Guiding cellular activity with polarized light

Actin, cytoskeleton protein forming microfilaments, play a crucial role in cellular motility. Here we show that exposure to very low levels of polarized light guide their orientation in‐vivo within the live cell. Using a simple model to describe the role of actin‐filament orientation in directional cellular motion, we demonstrate that the actin polymerization/depolymerization mechanism develops primarily along this direction and, under certain conditions, can lead to guidance of the cell movement. Our results also show a dose dependent increase in actin activity in direct correspondence to the level of laser irradiance. We found that total expression of Tau protein, which stabilize microtubules, was decreased by the irradiance, indicating that exposure to the light may change the activity of kinase, leading to increased cell activity.

     

Habitat‐related seed germination traits in alpine habitats

Understanding the key aspects of plant regeneration from seeds is crucial in assessing species assembly to their habitats. However, the regenerative traits of seed dormancy and germination are underrepresented in this context. In the alpine zone, the large species and microhabitat diversity provide an ideal context to assess habitat‐related regenerative strategies. To this end, seeds of 53 species growing in alpine siliceous and calcareous habitats (6230 and 6170 of EU Directive 92/43, respectively) were exposed to different temperature treatments under controlled laboratory conditions. Germination strategies in each habitat were identified by clustering with k‐means. Then, phylogenetic least squares correlations (PGLS) were fitted to assess germination and dormancy differences between species’ main habitat (calcareous and siliceous), microhabitat (grasslands, heaths, rocky, and species with no specific microhabitats), and chorology (arctic–alpine and continental). Calcareous and siliceous grasslands significantly differ in their germination behaviour with a slow, mostly overwinter germination and high germination under all conditions, respectively. Species with high overwinter germination occurs mostly in heaths and have an arctic–alpine distribution. Meanwhile, species with low or high germinability in general inhabit in grasslands or have no specific microhabitat (they belong to generalist), respectively. Alpine species use different germination strategies depending on habitat provenance, species’ main microhabitat, and chorotype. Such differences may reflect adaptations to local environmental conditions and highlight the functional role of germination and dormancy in community ecology.     

Fodis: Software for Protein Unfolding Analysis

The folding dynamics of proteins at the single-molecule level has been studied with single-molecule force spectroscopy experiments for 20 years, but a common standardized method for the analysis of the collected data and for sharing among the scientific community members is still not available. We have developed a new open-source tool—Fodis—for the analysis of the force-distance curves obtained in single-molecule force spectroscopy experiments, providing almost automatic processing, analysis, and classification of the obtained data. Our method provides also a classification of the possible unfolding pathways and the structural heterogeneity present during the unfolding of proteins.     

Post-translational modifications of VDAC1 and VDAC2 cysteines from rat liver mitochondria

VDACs three isoforms (VDAC1, VDAC2, VDAC3) are integral proteins of the outer mitochondrial membrane whose primary function is to permit the communication and exchange of molecules related to the mitochondrial functions. We have recently reported about the peculiar over-oxidation of VDAC3 cysteines. In this work we have extended our analysis, performed by tryptic and chymotryptic proteolysis and UHPLC/High Resolution ESI-MS/MS, to the other two isoforms VDAC1 and VDAC2 from rat liver mitochondria, and we have been able to find also in these proteins over-oxidation of cysteines. Further PTM of cysteines as succination has been found, while the presence of selenocysteine was not detected. Unfortunately, a short sequence stretch containing one genetically encoded cysteine was not covered both in VDAC2 and in VDAC3, raising the suspect that more, unknown modifications of these proteins exist. Interestingly, cysteine over-oxidation appears to be an exclusive feature of VDACs, since it is not present in other transmembrane mitochondrial proteins eluted by hydroxyapatite. The assignment of a functional role to these modifications of VDACs will be a further step towards the full understanding of the roles of these proteins in the cell.     

COX16 is required for assembly of cytochrome c oxidase in human cells and is involved in copper delivery to COX2

Cytochrome c oxidase (COX), complex IV of the mitochondrial respiratory chain, is comprised of 14 structural subunits, several prosthetic groups and metal cofactors, among which copper. Its biosynthesis involves a number of ancillary proteins, encoded by the COX-assembly genes that are required for the stabilization and membrane insertion of the nascent polypeptides, the synthesis of the prosthetic groups, and the delivery of the metal cofactors, in particular of copper. Recently, a modular model for COX assembly has been proposed, based on the sequential incorporation of different assembly modules formed by specific subunits.We have cloned and characterized the human homologue of yeast COX16. We show that human COX16 encodes a small mitochondrial transmembrane protein that faces the intermembrane space and is highly expressed in skeletal and cardiac muscle. Its knockdown in C. elegans produces COX deficiency, and its ablation in HEK293 cells impairs COX assembly. Interestingly, COX16 knockout cells retain significant COX activity, suggesting that the function of COX16 is partially redundant.Analysis of steady-state levels of COX subunits and of assembly intermediates by Blue-Native gels shows a pattern similar to that reported in cells lacking COX18, suggesting that COX16 is required for the formation of the COX2 subassembly module. Moreover, COX16 co-immunoprecipitates with COX2. Finally, we found that copper supplementation increases COX activity and restores normal steady state levels of COX subunits in COX16 knockout cells, indicating that, even in the absence of a canonical copper binding motif, COX16 could be involved in copper delivery to COX2.     

Nephronophthise und assoziierte Ziliopathien

medizinische genetik - Die Nephronophthise ist eine autosomal-rezessive tubulointerstitielle Nierenerkrankung und stellt die häufigste genetische Ursache für ein terminales Nierenversagen...     

The importance of using life cycle assessment in policy support to determine the sustainability of fishing fleets: a case study for the small-scale <Emphasis Type="Italic">xeito</Emphasis> fishery in Galicia,Spain

Purpose

Drift net fishing activities have undergone a thorough revision at a European Union level, since authorities argue that several loopholes still exist in the legislation that allow small-scale fisheries to use these gears. High incidental catches, or the lack of selectivity, are some of the primary scientific criteria behind this discussion. This new framework is of particular interest in the region of Galicia (NW Spain) due to the social importance of small-scale fishing vessels using drift nets. In fact, over 400 vessels have a licence to capture European pilchard (Sardina pilchardus) with a fishing gear called xeito, which is a small-scale drift net.

Methods

The main goal of this article is to provide stakeholders in the fishing sector with environmentally relevant results regarding the life cycle impacts linked to fishing practices performed by small-scale vessels using the xeito gear to target European pilchard. We hypothesize that environmental impacts computed with LCA will provide additional insights to the sustainability of the pilchard small-scale fishery in NW Spain, adding a series of criteria that may be useful for policy-makers to determine the consequences of forbidding this type of drift netting in the future.

Results and discussion

Results show that environmental impacts across impact categories and operational activities do not differ much from that of other similar fishing fleets examined in recent years, with fuel for propulsion being the main environmental burden in most impact categories. When conducting a statistical analysis, no significant difference in energy use was identified between this small-scale fleet and purse seiners targeting pilchard in Galicia. Moreover, the results obtained demonstrate, in line with previous studies, that European pilchard is still an energy-efficient source of animal protein option as compared to demersal fish alternatives, crustaceans, or livestock.

Conclusions

The results do not indicate that European pilchard landed with small-scale drift nets generates higher environmental life cycle impacts than pilchard landed by purse seiners in NW Spain. However, longer time frames for the analysis should be performed to attain results with lower uncertainty.

     

Diversity among peripheral populations: genetic and evolutionary differentiation of Salamandra atra at the southern edge of the Alps

Separate populations at the edge of a species range are receiving great attention and have been shown to be often different from populations in the core area. However, it has rarely been tested whether neighboring peripheral populations are genetically and evolutionarily similar to each other, as expected for their geographical proximity and similar ecological conditions, or differ due to historical contingency. We investigated isolation and differentiation, within‐population genetic diversity and evolutionary relationships among multiple peripheral populations of a cold‐adapted terrestrial salamander, Salamandra atra, at the southern edge of the species core range. We carried out population genetic, phylogeographic, and phylogenetic analyses on various molecular markers (10 autosomal microsatellite loci, three mitochondrial loci with total length >2,100 bp, two protein‐coding nuclear genes) sampled from more than 100 individuals from 13 sites along the southern Prealps. We found at least seven isolated peripheral populations, all highly differentiated from the remaining populations and differentiated from each other at various levels. The within‐population genetic diversity was variable in the peripheral populations, but consistently lower than in the remaining populations. All peripheral populations along the southern Prealps belong to an ancient lineage that is also found in the Dinarides but did not contribute to the postglacial recolonization of the inner and northern Alps. All fully melanistic populations from the Orobian mountains to the southern Dinarides represent a single clade, to the exclusion of the two yellow‐patched populations inhabiting the Pasubio massif and the Sette Comuni plateau, which are distinguished as S. atra pasubiensis and S. atra aurorae, respectively. In conclusion, multiple populations of S. atra at the southern edge of the species core area have different levels of differentiation, different amount of within‐population genetic diversity, and different evolutionary origin. Therefore, they should be regarded as complementary conservation targets to preserve the overall genetic and evolutionary diversity of the species.     

Epistatic fire blight resistance QTL alleles in the apple cultivar ‘Enterprise’ and selection X-6398 discovered and characterized through pedigree-informed analysis

Most cultivated apple cultivars are highly susceptible to fire blight, caused by Erwinia amylovora. However, differences in resistance levels are observed among cultivars and could be used in breeding. In this paper, we investigated the genetic basis of fire blight resistance of the cultivar ‘Enterprise’ and the advanced breeding selection X-6398. Genotyped pedigrees were used for validating and curating historic pedigree records. Various quantitative trait locus (QTL) discovery approaches were applied on the full-sib families ‘Gala’ × ‘Enterprise’ (GaEn) and X-6398 × X-6683 (IW) with the software FlexQTL? and MapQTL®. The paternal lineage of ‘Enterprise’ was reconstructed and showed to include ‘Cox’s Orange Pippin’. The QTLs found varied with the software used. Using FlexQTL?, two were found on linkage groups (LGs) 7 and 13, favourable alleles inherited by Enterprise from ‘Cox’s Orange Pippin’ and ‘Golden Delicious’, respectively. The former was identical to the previously named FB_F7 allele from ‘Fiesta’, while the latter is new and has been named FB_13GD. X-6398 had a QTL at the same position as FB_F7. Its favourable allele was new, originating from the unknown grandfather of X-4598, and was named FB_7X-6398. Using MapQTL® on GaEn, FB_F7 was also identified. Performing the same analysis on the subset of offspring that carried the favourable allele of FB_F7, two putative QTLs on LG8 and on top of LG13 were identified, which showed interactions with FB_F7. Implication of the findings for breeding for fire blight-resistant apples is discussed. Single nucleotide polymorphism data on Enterprise and its ancestors are provided.