Assessing the sensitivity of bivalve populations to global warming using an individual‐based modelling approach

Climate change exposes benthic species populations in coastal ecosystems to a combination of different stressors (e.g., warming, acidification and eutrophication), threatening the sustainability of the ecological functions they provide. Thermal stress appears to be one of the strongest drivers impacting marine ecosystems, acting across a wide range of scales, from individual metabolic performances to geographic distribution of populations. Accounting for and integrating the response of species functional traits to thermal stress is therefore a necessary step in predicting how populations will respond to the warming expected in coming decades. Here, we developed an individual‐based population model using a mechanistic formulation of metabolic processes within the framework of the dynamic energy budget theory. Through a large number of simulations, we assessed the sensitivity of population growth potential to thermal stress and food conditions based on a climate projection scenario (Representative Concentration Pathway; RCP8.5: no reduction of greenhouse gas emissions). We focused on three bivalve species with contrasting thermal tolerance ranges and distinct distribution ranges along 5,000 km of coastline in the NE Atlantic: the Pacific oyster (Magallana gigas), and two mussel species: Mytilus edulis and Mytilus galloprovincialis. Our results suggest substantial and contrasting changes within species depending on local temperature and food concentration. Reproductive phenology appeared to be a core process driving the responses of the populations, and these patterns were closely related to species thermal tolerances. The nonlinear relationship we found between individual life‐history traits and response at the population level emphasizes the need to consider the interactions resulting from upscaling across different levels of biological organisation. These results underline the importance of a process‐based understanding of benthic population response to seawater warming, which will be necessary for forward planning of resource management and strategies for conservation and adaptation to environmental changes.     

In Vivo Random Mutagenesis of Bacillus subtilis by Use of TnYLB-1, a mariner-Based Transposon

This report describes the construction and characterization of a mariner-based transposon system designed to be used in Bacillus subtilis, but potentially applicable to other gram-positive bacteria. Two pUC19-derived plasmids were created that contain the mariner-Himar1 transposase gene, modified for expression in B. subtilis, under the control of either σ^A- or σ^B-dependent promoters. Both plasmids also contain a transposable element (TnYLB-1) consisting of a Kan^r cassette bracketed by the Himar1-recognized inverse terminal repeats, as well as the temperature-sensitive replicon and Erm^r gene of pE194ts. TnYLB-1 transposes into the B. subtilis chromosome with high frequency (10⁻²) from either plasmid. Southern hybridization analyses of 15 transposants and sequence analyses of the insertion sites of 10 of these are consistent with random transposition, requiring only a “TA” dinucleotide as the essential target in the recipient DNA. Two hundred transposants screened for sporulation proficiency and auxotrophy yielded five Spo⁻ clones, three with insertions in known sporulation genes (kinA, spoVT, and yqfD) and two in genes (ybaN and yubB) with unknown functions. Two auxotrophic mutants were identified among the 200 transposants, one with an insertion in lysA and another in a gene (yjzB) whose function is unknown.     

Étude biostratigraphique et paléoenvironnementale des diatomées pyritisées de l'intervalle Paléocène supérieur-Éocène inférieur du sondage de Saint-Josse (France)

This paper presents the results of a biostratigraphic analysis of pyritized diatom assemblages in the Saint-Josse core (CC82) located in the northern part of the Paris basin (coordinates: X =555?000, Y =307?324 and Z =56.9 m). During the Paleocene-Eocene this locality was situated in a small bight of the North Sea Basin. The results are obtained from sediments of the Thanet and Mont-Bernon group equivalents belonging to the Paleocene-Eocene interval. Thirteen samples were studied and eleven contain pyritized diatoms. By epigenesis, the siliceous frustule of the diatom is changed into a pyritized skeleton with all the ornamentation very well preserved such as the velum, the areolae, the labiate processes, etc. Dispersive X-Ray analyses show this complete replacement of silica by pyrite. Another form of pyritization is crystallization of pyrite (in cubes, pyritohedrons, octahedrons, framboids) in internal cavities of the diatoms to produce internal moulds, also called steinkerns, which preserve the external morphology of the diatoms and some details such as the girdle. Despite pyritization, diatoms can often be recognized at the species level; brackish and marine species were observed but no fresh water specimens were encountered. Pyrite is easily altered into iron oxides. In outcrops, pyritized diatoms can be obscured or destroyed by oxidation. We have chosen borehole samples for this study to avoid the affects of weathering. Deposits from the Sorrus Unit (of the Thanet Group) have low abundances of pyritized diatoms (3 to 25 specimens per sample). This unit contains allochtonous diatom assemblages comprising Actinoptychussenarius, Coscinodiscus morsianus var. morsianus, and Coscinodiscus morsianus var. moelleri. Sample 34.31-34.45 from this unit is particularly interesting. It contains three specimens of Paralia siberica var. laevis, which is typical of an estuarine or littoral paleoenvironment, and corresponds to the more continental deposit of the Sorrus Unit. Seven samples, taken in the Argile de Saint-Aubin Unit (from the Mont-Bernon Group), contain more than 200 pyritized diatoms and between 9 to 16 different species per sample. A brackish assemblage (Actinoptychus senarius, Coscinodiscus commutatus and Stellarima microtrias) and a marine assemblage (C. morsianus var. morsianus, Coscinodiscus var. moelleri, Fenestrella antiqua, Odontellaheibergii, Rhizosolenia sp. 1 and Trinacria regina) are observed. The brackish assemblage expands in the upper part of the Saint-Aubin Unit indicating more widespread brackish paleoenvironmental conditions. Pyritized diatoms are important fossil markers in the Paris basin mainly when siliceous fossils (silicoflagellates or radiolarians) and others microfossils (foraminifers and dinoflagellates) are very poor or absent. Two diatom assemblages have been identified in the Saint-Josse borehole. The first assemblage D1, comprising C. morsianus var. moelleri (high occurrence), C. morsianus (a few) and T. regina (rare), is recorded in the Sorrus, La Calotterie, Bois Gorguette, Le Goulet and lower Saint-Aubin Units. The second assemblage D2, characterized by great abundance of F. antiqua and decreasing numbers of C. morsianus species, is found in the upper part of the Saint-Aubin Unit. These diatom assemblages can be correlated with other biozonations established in the North Sea basin and based on nannoplankton and diatoms (King, 1983), diatoms (Mitlehner, 1996) and calcareous nannoplankton (Martini, 1971). F. antiqua and C. morsianus var. moelleri are the more important diatom species encountered. F. antiqua (previously named Coscinodiscus sp. 1, King, 1983) is the fossil marker used by King to define his NSP4 biozone. The base of NSP4 corresponds to the lowest occurrence of F. antiqua and the top is marked by the highest occurrence of this species. The Sorrus, La Calotterie, Bois Gorguette, Le Goulet and Saint-Aubin (“Sparnacian” stage) Units, the last one comprising F. antiqua (increasing to acme), correspond to the NSP4 zone of King (1983). The Mont-Hulin and Château de la Bruyère Units correspond probably to the NSP5 zone of King (1983). F. antiqua and C. morsianus var. moelleri were also used by Mitlehner (1996) to differentiate the NSP4a zone (low abundance of F. antiqua and abundance of C. morsianus var. moelleri) from the NSP4b zone (great abundance and acme of F. antiqua). The abundance of C. morsianus var. moelleri is recorded in the lower part of Saint-Aubin Unit and the abundance of F. antiqua (high peak at 46% in the sample 17.87) is found in the upper part of Saint-Aubin Unit. Therefore, Sorrus, La Calotterie, Bois Gorguette, Le Goulet and the lower part of Saint-Aubin Units are correlated with the NSP4a zone and the upper part of Saint-Aubin Unit with the NSP4b zone. By correlating the calcareous nannoplankton biozonation (NP) of Martini (1971) with the biozonation of King (1983), adapted by Mitlehner (1996), the boundary between the NP9 and NP10 zones could be located in the 18.75-17.87 interval and the NP10-NP11 boundary at the top of Saint-Aubin Unit. Lithostratigraphic correlations between the units of the Saint-Josse borehole (Paris basin) and the formations of the North Sea basin can be established. The great abundance of C. morsianus var. moelleri and the great abundance (including acme) of F. antiqua are respectively recorded in the Sele and Balder Formations. Therefore, the interval Sorrus/lower Saint-Aubin Units is correlated with the Sele Formation and upper part of Saint-Aubin Unit with the Balder Formation.     

Cost-effectiveness of primary prophylaxis of AIDS associated cryptococcosis in Cambodia

Background

Cryptococcal infection is a frequent cause of mortality in Cambodian HIV-infected patients with CD4+ count ≤100 cells/µl. This study assessed the cost-effectiveness of three strategies for cryptococcosis prevention in HIV-infected patients.

Methods

A Markov decision tree was used to compare the following strategies at the time of HIV diagnosis: no intervention, one time systematic serum cryptococcal antigen (CRAG) screening and treatment of positive patients, and systematic primary prophylaxis with fluconazole. The trajectory of a hypothetical cohort of HIV-infected patients with CD4+ count ≤100 cells/µl initiating care was simulated over a 1-year period (cotrimoxazole initiation at enrollment; antiretroviral therapy within 3 months). Natural history and cost data (US$ 2009) were from Cambodia. Efficacy data were from international literature.

Results

In a population in which 81% of patients had a CD4+ count ≤50 cells/ µl and 19% a CD4+ count between 51–100 cells/µl, the proportion alive 1 year after enrolment was 61% (cost $ 472) with no intervention, 70% (cost $ 483) with screening, and 72% (cost $ 492) with prophylaxis. After one year of follow-up, the cost-effectiveness of screening vs. no intervention was US$ 180/life year gained (LYG). The cost-effectiveness of prophylaxis vs. screening was $ 511/LYG. The cost-effectiveness of prophylaxis vs. screening was estimated at $1538/LYG if the proportion of patients with CD4+ count ≤50 cells/µl decreased by 75%.

Conclusion

In a high endemic area of cryptococcosis and HIV infection, serum CRAG screening and prophylaxis are two cost effective strategies to prevent AIDS associated cryptococcosis in patients with CD4+ count ≤100 cells/µl, at a short-term horizon, screening being more cost-effective but less effective than prophylaxis. Systematic primary prophylaxis may be preferred in patients with CD4+ below 50 cells/µl while systematic serum CRAG screening for early targeted treatment may be preferred in patients with CD4+ between 51–100 cells/µl.     

Development of a URA5 integrative cassette for gene disruption in the Candida guilliermondii ATCC 6260 strain

We designed an efficient transformation system for Candida guilliermondii based on a ura5 ATCC 6260 derived recipient strain and a URA5 recyclable selection marker. This “URA5 blaster” disruption system represents a powerful tool to study the function of a large pallet of genes in this yeast of clinical and biotechnological interest.     

Phenotypic differentiation within a foundation grass species correlates with species richness in a subalpine community

The effects of species loss on ecosystems depend on the community’s functional diversity (FD). However, how FD responds to environmental changes is poorly understood. This applies particularly to higher trophic levels, which regulate many ecosystem processes and are strongly affected by human-induced environmental changes. We analyzed how functional richness (FRic), evenness (FEve), and divergence (FDiv) of important generalist predators—epigeic spiders—are affected by changes in woody plant species richness, plant phylogenetic diversity, and stand age in highly diverse subtropical forests in China. FEve and FDiv of spiders increased with plant richness and stand age. FRic remained on a constant level despite decreasing spider species richness with increasing plant species richness. Plant phylogenetic diversity had no consistent effect on spider FD. The results contrast with the negative effect of diversity on spider species richness and suggest that functional redundancy among spiders decreased with increasing plant richness through non-random species loss. Moreover, increasing functional dissimilarity within spider assemblages with increasing plant richness indicates that the abundance distribution of predators in functional trait space affects ecological functions independent of predator species richness or the available trait space. While plant diversity is generally hypothesized to positively affect predators, our results only support this hypothesis for FD—and here particularly for trait distributions within the overall functional trait space—and not for patterns in species richness. Understanding the way predator assemblages affect ecosystem functions in such highly diverse, natural ecosystems thus requires explicit consideration of FD and its relationship with species richness.     

Rapid production of functionalized recombinant proteins: marrying ligation independent cloning and in vitro protein ligation

Functional genomics and proteomics have been very active fields since the sequencing of several genomes was completed. To assign a physiological role to the newly discovered coding genes with unknown function, new generic methods for protein production, purification, and targeted functionalization are needed. This work presents a new vector, pCYSLIC, that allows rapid generation of Escherichia coli expression constructs via ligation-independent cloning (LIC). The vector is designed to facilitate protein purification by either Ni-NTA or GSH affinity chromatography. Subsequent proteolytic removal of affinity tags liberates an N-terminal cysteine residue that is then used for covalent modification of the target protein with different biophysical probes via protein ligation. The described system has been tested on 36 mammalian Rab GTPases, and it was demonstrated that recombinant GTPases produced with pCYSLIC could be efficiently modified with fluorescein or biotin in vitro. Finally, LIC was compared with the recently developed In-Fusion cloning method, and it was demonstrated that In-Fusion provides superior flexibility in choice of expression vector. By the application of In-Fusion cloning Cys-Rab6A GTPase with an N-terminal cysteine residue was generated employing unmodified pET30a vector and TVMV protease.