Netarts Bay chum salmon hatchery : an experiment in ocean ranching

Page 4 and 10 are blank pages in document.The recent pattern in Pacific salmon fisheries is one of overcapitalized vessels, facing escalating energy and labor costs, in pursuit of limited (in some cases decimated) stocks. In many areas of the Pacific Northwest, the fisheries depend heavily upon exploiting artificially propagated stocks. Since revenues from the fisheries do not offset the costs of hatchery programs, the propagative programs of state and federal agencies are a subsidy without which the fisheries could not exist. The fisheries are also dependent on market prices which place ocean-caught salmon in the luxury food class. The problems confronting the fisheries have resulted in increasing interest in salmon aquaculture as an alternative approach to salmon production

Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques

The discipline of synthetic biology emphasizes the application of engineering principles such as standardization, abstraction, modularity, and rational design to complex biological systems. The archetypical example of such standardization is BioBrick RFC[10], introduced in 2003 by Tom Knight at MIT. BioBricks are stored on a standard plasmid, pSB1C3, which contains prefix and suffix sequences flanking the DNA sequence specifying a biological part. The prefix and suffix sequences contain two pairs of 6 base-pair (bp) restriction enzyme sites (EcoRI+XbaI and SpeI+PstI), which can be used for both part assembly and quality control. BioBricks are intended to be well- characterized biological parts, such as genes or promoters, that function in a predictable fashion and can be readily combined to make complex systems. The rules of the RFC[10] BioBrick assembly method require that none of the restriction sites used in the prefix and suffix be present in the parts themselves. This requirement can be an onerous imposition for iGEM teams developing large, novel parts, such as genes or entire operons that are obtained by amplifying DNA sequences from environmental samples or microorganisms. While iGEM teams may use methods such as site-directed mutagenesis to remove illegal restriction sites from a part's sequence, it is certainly possible that this mutation will alter the functionality of the part – a very undesirable outcome. In addition, the mutagenesis of illegal restriction sites is an unnecessary burden on teams, given the limited time and resources available to teams during each year’s iGEM competition. Efforts spent mutagenizing sites would be better spent characterizing and improving parts. This RFC proposes an alternative submission standard to eliminate these problems

Heat Shock Protein 70 Expression in Juvenile Eastern Oysters, Crassostrea virginica (Gmelin, 1791), Exposed to Anoxic Conditions

Anoxic water events in conjunction with summer high temperatures are thought to be one of the causes of declines in natural oyster reefs on the eastern shore of Mobile Bay. Work is underway to determine whether tolerance to low oxygen can be selected for in hatchery-produced oysters. As a component of this work, the expression of heat shock protein 70 (HSP 70) was examined in control (normoxia) and anoxia-challenged juvenile oysters. Parental Eastern oysters, Crassostrea virginica were collected from 2 sites, Cedar Point Reef (CP), an area considered to have normoxic conditions, and White House Reef (WH), an area suspected to experience periodic anoxia. F1 generation oysters were produced from CP and WH parents that survived an anoxic exposure of 96 h. Control F1 generation oysters from both parental stocks not exposed to anoxia were also produced. The F1 generation oysters were subsequently exposed to anoxia or control normoxic conditions, and differences in expression of HSP 70 were examined. Nitrogen was used to create the anoxic conditions for both the parental and F1 generations. Three HSP 70 isoforms—2 constitutive forms (HSC 77 and HSC 72) and 1 inducible form (HSP 69)—were expressed in both anoxia- and normoxia-exposed oysters from all groups. Although there were differences among groups of oysters from the 2 sites, there were no differences in the expression of HSC 77 and HSC 72 between the control and anoxia-treated oysters within a group. Interestingly, the expression of HSP 69 was higher in oysters exposed to normoxia than the ones from anoxia treatments. These differences are thought to reflect a combination of responses to nutritional stress in the controls and facultative anaerobiosis and metabolic arrest in the anoxia groups

Differential glucocorticoid metabolism in patients with persistent versus resolving inflammatory arthritis

Introduction: Impairment in the ability of the inflamed synovium to generate cortisol has been proposed to be a factor in the persistence and severity of inflammatory arthritis. In the inflamed synovium, cortisol is generated from cortisone by the 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) enzyme. The objective of this study was to determine the role of endogenous glucocorticoid metabolism in the development of persistent inflammatory arthritis. Methods: Urine samples were collected from patients with early arthritis (symptoms ≤12 weeks duration) whose final diagnostic outcomes were established after clinical follow-up and from patients with established rheumatoid arthritis (RA). All patients were free of disease-modifying anti-rheumatic drugs at the time of sample collection. Systemic measures of glucocorticoid metabolism were assessed in the urine samples by gas chromatography/mass spectrometry. Clinical data including CRP and ESR were also collected at baseline. Results: Systemic measures of 11β-HSD1 activity were significantly higher in patients with early arthritis whose disease went on to persist, and also in the subgroup of patients with persistent disease who developed RA, when compared with patients whose synovitis resolved over time. We observed a significant positive correlation between systemic 11β-HSD1 activity and ESR/CRP in patients with established RA but not in any of the early arthritis patients group. Conclusions: The present study demonstrates that patients with a new onset of synovitis whose disease subsequently resolved had significantly lower levels of systemic 11β-HSD1 activity when compared with patients whose synovitis developed into RA or other forms of persistent arthritis. Low absolute levels of 11β-HSD1 activity do not therefore appear to be a major contributor to the development of RA and it is possible that a high total body 11β-HSD1 activity during early arthritis may reduce the probability of disease resolution

Caspase Inhibitors of the P35 Family Are More Active When Purified from Yeast than Bacteria

Many insect viruses express caspase inhibitors of the P35 superfamily, which prevent defensive host apoptosis to enable viral propagation. The prototypical P35 family member, AcP35 from Autographa californica M nucleopolyhedrovirus, has been extensively studied. Bacterially purified AcP35 has been previously shown to inhibit caspases from insect, mammalian and nematode species. This inhibition occurs via a pseudosubstrate mechanism involving caspase-mediated cleavage of a “reactive site loop” within the P35 protein, which ultimately leaves cleaved P35 covalently bound to the caspase's active site. We observed that AcP35 purifed from Saccharomyces cerevisae inhibited caspase activity more efficiently than AcP35 purified from Escherichia coli. This differential potency was more dramatic for another P35 family member, MaviP35, which inhibited human caspase 3 almost 300-fold more potently when purified from yeast than bacteria. Biophysical assays revealed that MaviP35 proteins produced in bacteria and yeast had similar primary and secondary structures. However, bacterially produced MaviP35 possessed greater thermal stability and propensity to form higher order oligomers than its counterpart purified from yeast. Caspase 3 could process yeast-purified MaviP35, but failed to detectably cleave bacterially purified MaviP35. These data suggest that bacterially produced P35 proteins adopt subtly different conformations from their yeast-expressed counterparts, which hinder caspase access to the reactive site loop to reduce the potency of caspase inhibition, and promote aggregation. These data highlight the differential caspase inhibition by recombinant P35 proteins purified from different sources, and caution that analyses of bacterially produced P35 family members (and perhaps other types of proteins) may underestimate their activity