Detection of Haplotypes Associated with Prenatal Death in Dairy Cattle and Identification of Deleterious Mutations in GART,SHBG and SLC37A2

The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10⁻⁴) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.     

Surface Area Loss and Increased Sphericity Account for the Splenic Entrapment of Subpopulations of Plasmodium falciparum Ring-Infected Erythrocytes

Ex vivo perfusion of human spleens revealed innate retention of numerous cultured Plasmodium falciparum ring-infected red blood cells (ring-iRBCs). Ring-iRBC retention was confirmed by a microsphiltration device, a microbead-based technology that mimics the mechanical filtering function of the human spleen. However, the cellular alterations underpinning this retention remain unclear. Here, we use ImageStream technology to analyze infected RBCs’ morphology and cell dimensions before and after fractionation with microsphiltration. Compared to fresh normal RBCs, the mean cell membrane surface area loss of trophozoite-iRBCs, ring-iRBCs and uninfected co-cultured RBCs (uRBCs) was 14.2% (range: 8.3–21.9%), 9.6% (7.3–12.2%) and 3.7% (0–8.4), respectively. Microsphilters retained 100%, ∼50% and 4% of trophozoite-iRBCs, ring-iRBCs and uRBCs, respectively. Retained ring-iRBCs display reduced surface area values (estimated mean, range: 17%, 15–18%), similar to the previously shown threshold of surface-deficient RBCs retention in the human spleen (surface area loss: >18%). By contrast, ring-iRBCs that successfully traversed microsphilters had minimal surface area loss and normal sphericity, suggesting that these parameters are determinants of their retention. To confirm this hypothesis, fresh normal RBCs were exposed to lysophosphatidylcholine to induce a controlled loss of surface area. This resulted in a dose-dependent retention in microsphilters, with complete retention occurring for RBCs displaying >14% surface area loss. Taken together, these data demonstrate that surface area loss and resultant increased sphericity drive ring-iRBC retention in microsphilters, and contribute to splenic entrapment of a subpopulation of ring-iRBCs. These findings trigger more interest in malaria research fields, including modeling of infection kinetics, estimation of parasite load, and analysis of risk factors for severe clinical forms. The determination of the threshold of splenic retention of ring-iRBCs has significant implications for diagnosis (spleen functionality) and drug treatment (screening of adjuvant therapy targeting ring-iRBCs).     

Chemical Compounds Related to the Predation Risk Posed by Malacophagous Ground Beetles Alter Self-Maintenance Behavior of Naive Slugs (Deroceras reticulatum)

Evidence that terrestrial gastropods are able to detect chemical cues from their predators is obvious yet scarce, despite the scientific relevance of the topic to enhancing our knowledge in this area. This study examines the influence of cuticular extracts from predacious ground beetles (Carabus auratus, Carabus hispanus, Carabus nemoralis and Carabus coriaceus), and a neutral insect species (Musca domestica) on the shelter-seeking behavior of naive slugs (Deroceras reticulatum). Slugs, known to have a negative phototactic response, were exposed to light, prompting them to make a choice between either a shelter treated with a cuticular extract or a control shelter treated with pure ethyl alcohol. Their behavioral responses were recorded for one hour in order to determine their first shelter choice, their final position, and to compare the percentage of time spent in the control shelters with the time spent in the treated shelters.The test proved to be very effective: slugs spent most of the experiment in a shelter. They spent significantly more time in the control shelter than in the shelter treated with either C. nemoralis (Z = 2.43; p = 0.0151; Wilcoxon matched-pairs signed-ranks test) or C. coriaceus cuticular extracts (Z = 3.31; p<0.01; Wilcoxon matched-pairs signed-ranks test), with a seemingly stronger avoidance effect when presented with C. coriaceus extracts. The other cuticular extracts had no significant effect on any of the behavioral items measured. Although it cannot be entirely excluded that the differences observed, are partly due to the intrinsic properties of the vehicle employed to build the cuticular extracts, the results suggest that slugs can innately discriminate amongst different potential predators and adjust their behavioral response according to the relevance of the threat conveyed by their predator’s chemical cues.     

How to efficiently determine the size at maturity of small-sized tropical fishes: A case study based on 144 species identified via DNA barcoding from southwestern Madagascar

In order to provide biological evidence of the real impact of mosquito seine nets in southwestern Madagascar, an efficient procedure for determining the size at maturity of small-sized tropical fishes was developed. The fishes caught by two small-scale fishermen were studied between October 2017 and April 2018. One catch per day was analyzed three days per month during the full-moon period. In the laboratory, fishes were all sorted by morphospecies, photographed and measured. One individual per morphospecies was selected for being identified using CO1 DNA barcoding. A total of 34,051 individual fishes belonging to 144 DNA bacoded species from 48 families was obtained from 42 samples, 467 individuals from 22 morphospecies that had not been successfully barcoded were excluded from the analyses. The macroscopic observations of 8,143 individuals between 0.7 and 10 cm SL indicated the proportion of individuals with clearly observable gonads was 15% only.Among the 144 species identified via DNA barcoding, 83 consisted of individuals that were all without clearly observable gonads, seven of individuals that were all with clearly observable gonads and 54 included of individuals with and without clearly observable gonads. As the determination of L₅₀ using logistic general linear models failed for most species, the minimum size at maturity was retained to determine the proportion of juveniles and adults for these 54 species. Compared to the data available in FishBase, the minimum size at maturity appears more adequate to discrimine juvenile from adult fish of small-sized tropical species.     

Divergent roles of HDAC1 and HDAC2 in the regulation of epidermal development and tumorigenesis

The histone deacetylases HDAC1 and HDAC2 remove acetyl moieties from lysine residues of histones and other proteins and are important regulators of gene expression. By deleting different combinations of Hdac1 and Hdac2 alleles in the epidermis, we reveal a dosage‐dependent effect of HDAC1/HDAC2 activity on epidermal proliferation and differentiation. Conditional ablation of either HDAC1 or HDAC2 in the epidermis leads to no obvious phenotype due to compensation by the upregulated paralogue. Strikingly, deletion of a single Hdac2 allele in HDAC1 knockout mice results in severe epidermal defects, including alopecia, hyperkeratosis, hyperproliferation and spontaneous tumour formation. These mice display impaired Sin3A co‐repressor complex function, increased levels of c‐Myc protein, p53 expression and apoptosis in hair follicles (HFs) and misregulation of HF bulge stem cells. Surprisingly, ablation of HDAC1 but not HDAC2 in a skin tumour model leads to accelerated tumour development. Our data reveal a crucial function of HDAC1/HDAC2 in the control of lineage specificity and a novel role of HDAC1 as a tumour suppressor in the epidermis.     

Pioneer marine biofilms on artificial surfaces including antifouling coatings immersed in two contrasting French Mediterranean coast sites

Marine biofilm communities that developed on artificial substrata were investigated using molecular and microscopic approaches. Polystyrene, Teflon® and four antifouling (AF) paints were immersed for 2 weeks at two contrasting sites near Toulon on the French Mediterranean coast (Toulon military harbour and the natural protected area of Porquerolles Island). Biofilms comprising bacteria and diatoms were detected on all the coatings. The population structure as well as the densities of the microorganisms differed in terms of both sites and coatings. Lower fouling densities were observed at Porquerolles Island compared to Toulon harbour. All bacterial communities (analysed by PCR-DGGE) showed related structure, controlled both by the sites and the type of substrata. Pioneer microalgal communities were dominated by the same two diatom species, viz. Licmophora gracilis and Cylindrotheca closterium, at both sites, irrespective of the substrata involved. However, the density of diatoms followed the same trend at both sites with a significant effect of all the AF coatings compared to Teflon and polystyrene.     

Conformational Equilibria of Bridled Chiroporphyrins in Solution Investigated by Vibrational Circular Dichroism

A series of bridled chiroporphyrins (BCP) and their metal complexes were prepared, in which two n‐methylene straps connect adjacent meso substituents by ester linkages. These compounds can exist as four atropisomers (αααα, αβαβ, αααβ, or ααββ) depending on the position of the meso groups relative to the macrocycle (α when above and β when below). We characterized the conformation of these chiral porphyrins and their metal (Zn, Ni, Mn) complexes by vibrational circular dichroism (VCD) associated with ab initio calculations. VCD spectra of the three metalloporphyrins were recorded in CDCl₃ and benzene solutions and ab initio calculations of their four atropoisomers were performed at the Density Functional Theory (DFT) level. The bridled chiroporphyrin with the longer straps (9 CH₂) and its nickel(II) complex can be isolated as the αβαβ atropisomer in the solid state and were found with the same conformation in CDCl₃ and benzene solutions. The bridled chiroporphyrin with the shortest straps (8 CH₂) and its zinc(II) complex can be isolated as the αααα atropisomer in the solid state, but in solution they are subject to atropisomeric equilibria, resulting in atropisomer distributions that are strongly solvent‐dependent. Comparison of the experimental VCD spectra with the predicted spectra of the four atropisomers allowed the quantification of these distributions. Finally, the manganese(III) complex also exhibits an atropisomeric equilibria in solution which is slightly solvent‐dependent. Chirality 25:480–486, 2013. © 2013 Wiley Periodicals, Inc.     

Chemical soil factors influencing plant assemblages along copper-cobalt gradients: implications for conservation and restoration

Aims

Define the chemical factors structuring plant communities of three copper-cobalt outcrops (Tenke-Fungurume, Katangan Copperbelt, D. R. Congo) presenting extreme gradients.

Methods

To discriminate plant communities, 172 vegetation records of all species percentage cover were classified based on NMDS and the Calinski criterion. Soil samples were analyzed for 13 chemical factors and means compared among communities with ANOVA. Partial canonical correspondence analysis (pCCA) was used to determine amount of variation explained individually by each factor and site effect.

Results

Seven communities were identified. Six of the studied communities were related to distinct sites. Site effect (6.0 % of global inertia) was identified as the most important factor related to plant communities’ variation followed by Cu (5.5 %), pH (3.6 %) and Co (3.5 %). Unique contribution of site effect (3.8 %) was higher than that of Cu (1.1 %) and Co (1.0 %).

Conclusions

In restoration, not only Cu and Co contents will be important to maintain vegetation diversity, attention should also be given to co-varying factors potentially limiting toxicity of metals: pH, organic matter, Ca and Mn. Physical parameters were also identified as important in the creation of adequate conditions for diverse communities. Further studies should focus on the effect of physical parameters and geology.     

Characterization of a Serine Hydrolase Targeted by Acyl-protein Thioesterase Inhibitors in Toxoplasma gondii

In eukaryotic organisms, cysteine palmitoylation is an important reversible modification that impacts protein targeting, folding, stability, and interactions with partners. Evidence suggests that protein palmitoylation contributes to key biological processes in Apicomplexa with the recent palmitome of the malaria parasite Plasmodium falciparum reporting over 400 substrates that are modified with palmitate by a broad range of protein S-acyl transferases. Dynamic palmitoylation cycles require the action of an acyl-protein thioesterase (APT) that cleaves palmitate from substrates and conveys reversibility to this posttranslational modification. In this work, we identified candidates for APT activity in Toxoplasma gondii. Treatment of parasites with low micromolar concentrations of β-lactone- or triazole urea-based inhibitors that target human APT1 showed varied detrimental effects at multiple steps of the parasite lytic cycle. The use of an activity-based probe in combination with these inhibitors revealed the existence of several serine hydrolases that are targeted by APT1 inhibitors. The active serine hydrolase, TgASH1, identified as the homologue closest to human APT1 and APT2, was characterized further. Biochemical analysis of TgASH1 indicated that this enzyme cleaves substrates with a specificity similar to APTs, and homology modeling points toward an APT-like enzyme. TgASH1 is dispensable for parasite survival, which indicates that the severe effects observed with the β-lactone inhibitors are caused by the inhibition of non-TgASH1 targets. Other ASH candidates for APT activity were functionally characterized, and one of them was found to be resistant to gene disruption due to the potential essential nature of the protein.     

Effects of elevated pCO2 on the metabolism of a temperate rhodolith Lithothamnion corallioides grown under different temperatures

Coralline algae are considered among the most sensitive species to near future ocean acidification. We tested the effects of elevated pCO₂ on the metabolism of the free‐living coralline alga Lithothamnion corallioides (“maerl”) and the interactions with changes in temperature. Specimens were collected in North Brittany (France) and grown for 3 months at pCO₂ of 380 (ambient pCO₂), 550, 750, and 1000 μatm (elevated pCO₂) and at successive temperatures of 10°C (ambient temperature in winter), 16°C (ambient temperature in summer), and 19°C (ambient temperature in summer +3°C). At each temperature, gross primary production, respiration (oxygen flux), and calcification (alkalinity flux) rates were assessed in the light and dark. Pigments were determined by HPLC. Chl a, carotene, and zeaxanthin were the three major pigments found in L. corallioides thalli. Elevated pCO₂ did not affect pigment content while temperature slightly decreased zeaxanthin and carotene content at 10°C. Gross production was not affected by temperature but was significantly affected by pCO₂ with an increase between 380 and 550 μatm. Light, dark, and diel (24 h) calcification rates strongly decreased with increasing pCO₂ regardless of the temperature. Although elevated pCO₂ only slightly affected gross production in L. corallioides, diel net calcification was reduced by up to 80% under the 1,000 μatm treatment. Our findings suggested that near future levels of CO₂ will have profound consequences for carbon and carbonate budgets in rhodolith beds and for the sustainability of these habitats.