On board sampling of the rockfish and lingcod commerical passenger fishing vessel industry in northern and central California, May 1987 to December 1991

From May 1987 to June 1990 and from August to December 1991 Fishery Technicians sampled catches on board 690 Commercial Passenger Fishing Vessel (CPFV) trips targeting rockfish and lingcod from the general port areas of Fort Bragg, Bodega Bay, San Francisco, Monterey, and Morro Bay. Data are presented for species composition by port area, year, and month, for catch-per-unit-effort, mean length, and length frequency of lingcod and the 18 most frequently observed rockfish species, and for trends in fishing effort related to fishing time, depth, and distance from port. Total catch estimates are presented based on unadjusted logbook records, logbook records adjusted by sampling data and compliance rates, and effort data from a marine recreational fishing statistics survey. Average catch of kept fish per angler day was 11.8 and average catch of kept fish per angler hour was 3.7. A trend of an increasing frequency of trips to deep (>40 fm) locations was observed in the Bodega Bay, San Francisco, and Monterey areas from 1988 to 1990-91. No trend was evident relative to trip frequency and distance from port. A total of 74 species was observed caught during the study. Rockfishes comprised 88.5% to 97.9% by number of the observed catch by port area. The five most frequently observed species were chilipepper, blue, yellowtail, and widow rockfishes, and bocaccio, with lingcod ranking seventh. In general, mean length and catch-per-angler-hour of sport fishes caught by CPFV anglers varied considerably and did not show steady declines during the study period. However, port-specific areas of major concern were identified for chilipepper, lingcod, and black rockfish, and to a lesser extent brown, canary, vermilion, yelloweye, olive, and widow rockfish. These areas of concern included steadily declining catch rate, steadily declining mean length, and a high percentage of sexually immature fish in the sampled-catch. Recent sampling of the commercial hook-and-line fishery in northern and central California indicated that most species of rockfishes taken by CPFV anglers are also harvested commercially. (261pp.

Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes.

Anti-CRISPRs (Acrs) are small proteins that inhibit the RNA-guided DNA targeting activity of CRISPR-Cas enzymes. Encoded by bacteriophage and phage-derived bacterial genes, Acrs prevent CRISPR-mediated inhibition of phage infection and can also block CRISPR-Cas-mediated genome editing in eukaryotic cells. To identify Acrs capable of inhibiting Staphylococcus aureus Cas9 (SauCas9), an alternative to the most commonly used genome editing protein Streptococcus pyogenes Cas9 (SpyCas9), we used both self-targeting CRISPR screening and guilt-by-association genomic search strategies. Here we describe three potent inhibitors of SauCas9 that we name AcrIIA13, AcrIIA14, and AcrIIA15. These inhibitors share a conserved N-terminal sequence that is dispensable for DNA cleavage inhibition and have divergent C termini that are required in each case for inhibition of SauCas9-catalyzed DNA cleavage. In human cells, we observe robust inhibition of SauCas9-induced genome editing by AcrIIA13 and moderate inhibition by AcrIIA14 and AcrIIA15. We also find that the conserved N-terminal domain of AcrIIA13-AcrIIA15 binds to an inverted repeat sequence in the promoter of these Acr genes, consistent with its predicted helix-turn-helix DNA binding structure. These data demonstrate an effective strategy for Acr discovery and establish AcrIIA13-AcrIIA15 as unique bifunctional inhibitors of SauCas9

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.

In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3' untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites

Technology transfer from NASA to targeted industries, volume 2

This volume contains the following materials to support Volume 1: (1) Survey of Metal Fabrication Industry in Alabama; (2) Survey of Electronics Manufacturing/Assembly Industry in Alabama; (3) Apparel Modular Manufacturing Simulators; (4) Synopsis of a Stereolithography Project; (5) Transferring Modular Manufacturing Technology to an Apparel Firm; (6) Letters of Support; (7) Fact Sheets; (8) Publications; and (9) One Stop Access to NASA Technology Brochure

Angiogenic Effect of Bioactive Borate Glass Microfibers and Beads in the Hairless Mouse

The purpose of this project was to investigate the angiogenic mechanism of bioactive borate glass for soft tissue repair in a \u27hairless\u27 SKH1 mouse model. Subcutaneous microvascular responses to bioactive glass microfibers (45S5, 13-93B3, and 13-93B3Cu) and bioactive glass beads (13-93, 13-93B3, and 13-93B3Cu) were assessed via: noninvasive imaging of skin microvasculature; histomorphometry of microvascular densities; and quantitative PCR measurements of mRNA expression of VEGF and FGF-2 cytokines. Live imaging via dorsal skin windows showed the formation at two weeks of a halo-like structure infused with microvessels surrounding implanted borate-based 13-93B3 and 13-93B3Cu glass beads, a response not observed with silicate-based 13-93 glass beads. Quantitative histomorphometry of tissues implanted with plugs of 45S5, 13-93B3, and 13-93B3Cu glass microfibers revealed microvascular densities that were 1.6-, 2.3-, and 2.7-times higher, respectively, than the sham control values whereas 13-93, 13-93B3, and 13-93B3Cu glass beads caused the microvascular density to increase 1.3-, 1.6-, and 2.5-fold, respectively, relative to sham controls. Quantitative PCR measurements indicate a marginally significant increased expression of VEGF mRNA in tissues with 13-93B3Cu glass beads, an outcome that supported the hypothesis that copper-doped borate glass could promote VEGF expression followed by angiogenesis for enhanced wound healing

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs

RNAs assume sophisticated structures that are active in myriad cellular processes. In this review, we highlight newly identified ribozymes, riboswitches, and small RNAs, some of which control the function of cellular metabolic and gene expression networks. We then examine recent developments in genome-wide RNA structure probing technologies that are yielding new insights into the structural landscape of the transcriptome. Finally, we discuss how these RNA ‘structomic’ methods can address emerging questions in RNA systems biology, from the mechanisms behind long non-coding RNAs to new bases for human diseases