The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization.

Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications - and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.

Recent advances and current challenges in population genomics of structural variation in animals and plants.

The field of population genomics has seen a surge of studies on genomic structural variation over the past two decades. These studies witnessed that structural variation is taxonomically ubiquitous and represent a dominant form of genetic variation within species. Recent advances in technology, especially the development of long-read sequencing platforms, have enabled the discovery of structural variants (SVs) in previously inaccessible genomic regions which unlocked additional structural variation for population studies and revealed that more SVs contribute to evolution than previously perceived. An increasing number of studies suggest that SVs of all types and sizes may have a large effect on phenotype and consequently major impact on rapid adaptation, population divergence, and speciation. However, the functional effect of the vast majority of SVs is unknown and the field generally lacks evidence on the phenotypic consequences of most SVs that are suggested to have adaptive potential. Non-human genomes are heavily under-represented in population-scale studies of SVs. We argue that more research on other species is needed to objectively estimate the contribution of SVs to evolution. We discuss technical challenges associated with SV detection and outline the most recent advances towards more representative reference genomes, which opens a new era in population-scale studies of structural variation.

Development of Antibacterial Protective Coatings Active against MSSA and MRSA on Biodegradable Polymers.

In this work the in vitro antimicrobial activity of colloidal solutions of nine different commercially available nanoparticles were investigated against Staphylococcus aureus strains, both methicillin-sensitive (MSSA) and methicillin-resistant (MRSA). Research covered antimicrobial investigation of different metal and metal-oxide nanoparticles, including Ag 10 nm, Ag 40 nm, Al2O3 100 nm, Au 20 nm, Pt 4 nm, TiO2 100 nm, Y2O3 100 nm, ZnO 100 nm and ZrO2 100 nm nanoparticles. Such materials were foreseen to be applied as coatings on 3D-printed biodegradable polymers: i.e., catheters, disposable materials, hospital bedding items, disposable antimicrobial linings and bandages for chronic wounds. Therefore, the antimicrobial activity of the nanoparticles was determined by agar well diffusion assays and serial microdilution broth assays. In addition, the chromatographic characterization of elements present in trace amounts was performed as a method for tracing the nanoparticles. Moreover, the potential of preparing the rough surface of biodegradable polymers for coating with antimicrobial nanoparticles was tested by 3D-printing fused deposition methodology. The in vitro results have shown that particular nanoparticles provided powerful antimicrobial effects against MSSA and MRSA strains, and can be easily applied on different biopolymers.