Many studies of global gene expression focus solely on studying the transcriptome thereby only assessing mRNA abundance. However, transcription is only a single layer of gene expression and recently, the influence of post-transcriptional regulation has become undeniable. Rather underrepresented players in post-transcriptional control are G-quadruplexes (G4s). These stable structures can form guanine tetrads in DNA and RNA via p-p-stacking of several planar arrangements of four guanine bases stabilized by Hoogsteen hydrogen bonds and a central metal cation. Recent reports have pointed to an important regulatory role of G4 motives in key cellular functions including pre-mRNA processing, RNA turnover, mRNA transport thereby suggesting intriguing links to human diseases as cancer and neurological disorders. G4 structures in mRNAs seem to act as signaling components that constitute an own post-transcriptional operon. Recruitment of G4-specific RBPs then determines the ultimate fate of G4-containing mRNAs. Not many RBPs or upstream regulatory factors of G4s have been identified and the functional consequences of these interactions are not known. In this proposal I will address these questions. First, I will identify mRNAs that are differentially translated and/or stabilized in the presence of the G4 specific ligand pyridostatin (PDS), which stabilizes G4 structures. The resulting comprehensive list of mRNAs will be the first data set that provides a mechanistically link of G4 motive regulation. Secondly, I will identify factors in the G4 regulatory network using a genome wide shRNA assay to determine proteins that modulate the stability and/or the translation of G4 motive containing mRNAs. It is important to understand G4 structure-function relationships and upstream regulatory processes as the emerging link between G4 formation and human disease opens up an exciting research direction that has potential implications for therapeutic intervention.

Tuberculosis has afflicted humans for about 70,000 years and continues to take a huge toll on human health. The increase of drug-resistant Mycobacterium tuberculosis and the limited effectiveness of the existing treatments make urgent a deeper understanding of its immunopathogenesis. The role of macrophages in the disease has been intensively studied, but little is known about the involvement of neutrophils. Recent findings indicate that neutrophils play crucial roles in the pathogenesis of tuberculosis that are unknown until the present. Thus, in this project I will use the recognized zebrafish-Mycobacterium marinum infection model, available in the host lab, to study the role played by neutrophils in mycobacterial infection. I propose to use this infection model combined with in vivo imaging of the interactions host-pathogen, gain and loss of gene function strategies, the use of zebrafish transgenic and mutant lines, gene expression analysis, and multitude of other techniques available in the host lab to study (1) how mycobacteria can evade neutrophil recruitment and phagocytosis, (2) what is the origin of the two functionally different neutrophil populations observed in mycobacterial infection, (3) how neutrophils can kill mycobacteria in the absence of macrophages and without any physical interaction, and (4) why neutrophils act as macrophage scavengers. The elucidation of all these questions never studied before will allow me to shed light on the involvement of neutrophils in the pathogenesis of tuberculosis, and will represent a relevant improvement in the field with biomedical implications. Moreover, it will be a crucial step in my scientific career thinking of becoming a group leader in the field of immunology and infectious diseases, since I will have the opportunity to work in a relevant biomedical question, with the support of the main experts in the field, in an unsurpassable scientific environment, and with the best facilities.

Photonic structures are extremely widespread in nature, and studying how light interacts with them is important. This contributes to understanding of the structures’ biological significance and also supports development of novel, bio-inspired optical materials. Natural photonic structures are, however, generally very challenging to model when one refuses to approximate their optical response to the one of simple periodic materials. The complications in describing light-matter interaction in such systems are introduced by the fact that natural structures are highly hierarchical (with features spread on different length-scales) and generally affected by disorder. With this proposal, we want to address these challenges by developing novel analysis tools, which will be used to increase understanding of disordered photonic structures. In particular, we will develop tools for two systems: One system is the striations found on a range of flower petals, which create iridescence due to their grating-like organisation. The other system is that of the helicoidal multilayer structure found in Pollia condensata fruit. This gives rise to a colour-selective, characteristic appearance, impossible to obtain using only pigmentation. The scientific goal of developing novel analysis tools for complex and disordered photonic structures is important in biology. Moreover, such tools will find application in the development of novel photonic structures, and they are relevant not only for natural photonics materials, but more in general, for self-assembled systems where disorder and hierarchical structuring are an inherent part of the fabrication process.