Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm

We have parallelized the FASTA algorithm for biological sequencecomparison using Linda, a machine-independent parallel programminglanguage. The resulting parallel program runs on a variety ofdifferent parallel machines. A straightforward parallelizationstrategy works well if the amount of computation to be doneis relatively large. When the amount of computation is reduced,however, disk I/O becomes a bottleneck which may prevent additionalspeed-up as the number of processors is increased. The paperdescribes the parallelization of FASTA, and uses FASTA to illustratethe I/O bottleneck problem that may arise when performing paralleldatabase search with a fast sequence comparison algorithm. Thepaper also describes several program design strategies thatcan help with this problem. The paper discusses how this bottleneckis an example of a general problem that may occur when parallelizing,or otherwise speeding up, a time-consuming computation. Received on July 25, 1990; accepted on October 15, 1990     

A framework for providing scientific advice for the management of new and developing invertebrate fisheries

A framework is developed for the provision of scientific advice to support the management of new and developing marine invertebrate fisheries. These fisheries often occur on species for which little biological or exploitation information is available. The framework explicitly endorses the precautionary approach to fisheries management and research. Three general management strategies (size/sex limits, regulation by total allowable catch, control of the exploitation rate) and their needs for supporting scientific information are identified. The significance of spatial pattern, and of recognizing the need for different approaches to obtain scientific information and to manage sedentary benthic and mobile pelagic species, is a central theme. Three 'phases' are proposed to obtain the necessary scientific information: (a) Phase 0, 'collecting existing information', consisting of syntheses of available biological and fisheries information on the target (and similar) species, leading to formulation of potential management strategies; (b) Phase 1, 'collecting new information', to obtain the essential information that is lacking or insufficient from the Phase 0 analysis, and to evaluate alternative management strategies and propose regulatory actions; and (c) Phase 2, 'fishing for commerce', to implement the chosen management actions and to monitor fishing operations, so as to increase the information base available to refine the results from previous phases. Phase 1 activities may consist of surveys, site-specific depletion experiments and studies to obtain biological information, and development of experimental management areas to test different exploitation rates. A strategy that includes establishing reserve areas recognises the inherent uncertainties associated with developing fisheries and provides a buffer against mistakes or 'surprises'; it also provides control areas to compare stock productivity in fished and unfished locations. The application of this framework to a developing sea cucumber fishery in British Columbia is presented as an example. Throughout, strong interaction and collaboration among science, management, and stakeholders is crucial to the provision of scientific advice for precautionary management of new invertebrate fisheries.     

Phosphatidic acid is a potent and selective inhibitor of protein phosphatase 1 and an inhibitor of ceramide-mediated responses.

In the present study, we report that phosphatidic acid (PA) functions as a novel, potent, and selective inhibitor of protein phosphatase 1 (PP1). The catalytic subunit of PP1alpha was inhibited by PA dose-dependently in a noncompetitive manner with a K(i) value of 80 nM. The inhibition by PA was specific to PP1 as PA failed to inhibit protein phosphatase 2A (PP2A) or PP2B. Furthermore, PA was the most effective and potent inhibitor of PP1 compared with other phospholipids. Because we recently showed that ceramides activated PP1, we next examined the effects of PA on ceramide stimulation of PP1. PA inhibited both basal and ceramide-stimulated PP1 activities, and ceramide showed potent and stereoselective activation of PP1 in the presence of PA. Next, the effects of PA on ceramide-induced responses were examined. Molt-4 cells took up PA dose- and time-dependently such that by 1 and 3 h, uptake of PA was 0.37 and 0. 65% of total PA added, respectively. PA at 30 microM and calyculin A at 10 nM (an inhibitor of PP1 and PP2A at low concentrations), but not okadaic acid at 10 nM (a PP2A inhibitor at low concentrations) prevented poly(ADP-ribose) polymerase proteolysis induced by C(6)-ceramide. Moreover, the combination of PA with okadaic acid prevented retinoblastoma gene product dephosphorylation induced by C(6)-ceramide. These data suggest that PA functions as a specific regulator of PP1 and may reverse or counteract those effects of ceramide that are mediated by PP1, such as apoptosis and retinoblastoma gene product dephosphorylation.     

Structural and Psycho-Social Limits to Climate Change Adaptation in the Great Barrier Reef Region

Adaptation, as a strategy to respond to climate change, has limits: there are conditions under which adaptation strategies fail to alleviate impacts from climate change. Research has primarily focused on identifying absolute bio-physical limits. This paper contributes empirical insight to an emerging literature on the social limits to adaptation. Such limits arise from the ways in which societies perceive, experience and respond to climate change. Using qualitative data from multi-stakeholder workshops and key-informant interviews with representatives of the fisheries and tourism sectors of the Great Barrier Reef region, we identify psycho-social and structural limits associated with key adaptation strategies, and examine how these are perceived as more or less absolute across levels of organisation. We find that actors experience social limits to adaptation when: i) the effort of pursuing a strategy exceeds the benefits of desired adaptation outcomes; ii) the particular strategy does not address the actual source of vulnerability, and; iii) the benefits derived from adaptation are undermined by external factors. We also find that social limits are not necessarily more absolute at higher levels of organisation: respondents perceived considerable opportunities to address some psycho-social limits at the national-international interface, while they considered some social limits at the local and regional levels to be effectively absolute.