No description available.

Cylindrospermopsin (CYN) is a toxic alkaloid produced by several freshwater cyanobacterial species, the most prevalent in Australian waters being Cylindrospermopsis raciborskii. The occurrence of CYN-producing cyanobacteria in drinking water sources worldwide poses a potential human health risk, with one well-documented case of human poisoning attributed to the toxin. While extensive characterisation of CYN-induced toxicity has been conducted in rodents both in vivo and in primary cell cultures, little is known about mechanisms of toxicity in human cell types. This thesis describes studies undertaken to further define the molecular mechanisms of CYN toxicity in human cells. Concentration-response relationships were determined in various cultured human cell types using standard toxicity assays. As expected, CYN caused dose-dependent decreases in the growth of three cell lines, HepG2, Caco-2 and HeLa, and one primary cell type, human dermal fibroblasts, according to tetrazolium reduction assays. CYN treatment did not disrupt cellular membranes according to the lactate dehydrogenase release assay in HepG2 or Caco-2 cells after 24, 48 or 72 h exposure, but did cause membrane disruption in fibroblasts after 72 h exposure to relatively high concentrations of the toxin. Apoptosis occurred more readily in HeLa cells than HepG2 cells or fibroblasts, with 72 h exposure to 1 &mug/mL required before statistically significant rates of apoptosis occurred in the latter cell types. CYN did not appear to directly affect the structure of actin filaments or microtubules under the conditions used in the present study. The major portion of the work presented in this thesis comprises a large-scale interrogation of changes in gene expression induced by the toxin in cultured cells. To assess the effects of CYN on global gene expression, relative messenger RNA (mRNA) levels in human dermal fibroblasts and HepG2 cells after 6 h and 24 h exposure to 1 &mug/mL CYN were determined using oligonucleotide microarrays representing approximately 19 000 genes. Overall, the number of transcripts significantly altered in abundance was greater in fibroblasts than in HepG2 cells. In both cell types, mRNA levels for genes related to amino acid biosynthesis, carbohydrate metabolism, and protein folding and transport were reduced after CYN treatment, while transcripts representing genes for apoptosis, RNA biosynthesis and RNA processing increased in abundance. More detailed data analyses revealed the modulation of a number of stress response pathways—genes regulated by NF-&kappaB were induced, DNA damage response pathways were up-regulated, and a large number of genes involved in endoplasmic reticulum stress were strongly down-regulated. Genes for the synthesis and processing of mRNA, tRNA and rRNA were strongly up-regulated, indicating that CYN treatment may increase the turnover of all forms of cellular RNA. A small group of genes were differentially expressed in HepG2 cells and fibroblasts, revealing cell-specific responses to the toxin. Selected changes in transcript level were validated using real-time quantitative reverse transcriptase PCR (qRT-PCR). The modulation of stress response pathways by CYN, indicated by microarray analysis, was further investigated using other methods. The role of tumour suppressor protein p53 in CYN-mediated gene expression was confirmed by measuring the expression of known p53-regulated genes following CYN treatment of HepG2 cells and human dermal fibroblasts using qRT-PCR. Western blotting of protein extracts from CYNtreated cells showed that p53 protein accumulation occurred in HepG2 cells, providing additional evidence of the activation of the p53 pathway by CYN in this cell line. The immediate-early genes JUN and FOS were found to be induced by CYN in a concentration-dependent manner, and MYC was induced to a lesser extent. The mitogen-activated protein kinase c-Jun NH2-terminal kinase, implicated in the ribotoxic stress response initiated by damage to ribosomal RNA, appeared to become phosphorylated in HeLa cells after CYN exposure, suggesting that ribotoxic stress may occur in response to CYN in at least some cell types. The expression of a reporter gene under the control of a response element specific for NF-&kappaB was induced at the mRNA level but inhibited at the protein level. This shows that while transcription factors such as p53 and NF-&kappaB are apparently activated in response to the toxin, transactivation of target genes may not necessarily manifest a corresponding increase at the protein level. The current work contributes significantly to the current understanding of cylindrospermopsin toxicity in human-derived cell types, and provides further insight into putative modes of action.

Metabolism of D-amino acids is of considerable interest due to their key importance in cellular functions. The enzymes D-serine dehydratase (DSD) and D-cysteine desulfhydrase (DCyD) are involved in the degradation of D-Ser and D-Cys, respectively. We determined the crystal structure of Salmonella typhimurium DSD (StDSD) by multiple anomalous dispersion method of phasing using selenomethione incorporated protein crystals. The structure revealed a fold typical of fold type II PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild type StDSD (WtDSD) and selenomethionine labeled StDSD (SeMetDSD), significant electron density was not observed for the co-factor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other fold type II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modeling suggested that Thr166 may be involved in abstraction of proton from the Cα atom of the substrate. Apart from the physiological reaction, StDSD catalyses α, β-elimination of D-Thr, D-Allothr and L-Ser to the corresponding α-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates. Salmonella typhimurium DCyD (StDCyD) is a fold type II PLP-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. We determined the crystal structure of StDCyD using molecular replacement method in two different crystal forms. The better diffracting crystal form obtained in presence of benzamidine illustrated the influence a small molecule in altering protein interfaces and crystal packing. The polypeptide fold of StDCyD consists of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) which resemble other fold type II PLP-dependent enzymes. X-ray crystal structures of StDCyD were also obtained in the presence of substrates, D-Cys and βCDA, and substrate analogs, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS). The structures obtained in the presence of D-Cys and βCDA show the product, pyruvate, bound at a site 4.0-6.0 Å away from the active site. ACC forms an external aldimine complex while D and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at Cα proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggested formation of PMP by the hydrolysis of cycloserines. Mutational studies suggested that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for Cα proton abstraction from D-Cys. Based on these studies, we proposed a probable mechanism for the degradation of D-Cys by StDCyD. The acid-induced arginine decarboxylase (ADC) is part of an enzymatic system in Salmonella typhimurium that contributes to making this organism acid resistant. ADC is a PLP-dependent enzyme that is active at acidic pH. It consumes a proton in the decarboxylation of arginine to agmatine, and by working in tandem with an arginine-agmatine antiporter, this enzymatic cycle protects the organism by preventing the accumulation of protons inside the cell. We have determined the structure of the acid-induced StADC to 3.1 Å resolution. StADC structure revealed an 800 kDa decamer composed as a pentamer of five homodimers. Each homodimer has an abundance of acidic surface residues, which at neutral pH prevent inactive homodimers from associating into active decamers. Conversely, acidic conditions favor the assembly of active decamers. Therefore, the structure of arginine decarboxylase presents a mechanism by which its activity is modulated by external pH.

Ο άξονας Υποθάλαμος – Υπόφυση – Επινεφρίδια και το συμπαθητικό νευρικό σύστημα είναι τα περιφερικά σκέλη του συστήματος απάντησης στο στρες, με στόχο τη διατήρηση της ομοιόστασης του οργανισμού. Ανεπάρκεια ανταπόκρισης των επινεφριδίων στη σοβαρή νόσο μπορεί να παρουσιαστεί χωρίς προφανή βλάβη στον άξονα ΥΥΕ. Σε πολλούς ασθενείς με σοβαρή νόσο, τα επίπεδα κορτιζόλης παρά το ότι είναι αυξημένα, δεν είναι αρκετά ώστε να εκδηλώσουν επαρκή επινεφριδιακή απάντηση σε σχέση με τη σοβαρότητα της νόσου. Η βέλτιστη απάντηση του άξονα ΥΥΕ σε καταστάσεις νόσου παραμένει υπό αμφισβήτηση. Η διάγνωση της πιθανής σχετικής με τη νόσο παροδικής επινεφριδιακής ανεπάρκειας και η ανάγκη για χορήγηση κορτικοστεροειδών είναι ακόμη υπό συζήτηση. Σκοπός της μελέτης αυτής είναι η εκτίμηση της επινεφριδιακής απάντησης ανάλογα με τη σοβαρότητα της νόσου στην οξεία φάση της νόσου και η μελέτη του άξονα ΥΥΕ τόσο στην οξεία φάση, όσο και στην ανάρρωση. Για το σκοπό αυτό μελετήθηκαν 56 νοσηλευόμενοι ασθενείς με διαφορετικής βαρύτητας νόσημα (ΑΕΕ, ήπια νόσο, σήψη και σοβαρή σήψη), καθώς και 15 υγιή άτομα – μάρτυρες. Σε όλους τους συμμετέχοντες, κατά την εισαγωγή τους (1η ημέρα), μετρήθηκε η κορτιζόλη και η ACTH. Κατόπιν εφαρμόστηκε η δοκιμασία με χαμηλή δόση (1μg) κορτικοτροπίνης και δύο ώρες αργότερα η δοκιμασία με τη συνήθη δόση (250μg) κορτικοτροπίνης. Τη δεύτερη ημέρα νοσηλείας στους ασθενείς μετρήθηκε η ημερήσια διακύμανση της κορτιζόλης. Κατά την 5η -6η ημέρα νοσηλείας (φάση ανάρρωσης) έγινε επανάληψη των δοκιμασιών σε 15 ασθενείς (7 με σήψη και 8 με σοβαρή σήψη). Από την επεξεργασία των αποτελεσμάτων, στην ομάδα των ΑΕΕ και της σοβαρής σήψης παρατηρούνται οι υψηλότερες τιμές κορτιζόλης, καθώς επίσης και εξάλειψη της ημερήσιας διακύμανσης της κορτιζόλης. Παράλληλα, σε όλους τους ασθενείς παρατηρείται διαχωρισμός των επιπέδων κορτιζόλης και ACTH. Η αύξηση της κορτιζόλης (Δmax κορτιζόλης) μετά από διέγερση με 1 μg κορτικοτροπίνης δεν διέφερε μεταξύ των ομάδων νόσου, ενώ η Δmax κορτιζόλης μετά από διέγερση με 250μg κορτικοτροπίνης παρουσίασε οριακά σημαντική διαφορά με μια τάση να είναι υψηλότερη στην ομάδα των υγιών μαρτύρων. Η συχνότητα της απάντησης ή μη στη συνήθη δοκιμασία με βάση το κριτήριο Δmax κορτιζόλης <9 δεν διέφερε μεταξύ των υγιών και των ομάδων ασθενών, ενώ όλοι οι ασθενείς επιβίωσαν χωρίς τη χορήγηση κορτικοειδών, ανεξάρτητα από την απάντηση ή μη στις δοκιμασίες με ACTH. Στους ασθενείς με σήψη, η Δmax κορτιζόλης μετά από διέγερση με 250 μg κορτικοτροπίνης ήταν υψηλότερη στη φάση ανάρρωσης σε σχέση με την οξεία φάση, ενώ στους ασθενείς με σοβαρή σήψη η αντίστοιχη διαφορά δεν ανεδείχθη σε σημαντικό βαθμό. Η βασική κορτιζόλη ήταν υψηλότερη στην οξεία φάση σε σχέση με τη φάση ανάρρωσης και στις δύο ομάδες νόσου. Συμπερασματικά, διαπιστώνονται ήπιες αλλαγές στον άξονα ΥΥΕ, ανάλογα με τη σοβαρότητα του νοσήματος. Παρόλα αυτά, δεν επιβεβαιώνεται η ύπαρξη σχετικής επινεφριδιακής ανεπάρκειας σε μη βαριά νοσούντες ασθενείς. / Relative corticosteroid insufficiency maybe is common in critically ill patients, associated with poor outcome; however it is not known the response of the hypothalamic-pituitary-adrenal (HPA) axis in nursed patients. Our aim was to evaluate the response of HPA axis in non-critically ill nursed (NCIN) patients. Fifty -six nursed patients, divided into four groups (stroke, mild disease, sepsis and severe sepsis) as well as a control group (n=15) were studied. At admission (day 1), cortisol and ACTH measured and a low - dose (1mug ) corticotropin test was performed, followed two hours later by a standard-dose (250 mug). Diurnal variation of cortisol was obtained on day 2. A second identical set of low and standard set of corticotropin tests were performed on day 5 or 6 (recovery phase). In patients with stroke and severe sepsis cortisol had the highest values and its diurnal variation was abolished. Dissociation of ACTH and cortisol was found in all patients. The Deltamax of cortisol after the 1 mug corticotropin test did not differ among the groups while after the 250 mug corticotropin test was borderline higher in controls. The ratio of responders (Deltamax of cortisol >/= 9 mug/dL) to non-responders after 1 mug or 250 mug corticotrophin tests did not differ among patients and controls. All patients had a good outcome without glucocorticoid treatment. In conclusion, mild alterations of the HPA axis, depending on the severity of illness occurred. However, relative corticosteroid insufficiency in non-critically ill nursed patients did not confirm.

A distinctive feature of host-pathogen interactions in the case of Mycobacterium tuberculosis is the asymptomatic latent phase of infection. The ability of the bacillus to survive for extended periods of time in the host suggests an adaptive mechanism in M. tuberculosis that can cope with a variety of environmental stresses and other host stimuli. Extensive genomic studies and analysis of knock-out phenotypes revealed elaborate cellular machinery in M. tuberculosis that ensures a rapid cellular response to host stimuli. Prominent amongst these are two-component systems and σ factors that exclusively govern transcription re-engineering in response to environmental stimuli. M. tuberculosis σK is a σ factor that was demonstrated to control the expression of secreted antigenic proteins. The study reported in this thesis was geared to understand the molecular basis for σK activity as well as to explore conditions that would regulate σK activity. Transcription in bacteria is driven by the RNA polymerase enzyme that can associate with multiple σ factors. σ factors confer promoter specificity and thus directly control the expression of genes. The association of different σ factors with the RNA polymerase is essential for the temporal and conditional re-engineering of the expression profile. Environment induced changes in expression rely on a subset of σ factors. This class of σ factors (also referred to as Class IV or Extra-cytoplasmic function (ECF) σ factors) is regulated by a variety of mechanisms. The regulation of an ECF σ factor activity at the transcriptional, translational or posttranslational steps ensures fidelity in the cellular concentration of free, active ECF σ factors. In general, ECF σ factors associate with an inhibitory protein referred to as an anti-σ factor. The release of a free, active σ factor from a σ /anti-σ complex is thus a mechanism that can potentially control the cellular levels of an active σ factor in the cell. M. tuberculosis σK is associated with a membrane bound anti-σK (also referred to as RskA) (Said-Salim et al., Molecular Microbiology 62: 1251-1263: 2006). The extracellular stimulus that is recognized by RskA remains unclear. However, recent studies have suggested the possibility of a regulated proteolytic cascade that can selectively degrade RskA and other membrane associated anti-σ factors. The goal of the study was to understand this regulatory mechanism with a specific focus on the M. tuberculosis σK/RskA complex. The structure of the cytosolic σK/RskA complex and the associated biochemical and biophysical characteristics revealed several features of this /anti-σ complex that were hitherto unclear. In particular, these studies revealed a redox sensitive regulatory mechanism in addition to a regulated proteolytic cascade. These features and an analysis of the M. tuberculosis σK/RskA complex vis-à-vis the other characterized σ/anti σfactor complexes are presented in this thesis. This thesis is organized as follows- Chapter 1 provides an overview of prokaryotic transcription. A brief description of the physiology of M. tuberculosis is presented along with a summary of characterized factors that contribute to the pathogenecity and virulence of this bacillus. The pertinent mechanistic issues of σ/anti-σ factor interactions are placed in the context of environment mediated changes in M. tuberculosis transcription. A summary of studies in this area provides a background of the research leading to this thesis. Chapters 2 and 3 of this thesis describe the structural and mechanistic studies on the σK/RskA complex. The crystal structure of the σK/RskA complex revealed a disulfide bond in domain 4 (σK4). σK4 interacts with the -35 element of the promoter DNA. The disulfide forming cysteines were seen to be conserved in more than 70% of σK homologs, across both gram-positive and gram-negative bacteria. The conservation of the disulfide-forming cysteines led us to further characterize the role of this disulfide in σK/RskA interactions. These were examined by several biochemical and biophysical experiments. The redox potential of these disulfide bond forming cysteine residues were consistent with the proposed role of a sensor. The crystal structure and biochemical studies thus suggest that M. tuberculosis σK is activated under reducing conditions. Chapter 4 of this thesis describes the progress made thus far in the structural and biochemical characterization of an intra-membrane protease, M. tuberculosis Rip1 (Rv2869c). This protein is an essential component of the proteolytic cascade that selectively cleaves RskA. The proteolytic steps that govern the selective degradation of an anti-σ factor were first characterized in the case of E. coli σE (Li, X. et al. Proc. Natl. Acad. Sci. USA, 106:14837-14842, 2009). This cascade is triggered by the concerted action of a secreted protease (also referred to as a site-1 protease) and a trans-membrane protease (also referred to as a site-2 protease). M. tuberculosis Rip1 was demonstrated to be bona-fide site 2 protease that acts on three anti-σ factors viz., RskA, RslA and RsmA (Sklar et al., Molecular Microbiology 77:605-617; 2010). To further characterize the role of Rip1 in the proteolytic cascade, this intra-membrane protease was cloned, expressed and purified for structural, biochemical and biophysical analysis. The preliminary data on this membrane protein is described in this chapter. The conclusions from the studies reported in this thesis and the scope for future work in this area is described in Chapter 5. Put together, the σK/RskA complex revealed facets of σ/anti-σ factor interactions that were hitherto unrecognized. The most prominent amongst these is the finding that an ECF σfactor can respond to multiple environmental stimuli. Furthermore, as seen in the case of the σK/RskA complex, the σ factor can itself serve as a receptor for redox stimuli. Although speculative, a hypothesis that needs further study is whether these features of the σK/RskA complex contribute to the variable efficacy of the M. bovis BCG vaccine. In this context it is worth noting that σK governs the expression of the prominent secreted antigens- MPT70 and MPT83. The studies reported in this thesis thus suggest several avenues for future research to understand mycobacterial diversity, immunogenicity and features of host-pathogen interactions. The appendix section is divided into two subparts- Appendix 1 of the thesis is a review on peptidase V. This is a chapter in The Handbook of Proteolytic enzymes (Elsevier Press, ISBN:9780123822192). Appendix 2 of the thesis includes technical details and an extended materials and methods section.

Die Genexpression ist ein stochastischer Prozess, dessen strenge Regulation einen ungestörten Zellzyklusverlauf ermöglicht. Jeglicher Stress löst eine Neuprogrammierung der Expression und somit einen Stillstand des Zellzyklus aus. Um ein besseres Verständnis des eukaryotischen Zellzyklus zu erlangen, wurde in dieser Arbeit die Fluoreszenzmikroskopie einzelner Zellen (S.cerevisiae) mit stochastischer Modellierung der Hauptregulatorgene des G1/S-Übergangs (SIC1, CLN2, CLB5) kombiniert. Mithilfe des MS2-CP-Systems wurden mRNA-Level von SIC1 in lebenden Zellen bestimmt und verschiedene Transportwege von SIC1-mRNA visualisiert. RNA-FISH in Kombination mit genetischen und morphologischen Markierungen ermöglichte es, die absolute Quantifizierung von SIC1-, CLN2- und CLB5-mRNA in allen Zyklusphasen vorzunehmen. Die Auswirkung von Osmostress, in Hinblick auf eine transkriptionale Verzerrung, wurde untersucht. Basierend auf den experimentellen-Daten wurde ein stochastisches Model entwickelt, dass die Expression von SIC1, CLN2 und CLB5 mRNA und Proteinlevel in Abhängigkeit von Osmostress über den gesamten Zellzyklus hinweg abbildet. Die Modellierung ermöglichte eine in silico Synchronisation und somit die Extraktion kinetischer Parameter. Die Expression der beobachteten Gene wurde im Verlauf des Zellzyklus nicht ein- und ausgeschaltet, stattdessen kam es zu Phasen hoher oder niedriger Expression. Niedriger SIC1 Expression gewährleistete niedriger Sic1 Protein Verzerrung und robustes G1/S Timing. CLN2 und CLB5 zeigten ein maximales Expressionslevel in G1 und auch eine erhöhte Expression in der späten Mitose. Osmostress induzierte einen langanhaltenden Effekt auf die Transkription und die Dauer der Zellzyklusphasen. Der hier vorgestellte Ansatz ermöglichte quantitative Einblicke in die Genexpression und zeitliche Koordination des Zellzyklus von S.cerevisiae. Einige der hier beobachteten Regulationsmechanismen könnten allgemeine Gültigkeit im eukaryotischen Zellzyklus besitzen. / Gene expression is a stochastic process and its appropriate regulation is critical for cell cycle progression. Cellular stress response requires expression reprogramming and cell cycle arrest. Time-resolved quantitative methods on single cells are needed to understand eukaryotic cell cycle in context of noisy gene expression and external perturbations. We applied single-cell fluorescence microscopy and stochastic modeling to SIC1, CLN2 and CLB5, the main G1/S regulators in S. cerevisiae. Using MS2-CP system we estimated SIC1 mRNA levels and visualized different types of transport for SIC1 mRNA particles in living cells. With RNA-FISH combined to genetic and morphological markers we monitored absolute numbers of mRNA and transcriptional noise over cell cycle phases with and without osmostress. Stochastic modeling enabled in silico synchronization, the extraction of kinetic parameters as well as expanded the static mRNA data into time courses for mRNAs, proteins and their noise. Based on our experimental data we developed a stochastic model of G1/S timing centered on SIC1 and a second one for the entire cell cycle involving SIC1, CLN2 and CLB5 and the response to osmostress. All three genes exhibited basal expression throughout cell cycle enlightening that transcription is not divided in on and off but rather in high and low phases. A low SIC1 transcript level ensured a low protein noise and a robust timing of the G1/S transition. CLN2 and CLB5 showed main expression peaks in G1 as well as an expression upshift in late mitosis. Osmostress induced different periods of transcriptional inhibition for CLN2 and CLB5 and long-term impact on cell cycle phase duration. Our approach disclosed detailed quantitative insights into gene expression and cell cycle timing, not available from bulk experiments. Importantly some regulation mechanisms specific to SIC1, CLN2 and CLB5 might be generalized to other genes as well as to other organisms.

Conditions which promote reversible growth arrest, such as hypoxia and high cell density, lead to activation of a diverse network of proteins known as growth arrest specific (GAS) genes. Fatty acid binding protein 4 (FABP4), a lipid chaperone involved in the regulation of metabolic and inflammatory responses, has been shown to be part of the GAS program. While the induction of FABP4 in oxygen-deprived environments is well characterized, its functionality and regulation in such conditions remains unclear. In this study, we describe how mis-expression of FABP4 affects cell viability and survival within low oxygen conditions. Loss of FABP4 using shRNA was shown to be associated with a significant increase in oxidative stress and lipid peroxidation, a reduction in lipid droplet formation and a greater incidence of apoptosis. Hypoxia-mediated expression of FABP4 was also found to be positively correlated with cellular levels of C/EBP-beta, an essential activator of p20K in quiescence. FABP4 and p20K are both lipocalins that have been shown to share similar induction patterns and ability to assist in the maintenance of lipid trafficking in cellular stress circumstances. Unexpectedly, the depletion of FABP4 or p20K results in loss of the other in limited oxygen concentrations. This occurs independently of disruption to the broad GAS gene program, suggesting the two proteins may be co-regulated in a shared hypoxic-signalling pathway. C/EBP-beta appears to be the transcriptional activator shared by FABP4 and p20K in quiescence, and the three may be part of an intricate system to sense and respond to reactive oxygen species and lipid radicals. However, the forced expression of either FABP4 or p20K when the other is repressed only moderately restores cell survival through alleviating oxidative stress, indicating the two are both necessary for optimal response to hypoxia. In all, these studies suggest that analogous to the p20K lipocalin, FABP4 plays a critical role in lipid homeostasis and cell survival in conditions of limited oxygen concentrations, and its stimulation is dependent on C/EBP-beta activity. / Thesis / Master of Science (MSc) / A study investigating the role of FABP4 and p20K in conditions of reversible growth arrest with an emphasis on cell survival, lipid homeostasis and mitigating the effects of oxidative stress, and regulation of the two lipocalins by C/EBP-beta.

Rainbow trout (Oncorhynchus mykiss) are introduced in large parts of the world and are commonly farmed for consumption as well as a valued sport fish. Many species of salmonids show large intraspecific variation in pigmentation, which has been shown to correlate with stress response and several other behavioral traits. In this study, the behavior and stress response of rainbow trout linked to pigmentation is investigated, depending on previous sport fishing experience. Through data from a previous study on rainbow trout in semi-natural ponds, locomotor activity was measured as a proxy of stress, under three different sport fishing treatments. From previous photos, the pigment spots of each rainbow trout are counted to test the correlation with locomotor activity. In addition, it is tested whether different previous experience of sport fishing means a higher stress response when re-exposed to fishing. No significant relationship between pigment spots and locomotor activity could be obtained for the three treatment groups. However, significant differences in locomotor activity due to angling experience between treatment groups upon re-exposure to fishing were found, with fish that were inexperienced in angling having higher locomotor activity compared to previously caught fish. Sport fishing and catch-and-release had the effect of reducing locomotor activity in rainbow trout, which can be interpreted as fishing could both stress them and trigger the fish's feeding response, depending on previous experience. Fishing is believed to create a passivation due to the negative association of being caught, while fish not previously caught were activated by sport fishing. The study's missing correlation between pigment spots and stress has been both confirmed and denied in other studies and may depend on the origin and the degree of domestication, which means that the correlation within other species of salmonids or fish with different origins would be relevant to investigate. / Regnbåge (Oncorhynchus mykiss) förekommer introducerade i stora delar av världen och är vanliga att odlas för konsumtion samt en uppskattad sportfisk. Många arter av salmonider visar stor intraspecifik variation i pigmentering, vilket visats korrelera med stressrespons och flera andra beteendemässiga karaktärsdrag. I denna studie undersöks regnbågarnas beteende och stressrespons kopplat till pigmentering, beroende på tidigare erfarenhet av sportfiske. Genom data från en tidigare studie på regnbåge i semi-naturliga dammar mäts rörelseaktivitet som indirektmått på stress, under tre olika sportfiskebehandlingar. Från tidigare foton räknas varje regnbåges pigmentfläckar för att testa korrelationen med rörelseaktivitet. Därtill testas om olika tidigare erfarenhet av sportfiske, innebär högre stressrespons vid återexponering för fiske. Inget signifikant samband mellan pigmentfläckar och rörelseaktivitet kunde erhållas för de tre behandlingsgrupperna. Signifikanta skillnader i rörelseaktivitet på grund av erfarenheten av sportfiske mellan behandlingsgrupperna vid återexponering för fiske fanns dock, där fisk som var oerfaren sportfiske hade högre rörelseaktivitet jämfört med fisk som fångats tidigare. Sportfiske och catch-and-release hade effekten att minska rörelseaktiviteten hos regnbågar, vilket kan tolkas som att fisket både kunde stressa och trigga fiskens födorespons, beroende på tidigare erfarenhet. Fisket tros skapa en passivisering på grund av den negativa associationen att bli fångad, medan fisk som inte fångats tidigare aktiverades av sportfisket. Studiens uteblivna samband mellan pigmentfläckar och stress har både bekräftats och dementerats i andra studier och kan bero på ursprung och graden av domesticering, vilket gör att sambandet inom andra arter av salmonider eller fisk med olika ursprung vore aktuellt att undersöka.

RNA ist ein zentrales Molekül in der Zelle und essentiell für ihre Lebensfunktionen. Die durchschnittliche Halbwertszeit von RNA-Molekülen limitiert jedoch die zeitliche Auflösung herkömmlicher RNA-Sequenzierung, da geringe Änderungen im Transkriptom kaum zu erkennen sind, bis eine gewisse Anzahl an Molekülen akkumuliert. Durch metabolische Markierung von RNA (SLAMseq) kann die Auflösung deutlich erhöht werden. Hierfür werden der Probe markierte Nucleotide (4sU/4sUTP) zugesetzt, die dann zufällig in neu transkribierte RNA inkorporiert werden und eine Unterscheidung zwischen ‚neuer‘ und ‚alter‘ RNA erlauben. In dieser Arbeit werden eine der ersten Einzelzell-SLAMseq-Methoden, die dazugehörige Datenanalyse-Software sowie drei Anwendungen der entwickelten Methoden vorgestellt. Die erste Anwendung verwendet Einzelzell-SLAMseq, um zwischen maternaler (alter) und zygotischer (neuer) RNA in sich entwickelnden Zebrafischembryos bis zur Gastrulation zu unterscheiden. Im Rahmen des Projekts entstand der erste Einzelzell-SLAMseq-Datensatz in einem vollständigen Wirbeltier, der es außerdem erlaubt, im Vorfeld identifizierten lokalisierten maternalen Transkripten zeitlich zu folgen. Diese – vorher uncharakterisierten –Transkripte wurden während der Gastrulation in den Keimzellen angereichert gefunden, was Rückschlüsse auf ihre mögliche Funktion erlaubt. Die zweite Anwendung konzentriert sich auf die neu transkribierte RNA und verwendet (Einzelzell-)SLAMseq, um Transkripte, die in Reaktion auf Stress während der Probenaufbereitung hergestellt wurden, zu identifizieren und rechnerisch zu entfernen. Die Vorteile der Methode werden in mehreren Systemen und Geweben (Mausherz, Zebrafischlarve, Maus-Microglia) demonstriert. In der dritten Anwendung wird eine Machbarkeitsstudie für in vivo SLAMseq zur Identifikation der initialen Immunantwort nach Makrophagenstimulation präsentiert, die auf einen deutlichen Gewinn an zeitlicher Auflösung durch SLAMseq hindeutet. / RNA is a central molecule in the cell and essential to its life functions. With the average RNA half life being multiple hours, regular RNA sequencing has an intrinsic limit on temporal resolution, where small changes in the transcriptome are not picked up until a certain amount of transcripts has build up. This resolution can be greatly improved using RNA metabolic labelling (SLAMseq), where labelled nucleotides (4sU/4sUTP) are added to the samples. These nucleotides are randomly incorporated into nascent transcripts and allow distinction between RNA produced before and after introduction of the labelling agent. This thesis presents one of the first high throughput single cell SLAMseq protocols, an accompanying computational pipeline for data analysis as well as three applications for the developed methods. The first application uses single cell SLAMseq to distinguish between maternal (unlabelled) and zygotic (labelled) transcripts in early zebrafish development (up to mid-gastrulation). This project generated the first single cell SLAMseq dataset in a whole vertebrate. Additionally the data allows to follow a previously discovered set of vegetally localised maternal transcripts in time and determine that these specific transcripts are mainly enriched in the primordial germ cells at gastrulation, therefore ascribing a potential function to a set of so far uncharacterised genes. The second application focuses on newly transcribed RNA and uses (single cell) SLAMseq as a technique to identify and remove transcripts generated in response to sample preparation stress. The method’s benefits are demonstrated in multiple systems and tissues, among them mouse cardiomyocytes, zebrafish larvae and mouse microglia. Finally as the third application an in vivo proof of concept study of SLAMseq to identify first response genes in macrophage stimulation is presented, where the introduction of 4sU shows clear advantages in temporal resolution compared to unlabelled data.

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