Applying the dark diversity concept to plants at the European scale

Large‐scale biodiversity maps are essential to macroecology. However, between‐region comparisons can be more useful if patterns of observed species richness are supplemented by variations in dark diversity – the absent portion of the species pool. We aim to quantify and map plant diversity across Europe by using a measure that accounts for both observed and dark diversity. To do this we need to delimit suitable species pools, and evaluate the potential and limitation of a large‐scale dataset. We used Atlas Florae Europaeae (ca 20% of European plant species mapped within 50 × 50 km grid cells) and defined for each grid cell several species pools by applying various geographical and environmental filters: geographic species pool (number of species within 500 km radius), biogeographic species pool (additionally incorporating species distribution patterns, i.e. dispersion fields), site‐specific species pool (additionally integrating environmental preferences of species based on species co‐occurrence). We integrated dark diversity and observed diversity at a relative scale to calculate the completeness of site diversity: logistic expression of observed and dark diversity. We tested whether our results are robust against regional variation in data availability. We used independent regional databases to test if Atlas Florae Europaeae is a representative subset of total species richness. Environmental filtering was the most influential determinant of species pool size with more species filtered out in southern Europe. Both observed and dark diversity adhered to the well‐known latitudinal gradient, but completeness of site diversity varied throughout Europe with no latitudinal trend. Dark diversity patterns were fairly insensitive to variations in regional sampling intensity. Atlas Florae Europaeae represented well the total variation in plant diversity. In summary, dark diversity and completeness of site diversity add valuable information to broad‐scale diversity patterns since observed diversity is expressed at a relative scale.     

Use of time in a decision‐making process by a parasitoid

1. Time perception is seldom studied in invertebrates, with the limited experimental evidence being insufficient to provide a comprehensive pattern of the capacity of invertebrates to measure time and use it in decision‐making processes. 2. In this study, it was hypothesized that insect parasitoids have evolved the capacity to measure time precisely and to use it to optimize foraging decisions related to host exploitation. To examine time perception in females of the gregarious egg parasitoid Trichogramma euproctidis, the present study used their ability to adjust their investment (number of eggs laid) in a host to the initial transit duration (interval between the first contact with the host and the following contact with the substrate). Females utilize this method to assess host egg size, as a large egg necessarily requires more time to evaluate than a small host. In this study, the initial transit duration for a given sized egg was artificially extended by suspending it. 3. For similar sized hosts, female T. euproctidis significantly increased both oviposition duration and progeny allocation following a longer initial transit duration. 4. These results demonstrate the intrinsic capacity of this parasitoid to measure time and to adjust their progeny investment accordingly. This is believed to be one of the few demonstrations of a retrospective measure of time in an invertebrate.     

Ammonium photo-production by heterocytous cyanobacteria: potentials and constraints

Over the last decades, production of microalgae and cyanobacteria has been developed for several applications, including novel foods, cosmetic ingredients and more recently biofuel. The sustainability of these promising developments can be hindered by some constraints, such as water and nutrient footprints. This review surveys data on N₂-fixing cyanobacteria for biomass production and ways to induce and improve the excretion of ammonium within cultures under aerobic conditions. The nitrogenase complex is oxygen sensitive. Nevertheless, nitrogen fixation occurs under oxic conditions due to cyanobacteria-specific characteristics. For instance, in some cyanobacteria, the vegetative cell differentiation in heterocyts provides a well-adapted anaerobic microenvironment for nitrogenase protection. Therefore, cell cultures of oxygenic cyanobacteria have been grown in laboratory and pilot photobioreactors (Dasgupta et al., 2010; Fontes et al., 1987; Moreno et al., 2003; Nayak & Das, 2013). Biomass production under diazotrophic conditions has been shown to be controlled by environmental factors such as light intensity, temperature, aeration rate, and inorganic carbon concentration, also, more specifically, by the concentration of dissolved oxygen in the culture medium. Currently, there is little information regarding the production of extracellular ammonium by heterocytous cyanobacteria. This review compares the available data on maximum ammonium concentrations and analyses the specific rate production in cultures grown as free or immobilized filamentous cyanobacteria. Extracellular production of ammonium could be coupled, as suggested by recent research on non-diazotrophic cyanobacteria, to that of other high value metabolites. There is little information available regarding the possibility for using diazotrophic cyanobacteria as cellular factories may be in regard of the constraints due to nitrogen fixation.     

From the Schnauzenorgan to the back: Morphological comparison of mormyromast electroreceptor organs at different skin regions of Gnathonemus petersii

The nocturnally active weakly electric fish Gnathonemus petersii is known to employ active electrolocation for the detection of objects and for orientation in its environment. The fish emits pulse‐type electric signals with an electric organ and perceives these signals with more than 3,000 epidermal electroreceptor organs, the mormyromasts, which are distributed over the animal's skin surface. In this study, we measured the metric dimensions of the mormyromasts from different body regions to find structural and functional specialization of the various body parts. We focused on the two foveal regions of G. petersii, which are located at the elongated and movable chin (the Schnauzenorgan; SO) and at the nasal region (NR), the skin region between the mouth and the nares. These two foveal regions were compared to the dorsal part (back) of the fish, which contains typical nonfoveal mormyromasts. While the gross anatomy of the mormyromasts from all skin regions is similar, the metric dimensions of the main substructures differed. The mormyromasts at the SO are the smallest and contain the smallest receptor cells. In addition, the number of receptor cells per organ is lowest at the SO. In contrast, at the back the biggest receptor organs with the highest amount of receptor cells per organ occur. The mormyromasts at the NR are in several respects intermediate between those from the back and the SO. However, mormyromasts at the NR are longer than those at all other skin regions, the canal leading from the receptor pore to the inner chambers were the longest and the overlaying epidermal layers are the thickest. These results show that mormyromasts and the epidermis they are embedded in at both foveal regions differ specifically from those found on the rest of the body. The morphological specializations lead to functional specialization of the two foveae. J. Morphol., 2012. © 2012 Wiley Periodicals, Inc.     

Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

Effect of microwave treatment on the shear bond strength of different types of commercial teeth to acrylic resin

doi:10.1111/j.1741‐2358.2009.00333.x
Effect of microwave treatment on the shear bond strength of different types of commercial teeth to acrylic resin Objective: The purpose of this study was to verify the effect of microwave treatment on the shear bond strength of commercial types of teeth to acrylic resin, when the glossy ridge laps were unmodified (groups 1 and 5), bur abraded (groups 2 and 6), bur grooved (groups 3 and 7) or etched by monomer (groups 4 and 8). Background: Controversial findings have shown that mechanical or chemical changes in ridge‐lap surface of the tooth increase or decrease the bond strength between tooth and acrylic resin, and the microwave disinfection may cause different changes on this bond strength. Materials and methods: Eighty specimens (n = 10) were made with the acrylic resin bonded to tooth glossy ridge lap, polymerised in water at 74°C for 9 h, and deflasked after flask cooling. Specimens of the groups 5, 6, 7 and 8 were individually immersed in 150 ml of water and submitted to microwave treatment in an oven at 650 W for 3 min. Control specimens (groups 1, 2, 3 and 4) were not microwave treated. Shear bond strength test was performed in an Instron machine with a cross‐speed of 1 mm/min. Collected data were submitted to anova and Tukey’s test (α = 0.05). Results: Microwave treatment decreased the shear bond strength values of the tooth/resin bond. In the microwaved and non‐microwaved procedures, mechanical retention improved the shear bond strength when compared with the control and monomer treatments. Conclusion: Shear bond strength of the tooth/resin bond was influenced by the microwave treatment and different commercial teeth association, and was lower for the Biotone tooth.     

Carbon System Measurements and Potential Climatic Drivers at a Site of Rapidly Declining Ocean pH

We explored changes in ocean pH in coastal Washington state, USA, by extending a decadal-scale pH data series, by reporting independent measures of dissolved inorganic carbon (DIC), spectrophotometric pH, and total alkalinity (TA), by exploring pH patterns over larger spatial scales, and by probing for long-term trends in environmental variables reflecting potentially important drivers of pH. We found that pH continued to decline in this area at a rapid rate, that pH exhibited high natural variability within years, that our measurements of pH corresponded well to spectrophotometric pH measures and expected pH calculated from DIC/TA, and that TA estimates based on salinity predicted well actual alkalinity. Multiple datasets reflecting upwelling, including water temperature, nutrient levels, phytoplankton abundance, the NOAA upwelling index, and data on local wind patterns showed no consistent trends over the period of our study. Multiple datasets reflecting precipitation change and freshwater runoff, including precipitation records, local and regional river discharge, salinity, nitrate and sulfate in rainwater, and dissolved organic carbon (DOC) in rivers also showed no consistent trends over time. Dissolved oxygen did not decline over time, indicating that long-term changes did not result from shifts in contributions of respiration to pH levels. These tests of multiple potential drivers of the observed rapid rate of pH decline indicate a primary role for inorganic carbon and suggest that geochemical models of coastal ocean carbon fluxes need increased investigation.