biogenic amine neurotransmitters, norepinephrine, octopamine, and dopamine on this activity. Adenyl cyclase activity was measured by a modification of the method of Krishna, et al., (1968). A summary of the results follows. In head extracts of fifth instar European corn borer larvae reared under both long day and short day photoperiodic regimens, adenyl cyclase activity in the presence of sodium fluoride increased as the larvae progressed through early, middle and mature stages. In long day larval heads, activity decreased in late prepupae and reached a low in pharate pupae. In contrast, adenyl cyclase activity in short day larval heads peaked in early diapause and then returned to prediapause levels during late diapause. Norepinephrine significantly enhanced adenyl cyclase activity only in early diapause larval head extracts, while octopamine significantly enhanced adenyl cyclase activity in head extracts of late short day mature and early diapause larvae. Dopamine was ineffective as an activator. An analysis of the combined effect of neurotransmitter and developmental stage revealed that in general, a given neurotransmitter in combination with short day larval head extracts resulted in higher adenyl cyclase levels than that neurotransmitter in combination with long day head extracts.Item Interannual and Regional Patterns of Abundance, Growth, and Feeding Ecology of Larval Bay Anchovy (Anchoa Mitchilli) in Chesapeake Bay(2003) Auth, Toby D.; Houde, Edward D.; Marine Estaurine and Environmental Science Program; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)Patterns in abundance, growth , and feeding by larval bay anchovy were examined in Chesapeake Bay from 1995-1999 to evaluate factors that contribute to variable recruitments of this abundant fish. The patterns were examined in relation to environmental factors, including hydrography and distributions of prey (zooplankton) and a probable predator (ctenophore). Larval abundances, sizes, feeding incidences, and growth rates varied annually and regionally. Averaged over five years, mean abundances in July decreased by almost two orders of magnitude from the mouth (38.l/m2) to the head (0.6/m) of the Bay, a long a declining salinity gradient. Yearly survey, bay-wide mean abundance varied nearly 10-fold; it was highest in 1998 (42. 7 /m2) and lowest in 1996 (4.6/m2). Feeding incidence was highest in 1998 (23%) and lowest in 1996 (9%), and varied regionally from 27% in the upper Bay to 13% in the mid Bay. Larvae fed predominantly during daylight. The most common prey ingested were copepod eggs and various life stages of calanoid copepods (primarily Acarlia Lonsa). Growth rates of larvae also differed annually and regionally. Mean growth rate was highest in 1998 (0.81 mm/d) and lowest in 1999 (0.68 mm/d), and varied regionally from 0.83 mm/d in the upper Bay to 0.71 mm/din the mid Bay. Zooplankton concentration was positively correlated with larval feeding incidence (r = +0.66) and growth rate (r = +0. 72). Larval feeding incidence was strongly correlated (r = +0.93) and summer larval abundance significantly correlated (r = +0.86) with fall recruitment of young-of-the-year bay anchovy.Item Ascidian gene-expression profiles(Springer Nature, 2002-09-25) Jeffery, William RWith the advent of gene-expression profiling, a large number of genes can now be investigated simultaneously during critical stages of development. This approach will be particularly informative in studies of ascidians, basal chordates whose genomes and embryology are uniquely suited for mapping developmental gene networks.Item Visualization and analysis of microarray and gene ontology data with treemaps(Springer Nature, 2004-06-28) Baehrecke, Eric H; Dang, Niem; Babaria, Ketan; Shneiderman, BenThe increasing complexity of genomic data presents several challenges for biologists. Limited computer monitor views of data complexity and the dynamic nature of data in the midst of discovery increase the challenge of integrating experimental results with information resources. The use of Gene Ontology enables researchers to summarize results of quantitative analyses in this framework, but the limitations of typical browser presentation restrict data access. Here we describe extensions to the treemap design to visualize and query genome data. Treemaps are a space-filling visualization technique for hierarchical structures that show attributes of leaf nodes by size and color-coding. Treemaps enable users to rapidly compare sizes of nodes and sub-trees, and we use Gene Ontology categories, levels of RNA, and other quantitative attributes of DNA microarray experiments as examples. Our implementation of treemaps, Treemap 4.0, allows user-defined filtering to focus on the data of greatest interest, and these queried files can be exported for secondary analyses. Links to model system web pages from Treemap 4.0 enable users access to details about specific genes without leaving the query platform. Treemaps allow users to view and query the data from an experiment on a single computer monitor screen. Treemap 4.0 can be used to visualize various genome data, and is particularly useful for revealing patterns and details within complex data sets.Item Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA(Springer Nature, 2004-09-16) Cummings, Michael P; Myers, Daniel SRNA editing is the process whereby an RNA sequence is modified from the sequence of the corresponding DNA template. In the mitochondria of land plants, some cytidines are converted to uridines before translation. Despite substantial study, the molecular biological mechanism by which C-to-U RNA editing proceeds remains relatively obscure, although several experimental studies have implicated a role for cis-recognition. A highly non-random distribution of nucleotides is observed in the immediate vicinity of edited sites (within 20 nucleotides 5' and 3'), but no precise consensus motif has been identified. Data for analysis were derived from the the complete mitochondrial genomes of Arabidopsis thaliana, Brassica napus, and Oryza sativa; additionally, a combined data set of observations across all three genomes was generated. We selected datasets based on the 20 nucleotides 5' and the 20 nucleotides 3' of edited sites and an equivalently sized and appropriately constructed null-set of non-edited sites. We used tree-based statistical methods and random forests to generate models of C-to-U RNA editing based on the nucleotides surrounding the edited/non-edited sites and on the estimated folding energies of those regions. Tree-based statistical methods based on primary sequence data surrounding edited/non-edited sites and estimates of free energy of folding yield models with optimistic re-substitution-based estimates of ~0.71 accuracy, ~0.64 sensitivity, and ~0.88 specificity. Random forest analysis yielded better models and more exact performance estimates with ~0.74 accuracy, ~0.72 sensitivity, and ~0.81 specificity for the combined observations. Simple models do moderately well in predicting which cytidines will be edited to uridines, and provide the first quantitative predictive models for RNA edited sites in plant mitochondria. Our analysis shows that the identity of the nucleotide -1 to the edited C and the estimated free energy of folding for a 41 nt region surrounding the edited C are the most important variables that distinguish most edited from non-edited sites. However, the results suggest that primary sequence data and simple free energy of folding calculations alone are insufficient to make highly accurate predictions.Item Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis(Springer Nature, 2004-09-28) Cummings, Michael P; Segal, Mark RMutations in rpoB, the gene encoding the β subunit of DNA-dependent RNA polymerase, are associated with rifampin resistance in Mycobacterium tuberculosis. Several studies have been conducted where minimum inhibitory concentration (MIC, which is defined as the minimum concentration of the antibiotic in a given culture medium below which bacterial growth is not inhibited) of rifampin has been measured and partial DNA sequences have been determined for rpoB in different isolates of M. tuberculosis. However, no model has been constructed to predict rifampin resistance based on sequence information alone. Such a model might provide the basis for quantifying rifampin resistance status based exclusively on DNA sequence data and thus eliminate the requirements for time consuming culturing and antibiotic testing of clinical isolates. Sequence data for amino acid positions 511–533 of rpoB and associated MIC of rifampin for different isolates of M. tuberculosis were taken from studies examining rifampin resistance in clinical samples from New York City and throughout Japan. We used tree-based statistical methods and random forests to generate models of the relationships between rpoB amino acid sequence and rifampin resistance. The proportion of variance explained by a relatively simple tree-based cross-validated regression model involving two amino acid positions (526 and 531) is 0.679. The first partition in the data, based on position 531, results in groups that differ one hundredfold in mean MIC (1.596 μg/ml and 159.676 μg/ml). The subsequent partition based on position 526, the most variable in this region, results in a > 354-fold difference in MIC. When considered as a classification problem (susceptible or resistant), a cross-validated tree-based model correctly classified most (0.884) of the observations and was very similar to the regression model. Random forest analysis of the MIC data as a continuous variable, a regression problem, produced a model that explained 0.861 of the variance. The random forest analysis of the MIC data as discrete classes produced a model that correctly classified 0.942 of the observations with sensitivity of 0.958 and specificity of 0.885. Highly accurate regression and classification models of rifampin resistance can be made based on this short sequence region. Models may be better with improved (and consistent) measurements of MIC and more sequence data.Item Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics(Springer Nature, 2005-06-14) Wang, Wenming; Tanurdzic, Milos; Luo, Meizhong; Sisneros, Nicholas; Kim, Hye Ran; Weng, Jing-Ke; Kudrna, Dave; Mueller, Christopher; Arumuganathan, K; Carlson, John; Chapple, Clint; de Pamphilis, Claude; Mandoli, Dina; Tomkins, Jeff; Wing, Rod A; Banks, Jo AnnThe lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants. Here we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from the lycophyte Selaginella moellendorffii. Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula, Diphaiastrum digita, Isoetes engelmanii and S. kraussiana. The arrayed BAC library consists of 9126 clones; the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes. The S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution.Item Microarray analysis of Pseudomonas aeruginosa reveals induction of pyocin genes in response to hydrogen peroxide(Springer Nature, 2005-09-08) Chang, Wook; Small, David A; Toghrol, Freshteh; Bentley, William EPseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, encounters toxicity from phagocyte-derived reactive oxidants including hydrogen peroxide during active infection. P. aeruginosa responds with adaptive and protective strategies against these toxic species to effectively infect humans. Despite advances in our understanding of the responses to oxidative stress in many specific cases, the connectivity between targeted protective genes and the rest of cell metabolism remains obscure. Pseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, encounters toxicity from phagocyte-derived reactive oxidants including hydrogen peroxide during active infection. P. aeruginosa responds with adaptive and protective strategies against these toxic species to effectively infect humans. Despite advances in our understanding of the responses to oxidative stress in many specific cases, the connectivity between targeted protective genes and the rest of cell metabolism remains obscure. This finding proposes that pyocin production might be another novel defensive scheme against oxidative attack by host cells.Item Genome re-annotation: a wiki solution?(Springer Nature, 2007-02-01) Salzberg, Steven LThe annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution.