Structure-function analysis of USP1: insights into the role of Ser313 phosphorylation site and the effect of cancer-associated mutations on autocleavage

Background: In complex with its cofactor UAF1, the USP1 deubiquitinase plays an important role in cellular processes related to cancer, including the response to DNA damage. The USP1/UAF1 complex is emerging as a novel target in cancer therapy, but several aspects of its function and regulation remain to be further clarified. These include the role of the serine 313 phosphorylation site, the relative contribution of different USP1 sequence motifs to UAF1 binding, and the potential effect of cancer-associated mutations on USP1 regulation by autocleavage. Methods: We have generated a large set of USP1 structural variants, including a catalytically inactive form (C90S), non-phosphorylatable (S313A) and phosphomimetic (S313D) mutants, deletion mutants lacking potential UAF1 binding sites, a mutant (GG/AA) unable to undergo autocleavage at the well-characterized G670/G671 diglycine motif, and four USP1 mutants identified in tumor samples that cluster around this cleavage site (G667A, L669P, K673T and A676T). Using cell-based assays, we have determined the ability of these mutants to bind UAF1, to reverse DNA damage-induced monoubiquitination of PCNA, and to undergo autocleavage. Results: A non-phosphorylatable S313A mutant of USP1 retained the ability to bind UAF1 and to reverse PCNA ubiquitination in cell-based assays. Regardless of the presence of a phosphomimetic S313D mutation, deletion of USP1 fragment 420-520 disrupted UAF1 binding, as determined using a nuclear relocation assay. The UAF1 binding site in a second UAF1-interacting DUB, USP46, was mapped to a region homologous to USP1(420-520). Regarding USP1 autocleavage, co-expression of the C90S and GG/AA mutants did not result in cleavage, while the cancer-associated mutation L669P was found to reduce cleavage efficiency. Conclusions: USP1 phosphorylation at S313 is not critical for PCNA deubiquitination, neither for binding to UAF1 in a cellular environment. In this context, USP1 amino acid motif 420-520 is necessary and sufficient for UAF1 binding. This motif, and a homologous amino acid segment that mediates USP46 binding to UAF1, map to the Fingers sub-domain of these DUBs. On the other hand, our results support the view that USP1 autocleavage may occur in cis, and can be altered by a cancer-associated mutation.

Improving Shepherd's Length Composition Analysis (SLCA) method for growth parameter estimations

Shepherd's "weekly parametric" method for estimating the parameter L sub( infinity ) and K of the von Bertalanffy growth function from length-frequency data often fails to converge, and usually overestimates K. It is shown that this is due to overcounting of the frequencies associated with large, slow growing fish, and that both of these problems can be completely overcome by a simple change in the way the scoring function is formulated.

Preliminary Analysis of the Feasibility of Transferring New Longline Technology to Small Artisanal Vessels off Northeastern Brazil

The catches of three longliners, including two recently converted small artisanal vessels and one large leased foreign longliner, were compared to provide some indication of the feasibility of transferring new longline technology to small vessels in the northeastern Brazilian pelagic longline fishery. Comparisons of catches between the two recently converted vessels operating across the same spatial and temporal scales showed no significant differences for the main target species, providing evidence to suggest that adoption of the technology was rapid and straightforward. A comparison of relative catch rates between one of the recently converted small longliners and the leased longliner across the same temporal scale, but in different areas, showed that while there were significant differences detected for some species, contributing to a significant reduction in total CPUE, the relative abundance of commercially important species within the operational range of the smaller vessels was sufficient for economically viable catches. The results showed that the net financial profit from the artisanal longliner was almost 10 times greater than that derived from existing fishing methods. The inclusion of some artisanal vessels in this fishery may help address the social and economic problems currently faced by fi

Biological Analysis of Two Management Options for the Atlantic Menhaden Fishery

Biological implications of two managment options (the closed corridor and the recommended shortened season (Option 7) options) for the Atlantic menhaden, Brevoortia tyrannus, fishery are reported based on purse-seine landings and port sampling data from 1970 to 1984 and captain's daily fishing reports from 1978 to 1982. Large catches of age-O menhaden raise concern for growth overfishing. Area-specific yield-per-recruit analyses are used to investigate the biological consequences of these management options. The closed corridor option indicates coastwide gains in yield-per-recruit ranging from 0.3 to 7.2% depending on changes in fishing activity with most areas showing gains. The shortened fishing season indicates coastwide gains in yield per recruit ranging from O. 4 to 10.2% depending onf ishing year with most geographic areas showing gains. The shortened fishing season option offers the greatest gains when large numbers ofy oung menhaden would be caught late in the fishing year, while gains from the closed corridor option depend on how the fishing fleet responds to that management plan. The shortened season offers greater potential coastwide gains to the fishery, but also may result in greater losses to the North Carolina fall fishery. The analytical approach is applicable to the management of other coastal migratory fish stocks that fall under the Atlantic States Marine Fisheries Commission or other interstate management groups.

Competing for the Recreational Dollar: An Analysis of the California Commercial Passenger-Carrying Fishing Vessel Industry

California has a large and diverse marine recreational fishery. Anglers on commercial passenger-carrying fishing vessels (CPFV's) harvest a substantial proportion of California's marine recreational fisheries landings, accounting for about 40 percent and 16 percent of the total 1986 marine recreational catch in southern and northern California, respectively (NMFS, 1987). In 1986, 459,369 CPFV anglers landed some 2,835,021 fish in southern California, while 200,925 CPFV anglers landed 1,240, 100 fish in central and northern California.

Surface temperature and precipitation variations in the western U.S. and their relation to large scale circulation indices [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): An analysis of the principal components of surface temperature and precipitation in the western U.S. is presented. Data consist of monthly mean temperature and total precipitation for 66 climate divisions west of the Continental Divide, for the years 1931-1984. The analysis is repeated for three separate combinations of months - the water year (Oct - Sept), the cool season (Oct - Mar) and the warm season (Apr - Sept). Inspection of monthly precipitation climatology indicates that selection of these combinations of months results in very few awkward splittings of the natural precipitation seasons found in the West.

Regulation of primary production in the Gulf of California through interaction of large-scale and local ocean processes [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): The suppression of primary productivity observed in eastern boundary ecosystems of the Pacific during El Nino episodes does not occur throughout the Gulf of California. On the contrary, analysis of the modern siliceous phytoplankton record from annually layered sediments and compilation of available primary productivity measurements indicate that production is significantly increased in the central Gulf during El Nino years compared to anti-El Nino years. Integrated observations of biological and physical variability during the spring of 1983, under the influence of the strong El Nino, show that very high primary productivity occurred along the eastern margin of the central Gulf. This resulted from the upwelling of a nutrient rich source provided by the locally formed Gulf water mass originating in the northern Gulf. Lower productivity and phytoplankton biomass were associated with the anomalous penetration of Tropical Surface Water along the western side of the Gulf.

Multiscale analysis of factors that affect the distribution of sharks throughout the northern Gulf of Mexico

Identification of the spatial scale at which marine communities are organized is critical to proper management, yet this is particularly difficult to determine for highly migratory species like sharks. We used shark catch data collected during 2006–09 from fishery-independent bottom-longline surveys, as well as biotic and abiotic explanatory data to identify the factors that affect the distribution of coastal sharks at 2 spatial scales in the northern Gulf of Mexico. Centered principal component analyses (PCAs) were used to visualize the patterns that characterize shark distributions at small (Alabama and Mississippi coast) and large (northern Gulf of Mexico) spatial scales. Environmental data on temperature, salinity, dissolved oxygen (DO), depth, fish and crustacean biomass, and chlorophyll-a (chl-a) concentration were analyzed with normed PCAs at both spatial scales. The relationships between values of shark catch per unit of effort (CPUE) and environmental factors were then analyzed at each scale with co-inertia analysis (COIA). Results from COIA indicated that the degree of agreement between the structure of the environmental and shark data sets was relatively higher at the small spatial scale than at the large one. CPUE of Blacktip Shark (Carcharhinus limbatus) was related positively with crustacean biomass at both spatial scales. Similarly, CPUE of Atlantic Sharpnose Shark (Rhizoprionodon terraenovae) was related positively with chl-a concentration and negatively with DO at both spatial scales. Conversely, distribution of Blacknose Shark (C. acronotus) displayed a contrasting relationship with depth at the 2 scales considered. Our results indicate that the factors influencing the distribution of sharks in the northern Gulf of Mexico are species specific but generally transcend the spatial boundaries used in our analyses.

Spatial and temporal analysis of bottlenose dolphin strandings in South Carolina, 1992-2005

This CD contains summary data of bottlenose dolphins stranded in South Carolina using a Geographical Information System (GIS) and contains two published manuscripts in .pdf files. The intent of this CD is to provide data on bottlenose dolphin strandings in South Carolina to marine mammal researchers and managers. This CD is an accumulation of 14 years of stranding data collected through the collaborations of the National Ocean Service, Center for Coastal Environmental Health and Biomolecular Research (CCEHBR), the South Carolina Department of Natural Resources, and numerous volunteers and veterinarians that comprised the South Carolina Marine Mammal Stranding Network. Spatial and temporal information can be visually represented on maps using GIS. For this CD, maps were created to show relationships of stranding densities with land use, human population density, human interaction with dolphins, high geographical regions of live strandings, and seasonal changes. Point maps were also created to show individual strandings within South Carolina. In summary, spatial analysis revealed higher densities of bottlenose dolphin strandings in Charleston and Beaufort Counties, which consist of urban land with agricultural input. This trend was positively correlated with higher human population levels in these coastal counties as compared with other coastal counties. However, spatial analysis revealed that certain areas within a county may have low human population levels but high stranding density, suggesting that the level of effort to respond to strandings is not necessarily positively correlated with the density of strandings in South Carolina. Temporal analysis revealed a significantly higher density of bottlenose dolphin strandings in the northern portion of the State in the fall, mostly due to an increase of neonate strandings. On a finer geographic scale, seasonal stranding densities may fluctuate depending on the region of interest. Charleston Harbor had the highest density of live bottlenose dolphin strandings compared to the rest of the State. This was due in large part to the number of live dolphin entanglements in the crab pot fishery, the largest source of fishery-related mortality for bottlenose dolphins in South Carolina (Burdett and McFee 2004). Spatial density calculations also revealed that Charleston and Beaufort accounted for the majority of dolphins that were involved with human activities. 1

Comparative analysis of three brevetoxin-associated bottlenose dolphin (Tursiops truncatus) mortality events in the Florida Panhandle region (USA)

In the Florida Panhandle region, bottlenose dolphins (Tursiops truncatus) have been highly susceptible to large-scale unusual mortality events (UMEs) that may have been the result of exposure to blooms of the dinoflagellate Karenia brevis and its neurotoxin, brevetoxin (PbTx). Between 1999 and 2006, three bottlenose dolphin UMEs occurred in the Florida Panhandle region. The primary objective of this study was to determine if these mortality events were due to brevetoxicosis. Analysis of over 850 samples from 105 bottlenose dolphins and associated prey items were analyzed for algal toxins and have provided details on tissue distribution, pathways of trophic transfer, and spatial-temporal trends for each mortality event. In 1999/2000, 152 dolphins died following extensive K. brevis blooms and brevetoxin was detected in 52% of animals tested at concentrations up to 500 ng/g. In 2004, 105 bottlenose dolphins died in the absence of an identifiable K. brevis bloom; however, 100% of the tested animals were positive for brevetoxin at concentrations up to 29,126 ng/mL. Dolphin stomach contents frequently consisted of brevetoxin-contaminated menhaden. In addition, another potentially toxigenic algal species, Pseudo-nitzschia, was present and low levels of the neurotoxin domoic acid (DA) were detected in nearly all tested animals (89%). In 2005/2006, 90 bottlenose dolphins died that were initially coincident with high densities of K. brevis. Most (93%) of the tested animals were positive for brevetoxin at concentrations up to 2,724 ng/mL. No DA was detected in these animals despite the presence of an intense DA-producing Pseudo-nitzschia bloom. In contrast to the absence or very low levels of brevetoxins measured in live dolphins, and those stranding in the absence of a K. brevis bloom, these data, taken together with the absence of any other obvious pathology, provide strong evidence that brevetoxin was the causative agent involved in these bottlenose dolphin mortality events.

Characterizing Jobos Bay, Puerto Rico: a watershed modeling analysis and monitoring plan

Land-based pollution is commonly identified as a major contributor to the observed deterioration of shallow-water coral reef ecosystem health. Human activity on the coastal landscape often induces nutrient enrichment, hypoxia, harmful algal blooms, toxic contamination and other stressors that have degraded the quality of coastal waters. Coral reef ecosystems throughout Puerto Rico, including Jobos Bay, are under threat from coastal land uses such as urban development, industry and agriculture. The objectives of this report were two-fold: 1. To identify potentially harmful land use activities to the benthic habitats of Jobos Bay, and 2. To describe a monitoring plan for Jobos Bay designed to assess the impacts of conservation practices implemented on the watershed. This characterization is a component of the partnership between the U.S. Department of Agriculture (USDA) and the National Oceanic and Atmospheric Administration (NOAA) established by the Conservation Effects Assessment Project (CEAP) in Jobos Bay. CEAP is a multi-agency effort to quantify the environmental benefits of conservation practices used by private landowners participating in USDA programs. The Jobos Bay watershed, located in southeastern Puerto Rico, was selected as the first tropical CEAP Special Emphasis Watershed (SEW). Both USDA and NOAA use their respective expertise in terrestrial and marine environments to model and monitor Jobos Bay resources. This report documents NOAA activities conducted in the first year of the three-year CEAP effort in Jobos Bay. Chapter 1 provides a brief overview of the project and background information on Jobos Bay and its watershed. Chapter 2 implements NOAA’s Summit to Sea approach to summarize the existing resource conditions on the watershed and in the estuary. Summit to Sea uses a GIS-based procedure that links patterns of land use in coastal watersheds to sediment and pollutant loading predictions at the interface between terrestrial and marine environments. The outcome of Summit to Sea analysis is an inventory of coastal land use and predicted pollution threats, consisting of spatial data and descriptive statistics, which allows for better management of coral reef ecosystems. Chapters 3 and 4 describe the monitoring plan to assess the ecological response to conservation practices established by USDA on the watershed. Jobos Bay is the second largest estuary in Puerto Rico, but has more than three times the shoreline of any other estuarine area on the island. It is a natural harbor protected from offshore wind and waves by a series of mangrove islands and the Punta Pozuelo peninsula. The Jobos Bay marine ecosystem includes 48 km² of mangrove, seagrass, coral reef and other habitat types that span both intertidal and subtidal areas. Mapping of Jobos Bay revealed 10 different benthic habitats of varying prevalence, and a large area of unknown bottom type covering 38% of the entire bay. Of the known benthic habitats, submerged aquatic vegetation, primarily seagrass, is the most common bottom type, covering slightly less than 30% of the bay. Mangroves are the dominant shoreline feature, while coral reefs comprise only 4% of the total benthic habitat. However, coral reefs are some of the most productive habitats found in Jobos Bay, and provide important habitat and nursery grounds for fish and invertebrates of commercial and recreational value.

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades.

An analysis of records of gillnet fishing in Pilkington Bay, Lake Victoria

Among the commercially valuable species occurring in Lake Victoria the two endemic species of Tilapia, T. esculenta (Graham) and T. variabilis (Boulenger) still provide the basis for the fishery in many areas, though in some places the non-cichlid species are more important, for example in the Kagera river area where large numbers of Labeo victorianus and Schilbe mystus migrate seasonally into the river. Although certain species show these habitat preferences. Most of the coastline of Lake Victoria supports a wide variety of species, all of which contribute to the commercial fishery. Over the past ten years the East African Fisheries Research Organisation has fished experimentally a number of stations within a radius of fifty miles from Jinja. These stations have been selected so as to cover a variety of habitats which range from sheltered bays to exposed coastlines. The records discussed in this paper are the result of fishing operations carried out in Pilkington Bay over the period December 1954 to November 1956. This series of fishing operations was carried out in an attempt to assess the composition of the fish populations contained in this area. To this end a variety of nets of differing mesh sizes were used. Pilkington Bay is about ten square miles in extent and is an irregular and deep indentation on the north coast of Buvuma Island. It lies within the sleeping siclmess area where fishing by Africans is prohibited. When selecting an experimental fishing ground, it is important to have some idea of the amount of commercial fishing being carried out in the area. Throughout the period of this experiment a few African fishermen were seen operating illegally in the area, but it is unlikely that their efforts greatly affected the results obtained. Pilkington Bay was fished by E.A.F.R.O. in 1949 and 1950 (Lowe McConnell 1956) but since then till the present experiment, fishing in the area has been infrequent.

Numerical analysis of the coupled circuit and cooling holes for an electromagnetic shaker

This paper presents a time-stepping shaker modeling scheme. The new method improves the accuracy of analysis of armature-position-dependent inductances and force factors, analysis of axial variation of current density in copper plates (short-circuited turns), and analysis of cooling holes in the magnetic circuit. Linear movement modeling allows armature position to be precisely included in the shaker analysis. A more accurate calculation of eddy currents in the coupled circuit is in particular crucial for the shaker analysis in a mid-or high-frequency operation range. Large currents in a shaker, including eddy currents, incur large Joule losses, which in turn require the use of a cooling system to keep temperature at bay. Sizable cooling holes have influence on the saturation state of iron poles, and hence have to be properly taken into account.