Studies of cap-independent mRNA translation in Drosophila melanogaster

Control of protein synthesis is a key step in the regulation of gene expression during apoptosis and the heat shock response. Under such conditions, cap-dependent translation is impaired and Internal Ribosome Entry Site (IRES)-dependent translation plays a major role in mammalian cells. Although the role of IRES-dependent translation during apoptosis has been mainly studied in mammals, its role in the translation of Drosophila apoptotic genes has not been yet studied. The observation that the Drosophila mutant embryos for the cap-binding protein, the eukaryotic initiation factor eIF4E, exhibits increased apoptosis in correlation with up-regulated proapoptotic gene reaper (rpr) transcription constitutes the first evidence for the existence of a cap-independent mechanism for the translation of Drosophila proapoptotic genes. The mechanism of translation of rpr and other proapoptotic genes was investigated in this work. We found that the 5 UTR of rpr mRNA drives translation in an IRES-dependent manner. It promotes the translation of reporter RNAs in vitro either in the absence of cap, in the presence of cap competitors, or in extracts derived from heat shocked and eIF4E mutant embryos and in vivo in cells transfected with reporters bearing a non functional cap structure, indicating that cap recognition is not required in rpr mRNA for translation. We also show that rpr mRNA 5 UTR exhibits a high degree of similarity with that of Drosophila heat shock protein 70 mRNA (hsp70), an antagonist of apoptosis, and that both are able to conduct IRES-mediated translation. The proapoptotic genes head involution defective (hid) and grim, but not sickle, also display IRES activity. Studies of mRNA association to polysomes in embryos indicate that both rpr, hsp70, hid and grim endogenous mRNAs are recruited to polysomes in embryos in which apoptosis or thermal stress was induced. We conclude that hsp70 and, on the other hand, rpr, hid and grim which are antagonizing factors during apoptosis, use a similar mechanism for protein synthesis. The outcome for the cell would thus depend on which protein is translated under a given stress condition. Factors involved in the differential translation driven by these IRES could play an important role. For this purpose, we undertook the identification of the ribonucleoprotein (RNP) complexes assembled onto the 5 UTR of rpr mRNA. We established a tobramycin-affinity-selection protocol that allows the purification of specific RNP that can be further analyzed by mass spectrometry. Several RNA binding proteins were identified as part of the rpr 5 UTR RNP complex, some of which have been related to IRES activity. The involvement of one of them, the La antigen, in the translation of rpr mRNA, was established by RNA-crosslinking experiments using recombinant protein and rpr 5 UTR and by the analysis of the translation efficiency of reporter mRNAs in Drosophila cells after knock down of the endogenous La by RNAi experiments. Several uncharacterized proteins were also identified, suggesting that they might play a role during translation, during the assembly of the translational machinery or in the priming of the mRNA before ribosome recognition. Our data provide evidence for the involvement of La antigen in the translation of rpr mRNA and set a protocol for purification of tagged-RNA-protein complexes from cytoplasmic extracts. To further understand the mechanisms of translation initiation in Drosophila, we analyzed the role of eIF4B on cap-dependent and cap-independent translation. We showed that eIF4B is mostly involved in cap-, but not IRES-dependent translation as it happens in mammals.

Artificial micro RNA system in Dictyostelium discoideum

Dictyostelium discoideum is a social amoeba that serves as a model system for RNA interference and related mechanisms. Its position between plants and animals enables evolutionary snapshot of mechanisms and protein machinery involved in investigated subjects. MiRNAs are small regulatory RNAs that are evolutionary conserved and present in animals, plants, viruses and some prokaryotes. They have roles in development, cell growth and differentiation, apoptosis and their miss-regulation is associated with many diseases such as cancer, neurodegenerative disorders and diabetes. Recently, through sequencing of DNA libraries miRNAs have been discovered in D. discoideum. In this work, it has been shown that heterologues miRNA let-7 can be expressed and processed in D. discoideum. Expression of let-7 miRNA in social amoeba resulted in a strong developmental phenotype suggesting an overload of the processing/silencing system or/and endogenous targets. The various effects on prel-7 strain have been observed and characterized, serving as a background for postulation of miRNA roles. An artificial miRNA system has been established and imposed to D. discoideum, showing that miRNAs in Dictyostelium could mediate gene expression on the level of mRNA stability and on the posttranscriptional level. Furthermore, presence of translational inhibition as a type of gene control was shown for the first time in this organism. Due to it new structures representing co-localities of miRNA and target mRNA have been detected. Taken together, this work shows functional artificial miRNA system and postulates roles of endogenous small RNA in social amoeba.

Non-University Higher Education and the Relationship of Its Graduates and the World of Work: Colombia

The non-university sector has been part of the Colombian higher education system for more than 50-years. Despite its long years of existence, it has never occupied such an important role within the education system as the one it is having today. Therefore, the aim of this work is to analyze the development of the non-university sector in the framework of the country’s social, educational and economic demands. Likewise, its actual situation and certain aspects of the relationship between its graduates and the world of work, i.e., graduates’ employment characteristics, the relationship of higher education studies and their work, as well as their early career success, are examined. In order to generate the required information, a graduate survey was carried out in Atlántico (Colombia). The target population was graduates from higher education institutions registered in Atlántico who were awarded a technical, technological or professional degree in 2008 from any of the following knowledge areas: Fine Arts, Health Science, Economy-Administration-Accountancy and similar, and Engineering-Architecture-Urban planning and similar. Besides, interviews with academic and administrative staff from non-university institutions were carried out, and higher education related documents were analyzed. As a whole, the findings suggest that the non-university sector is expanding and may help to achieve some of the goals, for which it is widely promoted i.e., access expansion for under-represented groups, enhancement of the higher education system, and the provision of programs pertinent to the needs of the market. Nevertheless, some aspects require further consideration, e.g., the sector’s consolidation within the system and its quality. As for the relationship between non-university higher education and the world of work, it was found to be close; particularly in those aspects related to the use of knowledge and skills in the work, and the relationship between graduates’ studies and their work. Additionally, the analysis of the graduates’ in their early career stages exposes the significant role that the socioeconomic stratum plays in their working life, particularly in their wages. This indicates that apart from education, other factors like the graduates’ economic or social capital may have an impact on their future work perspectives

Decent work?

Pastoralism and ranching are two different rangeland-based livestock systems in dryland areas of East Africa. Both usually operate under low and irregular rainfall and consequently low overall primary biomass production of high spatial and temporal heterogeneity. Both are usually located far from town centres, market outlets and communication, medical, educational, banking, insurance and other infrastructure. Whereas pastoralists can be regarded as self-employed, gaining their livelihood from managing their individually owned livestock on communal land, ranches mostly employ herders as wage labourers to manage the livestock owned by the ranch on the ranches’ own land property. Both production systems can be similarly labour intensive and – with regard to the livestock management – require the same type of work, whether carried out as self-employed pastoralist or as employed herder on a work contract. Given this similarity, the aim of this study was to comparatively assess how pastoralists and employed herders in northern Kenya view their working conditions, and which criteria they use to assess hardship and rewards in their daily work and their working life. Their own perception is compared with the concept of Decent Work developed by the International Labour Organisation (ILO). Samburu pastoralists in Marsabit and Samburu Districts as well as herders on ranches in Laikipia District were interviewed. A qualitative analysis of 47 semi-structured interviews yielded information about daily activities, income, free time, education and social security. Five out of 22 open interviews with pastoralists and seven out of 13 open interviews with employed herders fully transcribed and subjected to qualitative content analysis to yield life stories of 12 informants. Pastoralists consider it important to have healthy and satisfied animals. The ability to provide food for their family especially for the children has a high priority. Hardships for the pastoralists are, if activities are exhausting, and challenging, and dangerous. For employed herders, decent conditions are if their wages are high enough to be able to provide food for their family and formal education for their children. It is further most important for them to do work they are experienced and skilled in. Most employed herders were former pastoralists, who had lost their animals due to drought or raids. There are parallels between the ILO ‘Decent Work’ concept and the perception of working conditions of pastoralists and employed herders. These are, for example, that remuneration is of importance and the appreciation by either the employer or the community is desired. Some aspects that are seen as important by the ILO such as safety at work and healthy working conditions only play a secondary role to the pastoralists, who see risky and dangerous tasks as inherent characteristics of their efforts to gain a livelihood in their living environment.

Alley cropping of willows and grassland for bioenergy provision: productivity, tree-crop interactions and energy balance

The demand for biomass for bioenergy has increased rapidly in industrialized countries in the recent years. Biogenic energy carriers are known to reduce CO2 emissions. However, the resource-inefficient production of biomass often caused negative impacts on the environment, e.g. biodiversity losses, nitrate leaching, and erosion. The detrimental effects evolved mainly from annual crops. Therefore, the aim of modern bioenergy cropping systems is to combine yield stability and environmental benefits by the establishment of mixed-cropping systems. A particular emphasis is on perennial crops which are perceived as environmentally superior to annual crops. Agroforestry systems represent such mixed perennial cropping systems and consist of a mix of trees and arable crops or grassland within the same area of land. Agroforestry practices vary across the globe and alley cropping is a type of agroforestry system which is well adapted to the temperate zone, with a high degree of mechanization. Trees are planted in rows and crops are planted in the alleyways, which facilitates their management by machinery. This study was conducted to examine a young alley cropping system of willows and two grassland mixtures for bioenergy provision under temperate climate conditions. The first part of the thesis identified possible competition effects between willows and the two grassland mixtures. Since light seemed to be the factor most affecting the yield performance of the understory in temperate agroforestry systems, a biennial in situ artificial shade experiment was established over a separate clover-grass stand to quantify the effects of shade. Data to possible below- and aboveground interactions among willows and the two grassland mixtures and their effects on productivity, sward composition, and quality were monitored along a tree-grassland interface within the alleys. In the second part, productivity of the alley cropping system was examined on a triennial time frame and compared to separate grassland and willow stands as controls. Three different conversion technologies (combustion of hay, integrated generation of solid fuel and biogas from biomass, whole crop digestion) were applied to grassland biomass as feedstock and analyzed for its energetic potential. The energetic potential of willow wood chips was calculated by applying combustion as conversion technique. Net energy balances of separate grassland stands, agroforestry and pure willow stands evaluated their energy efficiency. Results of the biennial artificial shade experiment showed that severe shade (80 % light reduction) halved grassland productivity on average compared to a non-shaded control. White clover as heliophilous plant responded sensitively to limited radiation and its dry matter contribution in the sward decreased with increasing shade, whereas non-leguminous forbs (mainly segetal species) benefited. Changes in nutritive quality could not be confirmed by this experiment. Through the study on interactions within the alleys of the young agroforestry system it was possible to outline changes of incident light, soil temperature and sward composition of clover-grass along the tree-grassland interface. Nearly no effects of trees on precipitation, soil moisture and understory productivity occurred along the interface during the biennial experiment. Considering the results of the productivity and the net energy yield alley cropping system had lower than pure grassland stands, irrespective of the grassland seed mixture or fertilization, but was higher than that for pure willow stands. The comparison of three different energetic conversion techniques for the grassland biomass showed highest net energy yields for hay combustion, whereas the integrated generation of solid fuel and biogas from biomass (IFBB) and whole crop digestion performed similarly. However, due to the low fuel quality of hay, its direct combustion cannot be recommended as a viable conversion technique, whereas IFBB fuels were of a similar quality to wood chip from willow.