@phdthesis{RianoPachon2008,
  author    = {Ria{\~n}o-Pach{\´o}n, Diego Mauricio},
  title     = {Identification of transcription factor genes in plants},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-27009},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {In order to function properly, organisms have a complex control mechanism, in which a given gene is expressed at a particular time and place. One way to achieve this control is to regulate the initiation of transcription. This step requires the assembly of several components, i.e., a basal/general machinery common to all expressed genes, and a specific/regulatory machinery, which differs among genes and is the responsible for proper gene expression in response to environmental or developmental signals. This specific machinery is composed of transcription factors (TFs), which can be grouped into evolutionarily related gene families that possess characteristic protein domains. In this work we have exploited the presence of protein domains to create rules that serve for the identification and classification of TFs. We have modelled such rules as a bipartite graph, where families and protein domains are represented as nodes. Connections between nodes represent that a protein domain should (required rule) or should not (forbidden rule) be present in a protein to be assigned into a TF family. Following this approach we have identified putative complete sets of TFs in plant species, whose genome is completely sequenced: Cyanidioschyzon merolae (red algae), Chlamydomonas reinhardtii (green alga), Ostreococcus tauri (green alga), Physcomitrella patens (moss), Arabidopsis thaliana (thale cress), Populus trichocarpa (black cottonwood) and Oryza sativa (rice). The identification of the complete sets of TFs in the above-mentioned species, as well as additional information and reference literature are available at http://plntfdb.bio.uni-potsdam.de/. The availability of such sets allowed us performing detailed evolutionary studies at different levels, from a single family to all TF families in different organisms in a comparative genomics context. Notably, we uncovered preferential expansions in different lineages, paving the way to discover the specific biological roles of these proteins under different conditions. For the basic leucine zipper (bZIP) family of TFs we were able to infer that in the most recent common ancestor (MRCA) of all green plants there were at least four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments. Currently, following the approach described above, up to 57 TF and 11 TR families can be identified, which are among the most numerous transcription regulatory families in plants. Three families of putative TFs predate the split between rhodophyta (red algae) and chlorophyta (green algae), i.e., G2-like, PLATZ, and RWPRK, and may have been of particular importance for the evolution of eukaryotic photosynthetic organisms. Nine additional families, i.e., ABI3/VP1, AP2-EREBP, ARR-B, C2C2-CO-like, C2C2-Dof, PBF-2-like/Whirly, Pseudo ARR-B, SBP, and WRKY, predate the split between green algae and streptophytes. The identification of putative complete list of TFs has also allowed the delineation of lineage-specific regulatory families. The families SBP, bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA significantly differ in size between algae and land plants. The SBP family of TFs is significantly larger in C. reinhardtii, compared to land plants, and appears to have been lost in the prasinophyte O. tauri. The families bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA preferentially expanded with the colonisation of land, and might have played an important role in this great moment in evolution. Later, after the split of bryophytes and tracheophytes, the families MADS, AP2-EREBP, NAC, AUX/IAA, PHD and HRT have significantly larger numbers in the lineage leading to seed plants. We identified 23 families that are restricted to land plants and that might have played an important role in the colonization of this new habitat. Based on the list of TFs in different species we have started to develop high-throughput experimental platforms (in rice and C. reinhardtii) to monitor gene expression changes of TF genes under different genetic, developmental or environmental conditions. In this work we present the monitoring of Arabidopsis thaliana TFs during the onset of senescence, a process that leads to cell and tissue disintegration in order to redistribute nutrients (e.g. nitrogen) from leaves to reproductive organs. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. 76\% of these TFs are down-regulated during senescence, the remaining are up-regulated. The identification of TFs in plants in a comparative genomics setup has proven fruitful for the understanding of evolutionary processes and contributes to the elucidation of complex developmental programs.},
  language  = {en}
}
@phdthesis{GomezPorras2005,
  author    = {G{\´o}mez-Porras, Judith Lucia},
  title     = {In silico identification of genes regulated by abscisic acid in Arabidopsis thaliana (L.) Heynh.},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7401},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {Abscisic acid (ABA) is a major plant hormone that plays an important role during plant growth and development. During vegetative growth ABA mediates (in part) responses to various environmental stresses such as cold, drought and high salinity. The response triggered by ABA includes changes in the transcript level of genes involved in stress tolerance. The aim of this project was the In silico identification of genes putatively regulated by ABA in A. thaliana. In silico predictions were combined with experimental data in order to evaluate the reliability of computational predictions. Taking advantage of the genome sequence of A. thaliana publicly available since 2000, 1 kb upstream sequences were screened for combinations of cis-elements known to be involved in the regulation of ABA-responsive genes. It was found that around 10 to 20 percent of the genes of A. thaliana might be regulated by ABA. Further analyses of the predictions revealed that certain combinations of cis-elements that confer ABA-responsiveness were significantly over-represented compared with results in random sequences and with random expectations. In addition, it was observed that other combinations that confer ABA-responsiveness in monocotyledonous species might not be functional in A. thaliana. It is proposed that ABA-responsive genes in A. thaliana show pairs of ABRE (abscisic acid responsive element) with MYB binding sites, DRE (dehydration responsive element) or with itself. The analysis of the distances between pairs of cis-elements suggested that pairs of ABREs are bound by homodimers of ABRE binding proteins. In contrast, pairs between MYB binding sites and ABRE, or DRE and ABRE showed a distance between cis-elements that suggested that the binding proteins interact through protein complexes and not directly. The comparison of computational predictions with experimental data confirmed that the regulatory mechanisms leading to the induction or repression of genes by ABA is very incompletely understood. It became evident that besides the cis-elements proposed in this study to be present in ABA-responsive genes, other known and unknown cis-elements might play an important role in the transcriptional regulation of ABA-responsive genes. For example, auxin-related cis elements, or the cis-elements recognized by the NAM-family of transcription factors (Non-Apical meristem). This work documents the use of computational and experimental approaches to analyse possible interactions between cis-elements involved in the regulation of ABA-responsive genes. The computational predictions allowed the distinction between putatively relevant combinations of cis-elements from irrelevant combinations of cis-elements in ABA-responsive genes. The comparison with experimental data allowed to identify certain cis-elements that have not been previously associated to the ABA-mediated transcriptional regulation, but that might be present in ABA-responsive genes (e.g. auxin responsive elements). Moreover, the efforts to unravel the gene regulatory network associated with the ABA-signalling pathway revealed that NAM-transcription factors and their corresponding binding sequences are important components of this network.},
  subject      = {Bioinformatik},
  language  = {en}
}
@phdthesis{Schroth2016,
  author    = {Schroth, Maximilian},
  title     = {Microfinance and the enhancement of economic development in less developed countries},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94735},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XII, 287},
  year      = {2016},
  abstract  = {It is the intention of this study to contribute to further rethinking and innovating in the Microcredit business which stands at a turning point - after around 40 years of practice it is endangered to fail as a tool for economic development and to become a doubtful finance product with a random scope instead. So far, a positive impact of Microfinance on the improvement of the lives of the poor could not be confirmed. Over-indebtment of borrowers due to the pre-dominance of consumption Microcredits has become a widespread problem. Furthermore, a rising number of abusive and commercially excessive practices have been reported. In fact, the Microfinance sector appears to suffer from a major underlying deficit: there does not exist a coherent and transparent understanding of its meaning and objectives so that Microfinance providers worldwide follow their own approaches of Microfinance which tend to differ considerably from each other. In this sense the study aims at consolidating the multi-faced and very often confusingly different Microcredit profiles that exist nowadays. Subsequently, in this study, the Microfinance spectrum will be narrowed to one clear-cut objective, in fact away from the mere monetary business transactions to poor people it has gradually been reduced to back towards a tool for economic development as originally envisaged by its pioneers. Hence, the fundamental research question of this study is whether, and under which conditions, Microfinance may attain a positive economic impact leading to an improvement of the living of the poor. The study is structured in five parts: the three main parts (II.-IV.) are surrounded by an introduction (I.) and conclusion (V.). In part II., the Microfinance sector is analysed critically aiming to identify the challenges persisting as well as their root causes. In the third part, a change to the macroeconomic perspective is undertaken in oder to learn about the potential and requirements of small-scale finance to enhance economic development, particularly within the economic context of less developed countries. By consolidating the insights gained in part IV., the elements of a new concept of Microfinance with the objecitve to achieve economic development of its borrowers are elaborated. Microfinance is a rather sensitive business the great fundamental idea of which is easily corruptible and, additionally, the recipients of which are predestined victims of abuse due to their limited knowledge in finance. It therefore needs to be practiced responsibly, but also according to clear cut definitions of its meaning and objectives all institutions active in the sector should be devoted to comply with. This is especially relevant as the demand for Microfinance services is expected to rise further within the years coming. For example, the recent refugee migration movement towards Europe entails a vast potential for Microfinance to enable these people to make a new start into economic life. This goes to show that Microfinance may no longer mainly be associated with a less developed economic context, but that it will gain importance as a financial instrument in the developed economies, too.},
  language  = {en}
}