Preparing to Work with Big Data in Proteomics – A Report on the HUPO‐PSI Spring Workshop

The Human Proteome Organisation Proteomics Standards Initiative (HUPO‐PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data comparison, exchange and verification. The 2013 annual spring workshop was hosted by the University of Liverpool, UK and concentrated on updating and refining the existing standards in the light of new methodologies and technologies. To control the inflation of file sizes, strategies for file compression, particularly for mzML files, were explored. Best practices for encoding information such as protein grouping and PTM localisation were refined and documented. Additional example files for the mzQuantML format were designed to provide support for selected reaction monitoring techniques. Enhancements to the PSI Common Query Interface (PSICQUIC) and PSI‐MI XML were discussed. Finally, the group engaged in discussion on how the existing work of the HUPO‐PSI can be leveraged by the Metabolomics Standards Initiative to improve the capture of metabolite data.     

Can terrestrial ectotherms escape the heat of climate change by moving?

Whether movement will enable organisms to alleviate thermal stress is central to the biodiversity implications of climate change. We use the temperature-dependence of ectotherm performance to investigate the fitness consequences of movement. Movement to an optimal location within a 50 km radius will only offset the fitness impacts of climate change by 2100 in 5 per cent of locations globally. Random movement carries an 87 per cent risk of further fitness detriment. Mountainous regions with high temperature seasonality (i.e. temperate areas) not only offer the greatest benefit from optimal movement but also the most severe fitness consequences if an organism moves to the wrong location. Doubling dispersal capacity would provide modest benefit exclusively to directed dispersers in topographically diverse areas. The benefits of movement for escaping climate change are particularly limited in the tropics, where fitness impacts will be most severe. The potential of movement to lessen climate change impacts may have been overestimated.     

Influence of five commercial heparin preparations on the collagen induced platelet aggregation (author's transl)]

The ADP- and collagen-induced aggregation of platelets in PRP of healthy probands was tested in vitro in the presence of 4 heparin preparations (Novo, Vitrum, Liquemin, Haemoderivate) and of a heparinoid (Eleparon). None of the preparations caused a significant direct aggregation. The collagen-induced aggregation was inhibited by all mentioned preparations; thereby the heparins proved to be effective approx. to the same degree whereas the heparinoid proved to be significantly less effective. The ADP-induced aggregation was potentiated by all preparations. A considerably different sensitivity to heparin could be observed in the single PRP's. A special method was found out to exclude the influence of the heparin-sensitivity of the PRP's to compare the special effects of the heparins.     

Colour diversification in Malawi cichlids: evidence for adaptation,reinforcement or sexual selection?

The mechanisms responsible for the explosive radiations of haplochromine cichlid fishes in Africa's great lakes remain controversial. Since species thought to be closely related often differ most apparendy in male breeding colours, I examined patterns of male colour variation in rock-dwelling cichlids from Lake Malawi to test whether initial divergence between species is likely to have been caused by adaptation to differing habitats, by selection against hybridization (reinforcement or character displacement), or by sexual selection. I found that all significant variation in overall male colour occurs within, not between, species complexes, in contrast to variation in habitat and behavioural traits, which differed significandy between complexes. Male colour does not vary significandy with habitat characteristics such as water depth, and sympatric species differ no more in colour than allopatric ones. These results fail to provide support for adaptation or reinforcement as initial causes of colour divergence, and are consistent with the possibility that divergence may instead have been caused by sexual selection, but a direct test of sexual selection is not yet possible.     

Unusually fine-scale genetic structuring found in rapidly speciating Malawi cichlid fishes

Mechanisms behind the explosive radiation of over 500 cichlid fish species from a single founding population in Lake Malawi during the last 700 000 years are poorly understood. Recent studies have suggested that the degree of population subdivision among the habitat patches within the lake may be responsible, but the evidence has been circumstantial: lack of a dispersal stage in haplochromine cichlids; genetic and colour variation among populations separated by large-scale geographical barriers; and fluctuating lake levels. One reason for the rapidity of speciation in these fishes may be that population subdivision is on a much finer scale than previously thought. Here we quantify the level of population subdivision and estimate migration at a scale of 700-1400 m, in order to investigate whether cichlid populations are sufficiently isolated from each other for allopatric divergence and perhaps speciation to take place. Using six microsatellite loci, we demonstrate the existence of highly significant genetic differentiation between subpopulations on adjacent headlands in each of four rock-dwelling haplochromine cichlid species. Our results suggest that these fish populations are divided into thousands of subunits among which genetic divergence is currently occurring, and that this may provide unprecedented opportunities for allopatric speciation. <br>     

Sperm antibodies in vasectomized men and their effects on fertilization

Sera (vbs, n = 25) and seminal plasma (vsp, n = 21) from vasectomized men (n = 25) were analyzed for cross-reaction with lithium diiodosalicylate (LIS)-solubilized human sperm extract, protamine, and fertilization antigen (FA-1) with an enzyme-linked immunosorbent assay (ELISA). Among the vbs tested, 44% reacted with human sperm extract, 28% reacted with protamine, and 44% reacted with FA-1 for at least one class of antibodies (IgG, IgA, or IgM). In contrast to the sera, the seminal plasma showed minimal reactions. Neither the vbs nor vsp were found to contain immune complexes, indicating that the antibodies were present in free form. Vasectomized sera that reacted with FA-1 showed a significant (p less than 0.0001) inhibition of human sperm penetration of zona-free hamster ova. The immunoabsorption of FA-1-positive sera with purified FA-1 significantly increased the penetration rates. Affinity-purified human immunoglobulins reactive with FA-1 and not those reactive with protamine reduced sperm penetration rates. Thus, antibodies in vbs reactive with FA-1 are relevant to infertility, causing an inhibition of fertilization. These data will have clinical relevance for diagnosis and treatment of infertility after successful vasovasostomy.