This study focuses on relationships between individual condition, measures of ornament expression and mate choice in the Grey Partridge (Perdix perdix). It is based on the correlative data as well as results of manipulative experiments. I found positive correlation between the size of melanin- and carotenoid-based ornaments in partridges. The size and the redness of the carotenoid skin patch, and the size of the melanin-based feather ornamentation were associated with several measures of immunity and overall body condition (complement activity, ratio of immature erythrocytes, heterophil/leucocyte ratio, response to novel antigen). Furthermore, data from natural populations indicate that the expression of carotenoid-based ornamentation is associated with sexual attractiveness (measured as the ability to obtain a social mate) in partridges. Data from captive individuals indicate that carotenoid supplementation improves the redness of carotenoid-based ornament, while the stimulation of the immune system under increasing concentrations of supplemented carotenoids has no measurable effect on condition and physiological state. This seems to contradict predictions of the 'Carotenoid maintenance hypothesis'. Overall, results better understanding the role of carotenoid and melanin-based ornamentation in signaling...

Recent progress in fundamental biological sciences and medicine has considerably increased the quantity ofdata that can be studied and processed. The main limitation now is not retrieving data, but rather extractinguseful biological insights from the large datasets accumulated. More recent advances have provided detailedhigh-density data regarding metabolism (metabolomics) and protein expression (proteomics). Clearly, no single analytic methods, can provide a comprehensive understanding. Rather, the ability to link available datatogether in a coherent manner is required to obtain a complete view. The improving application of MachineLearning (ML) techniques provides the means to make continuous progress in processing complex data sets.A brief discussion is offered on the advantages of ML, the state-of-the-art in Deep Learning (DL) for proteinpredictions and the importance of ML in biological data processing. Noise stemming from incorrect classification or arbitrary/ambiguous labelling of data may arise when ML techniques are applied to large datasets. Furthermore, the stochasticity of biological systems needs to be considered for correctly evaluating theoutputs. Here we show the potential of a workflow to respond biological questions taking into consideration aperturbation of the biological data.  For controlling the applicability of models and maximizing the predictivity, in silico filtering schemescan usefully be applied as an “Ockham’s razor” before using any ML technique. After reviewing differentDL approaches for protein prediction purposes, this work shows that a computational approach in filteringsteps is a valuable tool for proteins classification when biological features are not fully annotated or reviewed.The in silico approach has identified putative proline transporters in fungi and plants as well as carotenoidbiosynthetic gene products in the plant family Brassicaceae. The proposed method is suitable for extractingfeatures of classification and then maximizing the use of a DL approach.

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Potato cultivars exhibit a wide variation in skin and flesh colour due to the presence of pigments. This study established that potato cultivars differ greatly with respect to types and concentrations of carotenoids in tubers. A total of 46 cultivars were evaluated for quantitative and qualitative carotenoid composition in different growing seasons, locations, storage conditions and disease symptoms. Factors controlling carotenoid accumulation were also tested by developing an in vitro minituber system as a new high-throughput model system for carotenogenesis in potato tubers. Tuber flesh colour was found to correlate with total carotenoid content in potato cultivars grown in both New Zealand and Netherlands. The main carotenoids identified in 32 potato cultivars in New Zealand were lutein, neoxanthin, violaxanthin and β-carotene. The ratio of these carotenoids varies between cultivars. Neoxanthin was detected in only 13 cultivars (10.59 to 69.21µg/g DW); violaxanthin was found only in 1 cultivar (32.76 µg/g DW). Whereas lutein and β-carotene were found in most of the cultivars but the concentration varied from (0.00 to 160.63 µg/g DW) and (0.00 to 13.62 µg/g DW) respectively. The main carotenoids identified in 12 cultivars grown in the Netherlands were neoxanthin, violaxanthin and lutein, whereas zeaxanthin was not found in any of the cultivars analysed. Marked differences were observed between the same potato cultivars grown in New Zealand and the Netherlands. Therefore cultivars were analysed over a second growing season to assess stability in carotenoids composition. The carotenoid profiles of the potato tubers grown for two different seasons showed highly significant differences between the cultivars, the seasons, the carotenoid pigments, and all combinations of interactions, indicating the complex nature of factors influencing carotenoid composition. Reflectance colorimeter measurement of yellow hue component in this study confirmed that the higher the total carotenoid content, the greater the yellow intensity colour. Eight cultivars were grown at three locations in New Zealand and Agria and Desiree were grown at eight locations in the Netherlands to further investigate the stability of carotenoid composition. Highly significant differences were observed between the cultivars, the locations, the carotenoid pigments, and all combinations of interactions, which emphasises that changes in carotenoid composition are complex and the responses are not consistent across cultivars. Reflectance colorimeter measurement of yellow hue component confirmed the relationship between the yellow colour intensity of tuber flesh, as well as confirming the interaction between colour and locations. Disease and post harvest storage conditions markedly influenced the levels of total carotenoid, neoxanthin, violaxanthin, zeaxanthin, lutein and β-carotene in potatoes. The magnitude of these effects depends on the cultivar, time of storage, and the intensity of powdery scab symptoms. Results showed that long term storage resulted in the accumulation of neoxanthin, violaxanthin and zeaxanthin with a concomitant decreased of lutein, β-carotene and total carotenoid content. Genotypes infected with disease (lower and higher scab score) resulted in accumulation of violaxanthin, β-carotene and total carotenoid with a concomitant decreased in neoxanthin and lutein. A high-throughput model system for investigating carotenoid biogenesis in potato tubers was developed. This involved in vitro potato minitubers and was validated by assessing the effects of environmental variables, such as drought stress, light intensity and nutrient availability on carotenoid accumulation. Light influenced the presence of zeaxanthin, whereas water stress and nutrient strength influenced the accumulation of neoxanthin and violaxanthin. Although these factors had an effect on the carotenoid content and profile, the most influential factor appeared to be cultivar selection.

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Evolution is a most fascinating feature of all living things in our world. The means of organismal evolution are diverse, comprising mainly of natural and sexual selection. Both of these phenomena may contribute to evolutionary adaptations in health and disease. The questions of immunity impact on the process of sexual selection and sexual selection for increased anti-parasite resistance are wide issues of the present research in natural sciences. Their clarification requires multidisciplinarily-based investigation combining a variety of partial results into a single united paradigm. My co-workers and I have chosen several specific issues to study, in order to fill some of the important gaps of the current knowledge. We proposed the Carotenoid maintenance handicap hypothesis to point out that optimisation instead of maximisation of the carotenoid intake and ornamental display may be physiologically convenient for the individual. In Scarlet rosefinch (Carpodacus erythrinus) we confirmed the role of the carotenoid-based ornamental colouration in the process of sexual selection and investigated several partial aspects of the association between immunogenetics, immune function, health and the ornament expression and mate choice. In Zebra finch (Taeniopygia guttata) we have shown that the present way of...