Philippe Grosjean

Optimization of gonad growth by manipulation of temperature and photoperiod in cultivated sea urchins, Paracentrotus lividus (Lamarck) (Echinodermata)

A starvation and then feeding method was developed to produce about 100% marketable sea urchins, Paracentrotus lividus, in 3 1/2 months. This method is needed because the reproduction cycle is desynchronized in the conditions imposed during the somatic growth stage in land-based closed systems. The major advantages of starving the animals are resetting the reproductive cycle to the spent stage (gonads almost devoid of sexual cells) and stressing the individuals so that they mobilize and restore the nutritive phagocytes, filling them with nutrients. Batches of sea urchins starved 2 months beforehand were fed ad libitum for 45 days with enriched food under eight combinations of four temperatures (12°C, 16°C, 20°C and 24°C) and two photoperiods (9 and 17 h daylight). In our system, the best combination was 24°C and 9 h daylight for growth as well as for gonad quality. The gonadal indices obtained (in dry weight) were over 9% at 16°C and over 12% at 24°C, which are better than what is found in the field for this population.

Reproductive cycle of the echinoid Paracentrotus lividus: analysis by means of the maturity index

Summary The gonad and maturity index cycles of the echinoid Paracentrotus lividus and their relations with environmental abiotic parameters are assessed after 2 years of observation in southern Brittany, France. The gonadal cycle is briefly described and eight gonadal stages are characterized. The annual cycle, the time of spawning and the period of gonadal growth are well established, suggesting they are controlled externally. The reproductive cycle has three main phases: the growing phase (late autumn and winter) when gonads accumulate reserve material; the maturation phase (spring and early summer) in which gametogenesis then spawning take place; and the spent/regenerating phase when relict gametes are resorbed by the nutritive phagocytes, the gonads being virtually devoid of sexual cells. The maturity index based on the histological diagnosis of gonads and the use of circular data and polar graphical representation make it possible to reliably determine the spawning period, the rate of gametogenesis a...

Experimental study of growth in the echinoid Paracentrotus lividus (Lamarck, 1816) (Echinodermata)

Abstract Multimodal size frequency distribution (i.e., a few individuals growing very fast and a few individuals growing very slowly) among an originally homogeneous cohort of juveniles Paracentrotus lividus is observed in reared conditions when they are 6–24 months old. The splitting of this cohort into homogeneous size-classed subgroups results in an increased growth of the smaller animals that catch up with the bigger ones in 4 months time. This indicates that the smaller animals are not genetically less productive and suggests they were inhibited in their growth due to the presence of larger ones. Supposing such growth inhibition also occurs in the natural environment, the observed mechanism could be very efficient in stabilizing field populations of aggregative echinoid species by maintaining a protected pool of small individuals with high growth potential but inhibited by the density of larger ones.

Studying Evolving Software Ecosystems based on Ecological Models

Research on software evolution is very active, but evolutionary principles, models and theories that properly explain why and how software systems evolve over time are still lacking. Similarly, more empirical research is needed to understand how different software projects co-exist and co-evolve, and how contributors collaborate within their encompassing software ecosystem.

Buffer capacity of the coelomic fluid in echinoderms.

The increase in atmospheric CO2 due to anthropogenic activity results in an acidification of the surface waters of the oceans. The impact of these chemical changes depends on the considered organisms. In particular, it depends on the ability of the organism to control the pH of its inner fluids. Among echinoderms, this ability seems to differ significantly according to species or taxa. In the present paper, we investigated the buffer capacity of the coelomic fluid in different echinoderm taxa as well as factors modifying this capacity. Euechinoidea (sea urchins except Cidaroidea) present a very high buffer capacity of the coelomic fluid (from 0.8 to 1.8mmolkg(-1) SW above that of seawater), while Cidaroidea (other sea urchins), starfish and holothurians have a significantly lower one (from -0.1 to 0.4mmolkg(-1) SW compared to seawater). We hypothesize that this is linked to the more efficient gas exchange structures present in the three last taxa, whereas Euechinoidea evolved specific buffer systems to compensate lower gas exchange abilities. The constituents of the buffer capacity and the factors influencing it were investigated in the sea urchin Paracentrotus lividus and the starfish Asterias rubens. Buffer capacity is primarily due to the bicarbonate buffer system of seawater (representing about 63% for sea urchins and 92% for starfish). It is also partly due to coelomocytes present in the coelomic fluid (around 8% for both) and, in P. lividus only, a compound of an apparent size larger than 3kDa is involved (about 15%). Feeding increased the buffer capacity in P. lividus (to a difference with seawater of about 2.3mmolkg(-1) SW compared to unfed ones who showed a difference of about 0.5mmolkg(-1) SW) but not in A. rubens (difference with seawater of about 0.2 for both conditions). In P. lividus, decreased seawater pH induced an increase of the buffer capacity of individuals maintained at pH7.7 to about twice that of the control individuals and, for those at pH7.4, about three times. This allowed a partial compensation of the coelomic fluid pH for individuals maintained at pH7.7 but not for those at pH7.4.

When GitHub Meets CRAN: An Analysis of Inter-Repository Package Dependency Problems

When developing software packages in a software ecosystem, an important and well-known challenge is how to deal with dependencies to other packages. In presence of multiple package repositories, dependency management tends to become even more problematic. For the R ecosystem of statistical computing, dependency management is currently insufficient to deal with multiple package versions and inter-repository package dependencies. We explore how the use of GitHub influences the R ecosystem, both for the distribution of R packages and for inter-repository package dependency management. We also discuss how these problems could be addressed.

On the maintainability of CRAN packages

When writing software, developers are confronted with a trade-off between depending on existing components and reimplementing similar functionality in their own code. Errors may be inadvertently introduced because of dependencies to unreliable components, and it may take longer time to fix these errors. We study such issues in the context of the CRAN archive, a long-lived software ecosystem consisting of over 5000 R packages being actively maintained by over 2500 maintainers, with different flavors of each package depending on the development status and target operating system. Based on an analysis of package dependencies and package status, we present preliminary results on the sources of errors in these packages per flavor, and the time that is needed to fix these errors.

Links between bacterial communities in marine sediments and trace metal geochemistry as measured by in situ DET/DGT approaches

Our current view about the relationship between metals and bacteria in marine sediments might be biased because most studies only use ex situ approaches to quantify metals. The aim of the present research was to compare ex situ and in situ methods of metal measurement (DET and DGT--diffusive equilibration or diffusive gradients in thin-films) and relate the results with two commonly used microbiological variables (bacterial biomass and bacterial diversity as revealed by DGGE). No previous studies have used such in situ approaches in microbial ecology. For biomass and most of the investigated trace metals (Ag, Cd, Sn, Cr, Ni, Cu, Pb, and Al) no significant correlations were found. The exceptions were Fe, Mn, Co, and As which behave like micronutrients. For bacterial diversity, no relevant relationships were found. We conclude that in situ methods are more adapted tools for microbial ecologists but that ex situ approaches are still necessary.

Optimizing food distribution in closed-circuit cultivation of edible sea urchins (Paracentrotus lividus: Echinoidea)

In the framework of echinoid cultivation, whose objective is to succeed in continuously producing large amounts of edible sea urchins (Paracentrotus lividus) under controlled conditions (aquaculture), gonadal growth is to be optimized. Among the various parameters influencing the production of roe, the quantity of food distributed was tested for optimization. After a 1-month fast, echinoids were fed artificial food pellets (enriched in soybean and fish proteins) for different periods of time over 48 h, the food thus being available ad libitum for 8, 16, 24, 32, 40, and 48 h; the cycles were repeated for a month. The results show that the quantity of food intake and the gonad index peak after about 35 h of food availability. This suggests food should be distributed discontinuously for optimal gonad production and minimal waste.

On the Development and Distribution of R Packages: An Empirical Analysis of the R Ecosystem

This paper explores the ecosystem of software packages for R, one of the most popular environments for statistical computing today. We empirically study how R packages are developed and distributed on different repositories: CRAN, BioConductor, R-Forge and GitHub. We also explore the role and size of each repository, the inter-repository dependencies, and how these repositories grow over time. With this analysis, we provide a deeper insight into the extent and the evolution of the R package ecosystem.