The Effects of Fish Trap Mesh Size on Reef Fish Catch off Southeastern Florida

Catch and mesh selectivity of wire-meshed fish traps were tested for eleven different mesh sizes ranging from 13 X 13 mm (0.5 x 0.5") to 76 x 152 mm (3 X 6"). A total of 1,810 fish (757 kg) representing 85 species and 28 families were captured during 330 trap hauls off southeastern Florida from December 1986 to July 1988. Mesh size significantly affected catches. The 1.5" hexagonal mesh caught the most fish by number, weight, and value. Catches tended to decline as meshes got smaller or larger. Individual fish size increased with larger meshes. Laboratory mesh retention experiments showed relationships between mesh shape and size and individual retention for snapper (Lutjanidae), grouper (Serranidae), jack (Carangidae), porgy (Sparidae), and surgeonfish (Acanthuridae). These relationships may be used to predict the effect of mesh sizes on catch rates. Because mesh size and shape greatly influenced catchability, regulating mesh size may provide a useful basis for managing the commercial trap fishery

Dominant Nuclear Outflow Driving Mechanisms in Powerful Radio Galaxies

In order to identify the dominant nuclear outflow mechanisms in Active Galactic Nuclei, we have undertaken deep, high resolution observations of two compact radio sources (PKS 1549-79 and PKS 1345+12) with the Advanced Camera for Surveys (ACS) aboard the Hubble Space Telescope. Not only are these targets known to have powerful emission line outflows, but they also contain all the potential drivers for the outflows: relativistic jets, quasar nuclei and starbursts. ACS allows the compact nature (<0.15") of these radio sources to be optically resolved for the first time. Through comparison with existing radio maps we have seen consistency in the nuclear position angles of both the optical emission line and radio data. There is no evidence for bi-conical emission line features on the large-scale and there is a divergance in the relative position angles of the optical and radio structure. This enables us to exclude starburst driven outflows. However, we are unable to clearly distinguish between radiative AGN wind driven outflows and outflows powered by relativistic radio jets. The small scale bi-conical features, indicative of such mechanisms could be below the resolution limit of ACS, especially if aligned close to the line of sight. In addition, there may be offsets between the radio and optical nuclei induced by heavy dust obscuration, nebular continuum or scattered light from the AGN.Comment: 9 pages, 8 figures, emulateapj, ApJ Accepte

DISTRIBUTED BROKERAGE OFFICES THROUGH INFORMATION TECHNOLOGY

This paper describes some novel ways in which Edward D. Jones and Co., a successful brokerage firm with 1650 offices nationwide, uses information technology to pursue a unique market niche: single-broker offices in communities too small to support a traditional, typically much larger, brokerage branch office. The paper focuses on the use of mainframes with "dumb" CRT terminals, rather than workstations or personal computers, to coordinate distributed operational work on a day-to-day basis.Information Systems Working Papers Serie

First Direct Double-Beta Decay Q-value Measurement of 82Se in Support of Understanding the Nature of the Neutrino

In anticipation of results from current and future double-beta decay studies, we report a measurement resulting in a 82Se double-beta decay Q-value of 2997.9(3) keV, an order of magnitude more precise than the currently accepted value. We also present preliminary results of a calculation of the 82Se neutrinoless double-beta decay nuclear matrix element that corrects in part for the small size of the shell model single-particle space. The results of this work are important for designing next generation double-beta decay experiments and for the theoretical interpretations of their observations.Comment: 5 pages, 2 figures, accepted for publication in Physical Review Letter

Annual Variation in Northern Bobwhite Survival and Raptor Migration

We estimated survival of radio-marked northern bobwhite (Colinus virginianus) on a managed prairie site in northeast Mississippi during 2 disparate winters (15 Sep-14 Apr 2000–2002). We retrospectively examined factors that may influence bobwhite survival. Pooled survival rates differed substantially between years (S 1⁄4 0.03 6 0.02 in 2000–2001 and S 1⁄4 0.36 6 0.16 in 2001–2002). Regional relative abundance of 3 species of raptors thought to be important predators of bobwhite was greater during 2000 compared to 2001 based on kriging of Christmas Bird Count (CBC) data. We demonstrate an approach for characterizing annual variation in spatial distribution of migratory raptors and suggest that annual variation in local winter predator context may be useful for explaining annual variation in winter survival of local bobwhite populations

RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome

BACKGROUND: Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MeCP2. Much of our understanding of MeCP2 function is derived from transcriptomic studies with the general assumption that alterations in the transcriptome correlate with proteomic changes. Advances in mass spectrometry-based proteomics have facilitated recent interest in the examination of global protein expression to better understand the biology between transcriptional and translational regulation. METHODS: We therefore performed the first comprehensive transcriptome-proteome comparison in a RTT mouse model to elucidate RTT pathophysiology, identify potential therapeutic targets, and further our understanding of MeCP2 function. The whole cortex of wild-type and symptomatic RTT male littermates (n = 4 per genotype) were analyzed using RNA-sequencing and data-independent acquisition liquid chromatography tandem mass spectrometry. Ingenuity(R) Pathway Analysis was used to identify significantly affected pathways in the transcriptomic and proteomic data sets. RESULTS: Our results indicate these two omics data sets supplement one another. In addition to confirming previous works regarding mRNA expression in Mecp2-deficient animals, the current study identified hundreds of novel protein targets. Several selected protein targets were validated by Western blot analysis. These data indicate RNA metabolism, proteostasis, monoamine metabolism, and cholesterol synthesis are disrupted in the RTT proteome. Hits common to both data sets indicate disrupted cellular metabolism, calcium signaling, protein stability, DNA binding, and cytoskeletal cell structure. Finally, in addition to confirming disrupted pathways and identifying novel hits in neuronal structure and synaptic transmission, our data indicate aberrant myelination, inflammation, and vascular disruption. Intriguingly, there is no evidence of reactive gliosis, but instead, gene, protein, and pathway analysis suggest astrocytic maturation and morphological deficits. CONCLUSIONS: This comparative omics analysis supports previous works indicating widespread CNS dysfunction and may serve as a valuable resource for those interested in cellular dysfunction in RTT

Large-scale discovery of enhancers from human heart tissue.

Development and function of the human heart depend on the dynamic control of tissue-specific gene expression by distant-acting transcriptional enhancers. To generate an accurate genome-wide map of human heart enhancers, we used an epigenomic enhancer discovery approach and identified ∼6,200 candidate enhancer sequences directly from fetal and adult human heart tissue. Consistent with their predicted function, these elements were markedly enriched near genes implicated in heart development, function and disease. To further validate their in vivo enhancer activity, we tested 65 of these human sequences in a transgenic mouse enhancer assay and observed that 43 (66%) drove reproducible reporter gene expression in the heart. These results support the discovery of a genome-wide set of noncoding sequences highly enriched in human heart enhancers that is likely to facilitate downstream studies of the role of enhancers in development and pathological conditions of the heart

Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli

OBJECTIVE Adherent-invasive Escherichia coli (AIEC) are a leading candidate bacterial trigger for Crohn's disease (CD). The AIEC pathovar is defined by in vitro cell-line assays examining specific bacteria/cell interactions. No molecular marker exists for their identification. Our aim was to identify a molecular property common to the AIEC phenotype. DESIGN 41 B2 phylogroup E. coli strains were isolated from 36 Australian subjects: 19 patients with IBD and 17 without. Adherence/invasion assays were conducted using the I-407 epithelial cell line and survival/replication assays using the THP-1 macrophage cell line. Cytokine secretion tumour necrosis factor ((TNF)-α, interleukin (IL) 6, IL-8 and IL-10) was measured using ELISA. The genomes were assembled and annotated, and cluster analysis performed using CD-HIT. The resulting matrices were analysed to identify genes unique/more frequent in AIEC strains compared with non-AIEC strains. Base composition differences and clustered regularly interspaced palindromic repeat (CRISPR) analyses were conducted. RESULTS Of all B2 phylogroup strains assessed, 79% could survive and replicate in macrophages. Among them, 11/41 strains (5 CD, 2 UCs, 5 non-IBD) also adhere to and invade epithelial cells, a phenotype assigning them to the AIEC pathovar. The AIEC strains were phylogenetically heterogeneous. We did not identify a gene (or nucleic acid base composition differences) common to all, or the majority of, AIEC. Cytokine secretion and CRISPRs were not associated with the AIEC phenotype. CONCLUSIONS Comparative genomic analysis of AIEC and non-AIEC strains did not identify a molecular property exclusive to the AIEC phenotype. We recommend a broader approach to the identification of the bacteria-host interactions that are important in the pathogenesis of Crohn's disease.This research was supported by an Australian Academy of Science France-Australia Science Innovation Collaboration early career fellowship; a Gastroenterological Society of Australia (GESA) Clinical Research grant; and funding from the Ministère de la Recherche et de la Technologie, Inserm (UMR1071), INRA (USC-2018); and Nouveau Chercheur EPST from Conseil Régional Auvergne

RIN4 Interacts with Pseudomonas syringae Type III Effector Molecules and Is Required for RPM1-Mediated Resistance in Arabidopsis

In Arabidopsis, RPM1 confers resistance against Pseudomonas syringae expressing either of two sequence unrelated type III effectors, AvrRpm1 or AvrB. An RPM1-interacting protein (RIN4) coimmunoprecipitates from plant cell extracts with AvrB, AvrRpm1, or RPM1. Reduction of RIN4 protein levels inhibits both the hypersensitive response and the restriction of pathogen growth controlled by RPM1. RIN4 reduction causes diminution of RPM1. RIN4 reduction results in heightened resistance to virulent Peronospora parasitica and P. syringae, and ectopic defense gene expression. Thus, RIN4 positively regulates RPM1-mediated resistance yet is, formally, a negative regulator of basal defense responses. AvrRpm1 and AvrB induce RIN4 phosphorylation. This may enhance RIN4 activity as a negative regulator of plant defense, facilitating pathogen growth. RPM1 may "guard" against pathogens that use AvrRpm1 and AvrB to manipulate RIN4 activity

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms