Fun in facets: A flexible new tool for population genomics in R

The landscape of analytical tools for population genomics continues to evolve. However, these tools are scattered across programming languages, making them largely inaccessible for many biologists. In this issue of Molecular Ecology Resources, Hemstrom and Jones, 2022 (Mol Ecol Resour; 962) introduce a new R package, snpR. This package combines a large number of existing analyses, to provide a one-stop shop for population genomics. F-statistics, admixture analyses, effective population size inferences, genome-wide association studies (GWAS), and parentage analyses are all implemented natively within the package. A variety of third-party software can also be run without leaving the R environment. The authors pay particular attention to data structure – avoiding redundancy – and allowing analyses to be run across multiple sample or single-nucleotide polymorphism (SNP) groupings. Because of its great accessibility and wide range of analyses, snpR has the potential to become a favourite within the Molecular Ecology community.     

The Role of Mitochondria in Glioma Pathophysiology

It has long been recognised that malignant tumours favour aerobic glycolysis to generate ATP and contain abnormalities of the intrinsic, mitochondria-dependent, apoptotic pathway, suggesting the involvement of dysfunctional mitochondria in tumour pathophysiology. However, the mechanisms underlying such processes in gliomas are poorly understood. Few recent studies have evaluated mitochondrial ultrastructure and proteomics in the pathophysiology of malignant gliomas. However, aberrant energy metabolism has been reported in gliomas and mitochondrial dysfunction links to glioma apoptotic signalling have been observed. Mitochondrial structural abnormalities and dysfunction in malignant gliomas is a neglected area of research. Definition of abnormalities in mitochondrial proteomics, membrane potential regulation, energy metabolism and intrinsic apoptotic pathway signalling in gliomas may open novel therapeutic opportunities.     

Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs

The recent availability of a genome‐wide SNP array for the goat genome dramatically increases the power to investigate aspects of genetic diversity and to conduct genome‐wide association studies in this important domestic species. We collected and analysed genotypes from 52 088 SNPs in Boer, Cashmere and Rangeland goats that had both polled and horned individuals. Principal components analysis revealed a clear genetic division between animals for each population, and model‐based clustering successfully detected evidence of admixture that matched aspects of their recorded history. For example, shared co‐ancestry was detected, suggesting Boer goats have been introgressed into the Rangeland population. Further, allele frequency data successfully tracked the altered genetic profile that has taken place after 40 years of breeding Australian Cashmere goats using the Rangeland animals as the founding population. Genome‐wide association mapping of the POLL locus revealed a strong signal on goat chromosome 1. The 769‐kb critical interval contained the polled intersex syndrome locus, confirming the genetic basis in non‐European animals is the same as identified previously in Saanen goats. Interestingly, analysis of the haplotypes carried by a small set of sex‐reversed animals, known to be associated with polledness, revealed some animals carried the wild‐type chromosome associated with the presence of horns. This suggests a more complex basis for the relationship between polledness and the intersex condition than initially thought while validating the application of the goat SNP50 BeadChip for fine‐mapping traits in goat.     

Ocular Histoplasmosis

Case reports of three residents of Ontario with clinical histoplasmic chorioretinitis are presented. The diagnosis was made on the basis of the clinical appearance, the presence of calcified lesions in the chest, a negative skin test to tuberculin, and a positive skin test to toxoplasmin. All patients were treated with intravenous amphotericin B. Except for transitory elevation of blood urea nitrogen, there were no serious complications from the drug and in all cases the lesions in the eyes were improved. Histologic or cultural proof of the presence of fungus in the eye is not available, but clinical and laboratory findings can combine to point to the diagnosis of histoplasmosis. In such cases, since vision is at stake, treatment with amphotericin B should be considered.     

ASSESSMENT OF VIABILITY OF FROZEN BONE MARROW CELLS USING A CELL-CULTURE METHOD

The survival of mouse bone marrow after freezing and thawing was assessed using two methods: the spleen-colony technique; and a cell-culture method. The results of these experiments indicate that both methods yield similar estimates of marrow cell viability. It is suggested that the cell-culture method be used as an assay of marrow-cell viability in situations where the spleen-colony technique is not applicable.     

Phylogeography reveals a North Island range extension for New Zealand's only sexually wing-dimorphic stonefly (Stenoperla helsoni)

Stenoperla helsoni is an endemic New Zealand stonefly characterised by distinctive sexually dimorphic wing loss. Previous distribution records indicated that this species was restricted to the South Island's Southern Alps, although our recent collections of wing-reduced specimens from a site in the Tararua Ranges suggest that this species may extend into the lower North Island. We amplified the mitochondrial COI gene to confirm the identity of North Island specimens, and to assess phylogeographic structuring within the species and genus. North Island specimens were confirmed as S. helsoni, indicating that this species has a much wider geographic range than previously thought. This broad distribution, combined with low levels of intraspecific divergence, suggests that female S. helsoni may be strong fliers, despite males being flightless. Distinct North Island and South Island populations were identified, with a 1.5% divergence between the two populations.     

Particle size influences fibronectin internalization and degradation by fibroblasts

The application of nanotechnology for drug targeting underlines the importance of controlling the kinetics and cellular sites of delivery for optimal therapeutic outcomes. Here we examined the effect of particle size on internalization and degradation of surface-bound fibronectin by fibroblasts using polystyrene nanoparticles (NPs; 51 nm) and microparticles (MPs; 1 μm). Fibronectin was strongly bound by NPs and MPs as assessed by immuno-dot blot analysis (5.1 ±0.4×10^{– 5} pg fibronectin per μm² of NP surface; 4.2±±0.3×10^–5 pg fibronectin per μm² of MP surface; p>0.2). We estimated that ~193 fibronectin molecules bound to a MP compared with 0.6 fibronectin molecules per NP, indicating that ~40% of nanoparticles were not bound by fibronectin. One hour after incubation, fibronectin-coated NPs and MPs were rapidly internalized by Rat-2 fibroblasts. MPs and NPs were engulfed partly by receptor-mediated endocytosis as indicated by decreased uptake when incubated at 4 °C, or by depletion of ATP with sodium azide. Pulse-chase experiments showed minimal exocytosis of NPs and MPs. Internalization of NPs and MPs was inhibited by jasplakinolide, whereas internalization of MPs but not NPs was inhibited by latrunculin B and by integrin-blocking antibodies. Extraction of plasma membrane cholesterol with methyl β-cyclodextrin inhibited internalization of fibronectin-coated NPs but not MPs. Biotinylated fibronectin internalized by cells was extensively degraded on MPs but not NPs. Particle size affects actin and clathrin-dependent internalization mechanisms leading to fibronectin degradation on MPs but not NPs. Thus either prolonged, controlled release or an immediate delivery of drugs can be achieved by adjusting the particle size along with matrix proteins such as FN.