Conspecific density and environmental complexity impact behaviour of turquoise killifish (Nothobranchius furzeri)

Fish models are essential for research in many biological and medical disciplines. With a typical lifespan of only 6 months, the Turquoise killifish (Nothobranchius furzeri) was recently established as a time- and cost-efficient model to facilitate whole-life and multigenerational studies in several research fields, including behavioural ecotoxicology. Essential information on the behavioural norm and on how laboratory conditions affect behaviour, however, is deficient. In the current study, we examined the impact of the social and structural environment on a broad spectrum of behavioural endpoints in N. furzeri. While structural enrichment affected only fish boldness and exploratory behaviour, fish rearing density affected the total body length, locomotor activity, boldness, aggressiveness and feeding behaviour of N. furzeri individuals. Overall, these results contribute to compiling a behavioural baseline for N. furzeri that increases the applicability of this new model species. Furthermore, our findings will fuel the development of improved husbandry protocols to maximize the welfare of N. furzeri in a laboratory setting.     

Establishment of a conditional Nomo1 mouse model by CRISPR/Cas9 technology

Molecular Biology Reports - The Nomo1 gene mediates a wide range of biological processes of importance in embryonic development. Accordingly, constitutive perturbation of Nomo1 function may result...     

Integrative modeling of protein-protein interactions with pyDock for the new docking challenges

The seventh CAPRI edition imposed new challenges to the modeling of protein-protein complexes, such as multimeric oligomerization, protein-peptide, and protein-oligosaccharide interactions. Many of the proposed targets needed the efficient integration of rigid-body docking, template-based modeling, flexible optimization, multiparametric scoring, and experimental restraints. This was especially relevant for the multimolecular assemblies proposed in the CASP12-CAPRI37 and CASP13-CAPRI46 joint rounds, which were described and evaluated elsewhere. Focusing on the purely CAPRI targets of this edition (rounds 38-45), we have participated in all 17 assessed targets (considering heteromeric and homomeric interfaces in T125 as two separate targets) both as predictors and as scorers, by using integrative modeling based on our docking and scoring approaches: pyDock, IRaPPA, and LightDock. In the protein-protein and protein-peptide targets, we have also participated with our webserver (pyDockWeb). On these 17 CAPRI targets, we submitted acceptable models (or better) within our top 10 models for 10 targets as predictors, 13 targets as scorers, and 4 targets as servers. In summary, our participation in this CAPRI edition confirmed the capabilities of pyDock for the scoring of docking models, increasingly used within the context of integrative modeling of protein interactions and multimeric assemblies.     

Antifouling substances of natural origin: Activity of benzoquinone compounds from Maesa Lanceolata against marine crustaceans

A screening of antifouling activity from plants extracts led to selection and further study of Maesa lanceolata Forssk. Two p‐benzoquinone compounds were isolated from the fruits and found to be active against Artemia salina. The anti‐crustacean activity of both p‐benzoquinones is reported for the first time.     

An optimized fine root sampling methodology balancing accuracy and time investment

Aims

Tree roots are spatially highly heterogeneous and it thus requires large numbers of samples to detect statistically significant changes in root biomass. The objectives of this study were to understand and quantify the sources of error in the assessment of fine root biomass (<2 mm) during the second year of a high-density Populus plantation.

Methods

Soil cores were collected in winter (n?=?35) and in summer (n?=?20), and fine roots were picked by hand for varying lengths of time: 1, 2, 5, 20, 40, and 60 min. The root biomass data were used to identify the best combination of the time spent for root picking and the number of samples collected, that minimizes the overall uncertainty (i.e. the combination of the spatial error due to the incomplete sampling and the temporal error due to the incomplete core processing).

Results

On average, 25 min was enough time to pick 90 % of the fine root biomass in winter, while in summer only 10 min were needed. In winter fewer samples were needed, but more time for picking was necessary as compared to summer when root biomass was higher.

Conclusions

Fine root sampling can be optimized by minimizing the uncertainty of the biomass estimates and simultaneously decreasing root sampling time investment.     

Soil CO2 efflux in a bioenergy plantation with fast-growing Populus trees – influence of former land use, inter-row spacing and genotype

Aims

In this study we quantified the annual soil CO₂ efflux (annual SCE) of a short rotation coppice plantation in its establishment phase. We aimed to examine the effect of former (agricultural) land use type, inter-row spacing and genotype.

Methods

Annual SCE was quantified during the second growth year of the establishment rotation in a large scale poplar plantation in Flanders. Automated chambers were distributed over the two former land use types, the two different inter-row spacings and under two poplar genotypes. Additional measurements of C, N, P, K, Mg, Ca and Na concentrations of the soil, pH, bulk density, fine root biomass, microbial biomass C, soil mineralization rate, distance to trees and tree diameters were performed at the end of the second growth year.

Results

Total carbon loss from soil CO₂ efflux was valued at 589 g m^?2 yr^?1. Annual SCE was higher in former pasture as compared to cropland, higher in the narrow than in the wider inter-row spacings, but no effect of genotype was found.

Conclusions

Spatial differences in site characteristics are of great importance for understanding the effect of ecosystem management and land use change on soil respiration processes and need to be taken into account in modeling efforts of the carbon balance.     

The Archaeal Diversity and Population in a Drained Alkaline Saline Soil of the Former Lake Texcoco (Mexico)

Draining soil of the former Lake Texcoco, Mexico with pH > 10.0 and electrolytic conductivity (EC) > 100 dS m^?1 for 17 years has reduced pH to 7.8 and EC to 0.68 dS m^?1. Metagenomic DNA from the archaeal community was extracted directly from this soil and used as template to amplify the 16S ribosomal genes by PCR to construct gene libraries. Most of the cloned Archaea were related to mesophilic crenarchaeota and were not-yet-cultured. Sequence and phylogenetic analyses of these clones identified a group of Archaea with close affiliation to the ammonia-oxidizing Archaea. The cloned sequences from the drained soil diverged clearly from Haloarchaea found in the undrained soil from the lake.     

hCOA3 Stabilizes Cytochrome c Oxidase 1 (COX1) and Promotes Cytochrome c Oxidase Assembly in Human Mitochondria

Cytochrome c oxidase (COX) or complex IV of the mitochondrial respiratory chain plays a fundamental role in energy production of aerobic cells. In humans, COX deficiency is the most frequent cause of mitochondrial encephalomyopathies. Human COX is composed of 13 subunits of dual genetic origin, whose assembly requires an increasing number of nuclear-encoded accessory proteins known as assembly factors. Here, we have identified and characterized human CCDC56, an 11.7-kDa mitochondrial transmembrane protein, as a new factor essential for COX biogenesis. CCDC56 shares sequence similarity with the yeast COX assembly factor Coa3 and was termed hCOA3. hCOA3-silenced cells display a severe COX functional alteration owing to a decreased stability of newly synthesized COX1 and an impairment in the holoenzyme assembly process. We show that hCOA3 physically interacts with both the mitochondrial translation machinery and COX structural subunits. We conclude that hCOA3 stabilizes COX1 co-translationally and promotes its assembly with COX partner subunits. Finally, our results identify hCOA3 as a new candidate when screening for genes responsible for mitochondrial diseases associated with COX deficiency.     

Révision du genre Pycnomorphus Thomson, 1864. Systématique et phylogénie (Coleoptera : Lamiinae,Acanthoderini)

Le genre Pycnomorphus Thomson est révisé et quatre espèces nouvelles sont décrites: Pycnomorphus guyanensis n. sp., P. pradosiae n. sp.et P. sarryi n. sp. de Guyane, et P. batesi n. sp. du Nicaragua. Un genre nouveau Pycnomorphidiellus n. gen. est créé pour une nouvelle espèce de Guyane, P. polyphagus n. sp. Une analyse cladistique et une clef d’identification des espèces complètent ce travail.     

The novel Fh8 and H fusion partners for soluble protein expression in Escherichia coli: a comparison with the traditional gene fusion technology

The Escherichia coli host system is an advantageous choice for simple and inexpensive recombinant protein production but it still presents bottlenecks at expressing soluble proteins from other organisms. Several efforts have been taken to overcome E. coli limitations, including the use of fusion partners that improve protein expression and solubility. New fusion technologies are emerging to complement the traditional solutions. This work evaluates two novel fusion partners, the Fh8 tag (8 kDa) and the H tag (1 kDa), as solubility enhancing tags in E. coli and their comparison to commonly used fusion partners. A broad range comparison was conducted in a small-scale screening and subsequently scaled-up. Six difficult-to-express target proteins (RVS167, SPO14, YPK1, YPK2, Frutalin and CP12) were fused to eight fusion tags (His, Trx, GST, MBP, NusA, SUMO, H and Fh8). The resulting protein expression and solubility levels were evaluated by sodium dodecyl sulfate polyacrylamide gel electrophoresis before and after protein purification and after tag removal. The Fh8 partner improved protein expression and solubility as the well-known Trx, NusA or MBP fusion partners. The H partner did not function as a solubility tag. Cleaved proteins from Fh8 fusions were soluble and obtained in similar or higher amounts than proteins from the cleavage of other partners as Trx, NusA or MBP. The Fh8 fusion tag therefore acts as an effective solubility enhancer, and its low molecular weight potentially gives it an advantage over larger solubility tags by offering a more reliable assessment of the target protein solubility when expressed as a fusion protein.