Germline variants in oculocutaneous albinism genes and predisposition to familial cutaneous melanoma

Approximately 1%–2% of cutaneous melanoma (CM) is classified as strongly familial. We sought to investigate unexplained CM predisposition in families negative for the known susceptibility genes using next‐generation sequencing of affected individuals. Segregation of germline variants of interest within families was assessed by Sanger sequencing. Several heterozygous variants in oculocutaneous albinism (OCA) genes: TYR, OCA2, TYRP1 and SLC45A2, were present in our CM cohort. OCA is a group of autosomal recessive genetic disorders, resulting in pigmentation defects of the eyes, hair and skin. Missense variants classified as pathogenic for OCA were present in multiple families and some fully segregated with CM. The functionally compromised TYR p.T373K variant was present in three unrelated families. In OCA2, known pathogenic variants: p.V443I and p.N489D, were present in three families and one family, respectively. We identified a likely pathogenic SLC45A2 frameshift variant that fully segregated with CM in a family of four cases. Another four‐case family harboured cosegregating variants (p.A24T and p.R153C) of uncertain functional significance in TYRP1. We conclude that rare, heterozygous variants in OCA genes confer moderate risk for CM.     

The roles of age,parentage and environment on bacterial and algal endosymbiont communities in Acropora corals

The bacterial and microalgal endosymbiont (Symbiodiniaceae spp.) communities associated with corals have important roles in their health and resilience, yet little is known about the factors driving their succession during early coral life stages. Using 16S rRNA gene and ITS2 metabarcoding, we compared these communities in four Acropora coral species and their hybrids obtained from two laboratory crosses (Acropora tenuis × Acropora loripes and Acropora sarmentosa × Acropora florida) across the parental, recruit (7 months old) and juvenile (2 years old) life stages. We tested whether microbiomes differed between (a) life stages, (b) hybrids and purebreds, and (c) treatment conditions (ambient/elevated temperature and pCO₂). Microbial communities of early life stage corals were highly diverse, lacked host specificity and were primarily determined by treatment conditions. Over time, a winnowing process occurred, and distinct microbial communities developed between the two species pair crosses by 2 years of age, irrespective of hybrid or purebred status. These findings suggest that the microbial communities of corals have a period of flexibility prior to adulthood, which can be valuable to future research aimed at the manipulation of coral microbial communities.     

Virulence‐associated protein A from Rhodococcus equi is an intercompartmental pH‐neutralising virulence factor

Professional phagocytic cells such as macrophages are a central part of innate immune defence. They ingest microorganisms into membrane‐bound compartments (phagosomes), which acidify and eventually fuse with lysosomes, exposing their contents to a microbicidal environment. Gram‐positive Rhodococcus equi can cause pneumonia in young foals and in immunocompromised humans. The possession of a virulence plasmid allows them to subvert host defence mechanisms and to multiply in macrophages. Here, we show that the plasmid‐encoded and secreted virulence‐associated protein A (VapA) participates in exclusion of the proton‐pumping vacuolar‐ATPase complex from phagosomes and causes membrane permeabilisation, thus contributing to a pH‐neutral phagosome lumen. Using fluorescence and electron microscopy, we show that VapA is also transferred from phagosomes to lysosomes where it permeabilises the limiting membranes for small ions such as protons. This permeabilisation process is different from that of known membrane pore formers as revealed by experiments with artificial lipid bilayers. We demonstrate that, at 24 hr of infection, virulent R. equi is contained in a vacuole, which is enriched in lysosome material, yet possesses a pH of 7.2 whereas phagosomes containing a vapA deletion mutant have a pH of 5.8 and those with virulence plasmid‐less sister strains have a pH of 5.2. Experimentally neutralising the macrophage endocytic system allows avirulent R. equi to multiply. This observation is mirrored in the fact that virulent and avirulent R. equi multiply well in extracts of purified lysosomes at pH 7.2 but not at pH 5.1. Together these data indicate that the major function of VapA is to generate a pH‐neutral and hence growth‐promoting intracellular niche. VapA represents a new type of Gram‐positive virulence factor by trafficking from one subcellular compartment to another, affecting membrane permeability, excluding proton‐pumping ATPase, and consequently disarming host defences.     

Analytical comparison of absolute quantification strategies to investigate the insulin signaling pathway in fat cells

So far, mass spectrometry-based targeted proteomics is the most sensitive approach to answer and address specific biological questions in an accurate and quantitative fashion. However, the data analysis design used for such quantification varies in the field leading to discrepancies in the reported values. In this study, different quantification strategies based on calibration curves were evaluated and compared. The best accuracy and coefficient of variation was achieved by ratio to ratio calibration curves. We applied the ratio to ratio quantification approach to analyze very low abundant insulin signaling proteins such as PIK3RA (0.10–0.93 fmol/μg), AKT1 (0.1–0.39 fmol/μg), and the insulin receptor (0.22–2.62 fmol/μg) in a fat cell model and demonstrated the adaptation of this pathway at different states of insulin sensitivity.     

Spatial scale,topography and thermoregulatory behaviour interact when modelling species’ thermal niches

The spatial scale at which climate and species’ occupancy data are gathered, and the resolution at which ecological models are run, can strongly influence predictions of species performance and distributions. Running model simulations at coarse rather than fine spatial resolutions, for example, can determine if a model accurately predicts the distribution of a species. The impacts of spatial scale on a model's accuracy are particularly pronounced across mountainous terrain. Understanding how these discrepancies arise requires a modelling approach in which the underlying processes that determine a species’ distribution are explicitly described. Here we use a process‐based model to explore how spatial resolution, topography and behaviour alter predictions of a species thermal niche, which in turn constrains its survival and geographic distribution. The model incorporates biophysical equations to predict the operative temperature (T_e), thermal‐dependent performance and survival of a typical insect, with a complex life‐cycle, in its microclimate. We run this model with geographic data from a mountainous terrain in South Africa using climate data at three spatial resolutions. We also explore how behavioural thermoregulation affects predictions of a species performance and survival by allowing the animal to select the optimum thermal location within each coarse‐grid cell. At the regional level, coarse‐resolution models predicted lower T_e at low elevations and higher T_e at high elevations than models run at fine‐resolutions. These differences were more prominent on steep, north‐facing slopes. The discrepancies in T_e in turn affected estimates of the species thermal niche. The modelling framework revealed how spatial resolution and topography influence predictions of species distribution models, including the potential impacts of climate change. These systematic biases must be accounted for when interpreting the outputs of future modelling studies, particularly when species distributions are predicted to shift from uniform to topographically heterogeneous landscapes.     

Dynamics of polymorphism of acidocalcisomes in<Emphasis Type="Italic"> Leishmania</Emphasis> parasites

Growth of Leishmania mexicana amazonensis promastigotes in different culture media resulted in structurally and chemically different acidocalcisomes. When grown in SDM-79 medium, the promastigotes showed large spherical acidocalcisomes of up to 1.2 m diameter distributed throughout the cell. X-ray microanalysis and elemental mapping of the organelles showed large amounts of oxygen, phosphorus, sodium, potassium, magnesium, calcium, and zinc. Immunofluorescence microscopy using antisera raised against a peptide sequence of the vacuolar-type proton pyrophosphatase of Arabidopsis thaliana that is conserved in the Leishmania enzyme, indicated localization in acidocalcisomes. When cells were transferred to Warrens medium, the acidocalcisomes transformed from spherical into branched tubular organelles. The labeling pattern of the vacuolar proton-pyrophosphatase, considered as a marker for the organelle, changed accompanying the structural changes of the acidocalcisomes, and the enzyme showed an apparently lower proton-transporting activity when measured in digitonin-permeabilized promastigotes. X-ray microanalysis and elemental mapping of these structures revealed the additional presence of iron. Together, the results reveal that the morphology and composition of acidocalcisomes are greatly influenced by the culture conditions.Electronic Supplementary Material Supplementary material is available in the online version of this article at     

Changes in plasma gonadotropin concentrations and urethral closure pressure in the bitch during the 12 months following ovariectomy

Urinary incontinence due to acquired urethral sphincter incompetence is a common side effect of spaying, for which the underlying cause remains unknown. Spaying not only results in a significant reduction in the urethral closure pressure within 1 year but also in an increase in the plasma gonadotropin concentrations. To investigate the possible link between the post-ovariectomy changes in plasma gonadotropins and in urethral closure pressure, gonadotropin and urodynamic measurements were performed in 10 Beagle bitches before and for a period of 1 year after spaying. Plasma gonadotropin concentrations rose quickly after ovariectomy and peak levels were seen within 3-5 weeks, followed by a sharp drop until week 10. A steady increase was observed subsequently until week 42, when a plateau was reached. One year after spaying, the mean FSH concentration was 75.3 +/- 32.1 ng/ml, a 17-fold increase, and the LH was 8.3 +/- 3.8 ng/ml, an eightfold increase over the pre-spaying values. Ten months after spaying, the mean urethral closure pressure (9.7 cm H2O) was significantly reduced when compared to the mean pre-operative value of 15.4 cm H2O. However, there was no clear relationship between the gonadotropin concentrations and the urethral closure pressure. From these results it seems unlikely that chronically elevated gonadotropins are the underlying cause for reduced urethral closure pressure after spaying resulting in urinary incontinence.     

Discovery of the novel candidate phylum "Poribacteria" in marine sponges

Marine sponges (Porifera) harbor large amounts of commensal microbial communities within the sponge mesohyl. We employed 16S rRNA gene library construction using specific PCR primers to provide insights into the phylogenetic identity of an abundant sponge-associated bacterium that is morphologically characterized by the presence of a membrane-bound nucleoid. In this study, we report the presence of a previously unrecognized evolutionary lineage branching deeply in the domain Bacteria that is moderately related to the Planctomycetes, Verrucomicrobia, and Chlamydia lines of decent. Because members of this lineage showed <75% 16S rRNA gene sequence similarity to known bacterial phyla, we suggest the status of a new candidate phylum, named "Poribacteria", to acknowledge the affiliation of the new bacterium with sponges. The affiliation of the morphologically conspicuous sponge bacterium with the novel phylogenetic lineage was confirmed by fluorescence in situ hybridization with newly designed probes targeting different sites of the poribacterial 16S rRNA. Consistent with electron microscopic observations of cell compartmentalization, the fluorescence signals appeared in a ring-shaped manner. PCR screening with "Poribacteria"-specific primers gave positive results for several other sponge species, while samples taken from the environment (seawater, sediments, and a filter-feeding tunicate) were PCR negative. In addition to a report for Planctomycetes, this is the second report of cell compartmentalization, a feature that was considered exclusive to the eukaryotic domain, in prokaryotes.