Related calcium-binding proteins map to the same subregion of chromosome 1q and to an extended region of synteny on mouse chromosome 3

The serum protein cystic fibrosis-associated antigen (CFAG), present at elevated levels in CF homozygotes and heterozygotes, is now known to consist of two distinct but related subunits (calgranulins A (CAGA) and B (CAGB)). Both show similarity to the S100-related calcium-binding proteins. We have previously assigned CAGA to human chromosome 1q12-q21 and demonstrate here that the cDNA probe for CAGB cosegregates with it in our somatic cell hybrid panel. cDNA probes for the related genes calcyclin (CACY) and a mouse placental protein (18A2, suggested name Capl) enabled us to confirm and refine the in situ hybridization result assigning CACY to chromosome 1q21-25 and to demonstrate that both genes cosegregate with CAGA and CAGB. Capl was mapped to a region of chromosome 3 in the mouse using the BXD recombinant inbred strain mice where the p11 protein (calpactin light chain Cal1l), another S100 family member, has been localized. Cacy is shown to be within 8 kb of Capl in the mouse genome.     

Calcium influences the stability and conformation of rotavirus SAH glycoprotein VP7 expressed in Dictyostelium discoideum

We have previously reported expression of the rotavirus outer capsid glycoprotein, VP7, in the relatively new expression host, Dictyostelium discoideum. To optimise yields of recombinant VP7, we examined the role of Ca²⁺ since stability of both VP7 and mature rotavirus during a rotavirus infection are calcium-dependent. Low micromolar levels of free extracellular Ca²⁺ were required to maximise yields of VP7 in D. discoideum whilst levels of VP7 were reduced following depletion of intracellular Ca²⁺ reserves using A23187 and EGTA. Immunoblot analysis suggested that VP7 was being degraded in an intracellular compartment. Immunoprecipitation with a conformation-dependent neutralising antibody confirmed that EGTA-induced Ca²⁺ chelation alters the conformation of VP7. These results suggest that stability of VP7 is dependent on maintaining adequate levels of intracellular Ca²⁺ and that conformational changes in VP7 which occur following depletion of Ca²⁺ reserves induce rapid proteolysis of the protein. Since these results establish conditions for expressing optimal levels of VP7 in the correct conformation they have important implications for the development of a subunit vaccine based on recombinant VP7.     

The importance of mate retention and experience on breeding success in Cassin's auklet (Ptychoramphus aleuticus)

We studied the relative effects of mate retention and breedingexperience on reproductive success in Cassin's auklet (Ptychoramphusaleuticus) on Southeast Farallon Island, California, USA. Breedingsuccess of banded birds was monitored from 1985 to 1990 andanalyzed using linear and logistic regression. Breeding performanceimproved with experience and mate retention, but their relativeeffects differed. Hatching success improved with both femaleand male experience but declined with advanced experience inmales, perhaps due to reproductive senescence. In males, butnot in females, hatching success showed a quadratic relationshipwith length of the pair-bond when adjusted for experience, indicatinga greater benefit to males for mate retention. Fledging andbreeding success and weight at fledging also increased asymptoticallywith length of the pair-bond for both sexes. There was no correlationbetween mate switching and previous reproductive failure. Anincrease in weight at fledging with experience in females, butnot in males, suggests that females either became more efficientat foraging or invested greater effort in chick rearing withexperience than males.     

Great Barrier Reef butterflyfish community structure: the role of shelf position and benthic community type

The extent to which fish communities are structured by spatial variability in coral reef habitats versus stochastic processes (such as larval supply) is very important in predicting responses to sustained and ongoing habitat degradation. In this study, butterflyfish and benthic communities were surveyed annually over 15 years on 47 reefs (spanning 12° of latitude) of the Great Barrier Reef (GBR). Spatial autocorrelation in the structure of butterflyfish communities versus key differences in reef habitats was investigated to assess the extent to which the structure of these fish communities is influenced by habitat conditions. Benthic communities on each of the 47 reefs were broadly categorised as either: 1. Poritidae/Alcyoniidae, 2. mixed taxa, 3. soft coral or 4. Acropora-dominated habitats. These habitat types most reflected increases in water clarity and wave exposure, moving across the GBR shelf from coastal to outer-shelf environments. In turn, each habitat type also supported very distinct butterflyfish communities. Hard coral feeders were always the dominant butterflyfish species in each community type. However, the numerically dominant species changed according to habitat type, representing spatial replacement of species across the shelf. This study reveals clear and consistent differences in the structure of fish communities among reefs associated with marked differences in habitat structure.     

Genome skimming identifies polymorphism in tern populations and species

Background

Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons.

Findings

We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH.

Conclusions

ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.     

Fluctuations in Adélie penguin prey size in the mid to late Holocene, northern Marguerite Bay, Antarctic Peninsula

We investigated temporal changes in Adélie penguin prey size in northern Marguerite Bay, Antarctic Peninsula, through excavations of three abandoned and one active colony at Lagoon (67°35'S, 68°16'W) and Ginger Islands (67°45'S, 68°41'W), respectively, in austral summer 1999/2000. Radiocarbon dates on penguin bones and eggshell fragments collected at each site indicate that Lagoon Island was first occupied after 6000 BP and Ginger Island near 2275 BP. Identifiable non-krill prey remains (otoliths and squid beaks) were recovered from ornithogenic soils at all sites, with Antarctic silverfish (Pleuragramma antarcticum) and squid (Psychroteuthis glacialis) being the most abundant species represented in the deposits. Estimated mean standard lengths and mantle lengths of these two prey taxa, based on regressions with otolith and beak measurements respectively, indicate that Adélie penguins primarily select these prey within a mean size range of 95-117 mm. Prey size also varied significantly across seven occupation periods from 6000 BP to the present, but did not correlate with climate change.     

Cost of reproduction and the evolution of deferred breeding in the western gull

Survival patterns in a population of western gulls (Larus occidentalis)of known age of first breeding, a, indicate a cost of reproductionrelated to the age of initial breeding. Among both sexes, birdsthat commenced breeding at the earliest ages (3 years in malesand 4 years in females) had higher annual mortality than thosethat deferred breeding one or more years. In addition, females(but not males) evidenced a cumulative cost of reproduction:holding age constant, females with more annual breeding attemptsdemonstrated poorer survival. These patterns of -specific survivalwere statistically significant after controlling for interannualvariation in food availability and are not explained simplyby variation in the intrinsic quality of individuals. To assessthe effects of these sex-specific costs on fitness, we combinedthe observed survival patterns with data on prebreeding survivorshipand -specific reproductive success to estimate rates of populationgrowth and lifetime reproductive success for different agesat first reproduction. Males showed a clearly defined fitnessoptimum at = 4 years, which coincided with the modal for malesin the population. Females showed no clear optimum, except thatbreeding at age 4 was suboptimal, hence females benefited fromdeferring breeding to ages 5-7 years. Observed age of firstbreeding also showed no clear mode for females, with slightpeaks at ages 5 and 7. As a result, in both sexes, the fitnesssurface for corresponded well with observed frequencies of. We suggest that stabilizing selection has acted to shape thephenotypic distribution of in males but, due to trade-offsbetween survival and early reproduction, stabilizing selectionis weak or absent in females