No description available.

Glucosyltransferases catalyze the transfer of glucose molecules from an active donor to acceptor molecules and are involved in many plant processes. SIP68, a tobacco glucosyltransferase protein, is a SABP2-interacting protein. It was identified in a yeast two-hybrid screen using SABP2 as bait and tobacco proteins as prey. SABP2, converts methyl salicylate to salicylic acid (SA) as a part of the signal transduction pathways in SA-mediated defense signaling. Subcellular localization is a crucial aspect of protein functional analysis to assess its biological function. The recombinant SIP68 tagged with eGFP was expressed transiently in Nicotiana benthamiana and observed under confocal microscopy. Fluorescent signals were observed in the epidermal cells. Subcellular fractionation of the tobacco leaves transiently expressing SIP68-+eGFP confirmed that SIP68 is localized in the cytosol. To study the role of SIP68 in plant stress signaling, transgenic lines with altered SIP68 expression were generated using RNAi and CRISPR Cas9 and analyzed.

MicroRNAs (miRNAs) are non-coding RNAs that often play a fundamental role in gene regulation. Currently, hundreds to over a thousand miRNAs are predicted to be present in many eukaryote species, with many to be discovered; the functions of most are unknown. While much attention has gone towards model organisms, a much greater depth of understanding remains to be gained for the miRNAs of many organisms directly important to humans. There are few verified miRNAs for any mosquito species, despite the role of mosquitoes in many of humanity’s worst diseases. Anopheles gambiae and Aedes aegypti, carriers of malaria and dengue, respectively, are responsible for over a million deaths a year. To date, there are sixty-six microRNAs in An. gambiae in miRBase, a central repository for miRNA sequences. Many of these are based on homology to primarily Drosophila miRNAs. While sequence conservation suggests an important function for these miRNAs, expression has not been experimentally verified for most mosquito miRNAs. Using small RNA cloning and northern blots, I discovered and analyzed 27 different microRNAs in aged female An. stephensi mosquitoes, the age group responsible for transmission of malarial parasites. Three of these miRNAs are only found in mosquitoes (miR-1889, -1890, and –1891). Cloning and northern analysis revealed an abundance of a miRNA that is linked to longevity in flies, miR-14, across different life stages of mosquitoes. It was also shown that miR-989 was expressed almost exclusively in the adult ovary and its expression fluctuated in response to bloodfeeding, suggesting a possible role in reproduction, an area of great importance to controlling mosquito populations. Building upon the above cloning experiment, a later high-throughput sequencing effort uncovered 98 miRNA precursors from Ae. aegypti. There are a total of 13 novel miRNAs that have not been found in other organisms by bioinformatic predictions or experiments. These “mosquito-specific” miRNAs may play a role in processes such as blood-feeding or vector-host interactions. A detailed examination of the expression of eight of these miRNAs was conducted in An. gambiae, An. stephensi, Ae. aegypti, and T. amboinensis to determine their expression profile, conservation, and provide hints to their function. My work revealed conserved and sometime stage-specific expression profiles of some of the mosquito-specific miRNAs. I also provided evidence for three lineage-specific miRNAs that may shed light on the divergence of different mosquito lineages. Extending the finding that miR-989 may be involved in mosquito reproduction, we conducted a detailed analysis of its evolution, expression, possible targets and regulation. miR-989 is conserved in holometabolous insects. miR-989 expression in female An. stephensi and Ae. aegypti dramatically rises following pupal emergence until strong signal is observed, until a blood meal is taken. Expression remains quite strong then begins a steep decline in expression at 32-40 hours post blood meal (PBM), and even by 96 hours PBM, remains weak. Bioinformatic predictions of miR-989 targets coupled with a PCR-based approach uncovered three potential target leads, though preliminary results were artifacts. Although the miR-989 post-emergence expression profile correlates with the expression of Juvenile Hormone, a key reproductive hormone in mosquitoes, no observable induction occurred when abdominal ligation samples were administered methoprene, a JH analog. However, methoprene impacted a number of other miRNAs, with up to a 3.87 fold induction (miR-1891), and a 3.15 fold suppression (miR-9a) of signal. Subsequent northern analysis provided visual confirmation of observable fold changes for miR-1891 and miR-9a, but not for miRNAs that showed changes below two fold. This analysis provides a foundation to study Juvenile Hormone regulation of miRNAs in mosquitoes. In summary, we have expanded the understanding of microRNAs in mosquitoes. An improved understanding of mosquito physiology can assist in efforts to control mosquito-borne infectious diseases. / Ph. D.

No description available.

More than 40 neurological diseases are known to be caused by large expansions oftandem repeat sequences scattered throughout the human genome in introns, exons and untranslated regions. The GGGGCC (G4C2) repeat expansion located in the first intron of the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). In C9 FTD/ALS, expanded transcripts are known to aggregate and accumulate in the cell nucleus, sequestering RNA binding proteins. Other expanded RNA species are exported to the cytoplasm to undergo a non-canonical form of translation termed ‘repeat-associated non-AUG (RAN) translation’. RAN translation leads to the production of toxic polydipeptide repeat proteins in the absence of a canonical AUG start codon. This dissertation will highlight new mechanistic features of translation across the G4C2 repeat expansion, identify a potential therapeutic for C9 FTD/ALS using RNAi and develop a cellular system to explore the G4C2 repeat RNA lifecycle. First, we demonstrate that increasing G4C2 repeat expansion size results in suppression of translation from both canonical and non-canonical start codons, suggesting that large polydipeptide repeats are rarely fully translated. We further find that initiation does not occur from within the repeat expansion, relying on upstream sequence for initiation. However, some reading frames are prone to substantial frameshifting, such as poly-GA. We also show that a bias in ii codon usage efficiency contributes to previously observed variations in the levels of each polydipeptide. Our results support and extend previous studies by identifying two new mechanisms that bias production of poly-dipeptides toward poly-GA in C9 FTD/ALS. Further, we generated central mismatch-containing short hairpin RNAs (shRNAs) targeting the G4C2 repeat expansion to reduce aggregation or block translation of repeatcontaining transcripts. Iterative design was able to improve shRNA processing efficiency and cellular abundance, yet they were unable to reduce nuclear RNA foci in patient-derived cells. Despite this, we show preliminary data suggesting that these shRNAs are able to target cytoplasmic repeat-containing transcripts and resulting in a reduced translation of poly-GP. Finally, we optimized the previously published RNA-protein interaction detection (RaPID) technique, which uses proximity dependent labelling by a mutant biotin ligase and mass spectrometry for protein identification in living cells, to identify proteins interacting with the G4C2 repeat expansion. We embedded the box B RNA hairpin between G4C2 repeats and tested the ability for λN fused to a biotin ligase mutant, BASU, to specifically bind the box B hairpin in vitro. We show that 6 repeats each side of the hairpin combined with an extended hairpin stem promotes specific binding of the λN-BASU fusion protein and is likely to be successful in cells. C9 FTD/ALS is a currently incurable neurodegenerative disorder largely due to the limited understanding of disease mechanism. This dissertation demonstrates new mechanisms of translation across the G4C2 repeat expansion that results in toxic DPR production while also developing a nucleic acid therapeutic for long-term treatment of C9 FTD/ALS and further developing systems to explore RNA-mediated toxicity in cells.

Aedes aegypti is an important vector of human pathogens including the viruses yellow fever, dengue and chikungunya. The small interfering RNA (siRNA) pathway is a critical immune response for controlling viral replication in Aedes aegypti. The goal of this research is to identify components of the Aedes aegypti genome that influence this pathway. A transgenic mosquito strain that reports the status of the siRNA pathway via enhanced green fluorescent protein (EGFP) intensity was employed to differentiate silencing abilities among individuals. Extreme EGFP expression phenotypes, representing efficient and poor silencing abilities, were enriched over five generations. Transcriptome sequencing and analyses were performed from pools of individuals from each enriched phenotype, revealing potential RNAi contributors. 1,120 transcripts were significantly different (FDR<0.0001) among the extreme phenotypes. Four genes were chosen, amplified, sequenced for SNP analysis. These analyses were performed on samples obtained by crossing enriched, extreme phenotype F0 individuals, intercrossing their progeny, then selecting individuals representing the extreme phenotypes from the F2 population. Though further verification is needed, findings from these analyses imply the regions of Aedes aegypti, Liverpool strain (AAEL) gene identifiers AAEL005026, AAEL013438 and AAEL011704 amplified do not contribute to the two extreme, opposite RNAi silencing in the sensor strain used here. SNP analyses of AAEL000817 indicate this gene either influences extreme RNAi phenotypes or is closely linked to a gene(s) that contributes to RNAi in Aedes aegypti. The 1,120 genes identified can be validated or eliminated as potential targets in the quest to mitigate the impact of Aedes aegypti. / Master of Science in Life Sciences

RNA interference (RNAi) is a gene regulation mechanism conserved among eukaryotes. To silence gene expression, RNAi relies on a short single-stranded guide RNA to steer the RNA-induced Silencing Complex (RISC) to mRNAs with guide strand-complementary sequences. RNAi is a highly membrane-associated process. The RISC complex is likely loaded at the rough Endoplasmic Reticulum, where it can bind to and degrade mRNAs. Components of the RISC complex also colocalize to late endosomes, and the efficiency of RNAi-mediated silencing is affected by changes in late endosome to lysosome fusion. RNAi can be systemic and inherited, effecting gene silencing in distal tissues and in the offspring. In this thesis, the model organism Caenorhabditis elegans was used to identify and characterize factors connecting systemic and inherited RNAi to the endomembrane system. We identify two SNARE proteins, SEC-22 and SYX-6, that both act as negative regulators of RNAi. SNAREs are necessary for vesicle fusion. Both SEC-22 and SYX-6 localize to late endosomes, and both interact with systemic RNAi protein SID-5 in a yeast two-hybrid (Y2H) screen. We find that in addition to its function in systemic RNAi, SID-5 is required for proper maturation of late endosomes. Furthermore, we identify the putative RNA-binding protein C12D8.1 as a novel regulator of RNAi inheritance. Mutant C12D8.1 animals will have enhanced inheritance of RNAi silencing, which negatively affects the ability of the progeny to silence new targets using RNAi. Finally, we describe a novel, object-based method for estimating significance in colocalization studies. This method helped us describe and quantify spatial relations between fluorophore-labeled proteins in situations where such analyses would otherwise be impossible. In conclusion, the work presented here further elucidates the connection between cellular RNAi, the endomembrane system, and the outside world.

Ziel der vorliegenden Dissertation war es, zum Verständnis der genetischen Grundlagen des akustischen Kommunikationssystems der Grille Gryllus bimaculatus beizutragen (s. auch 1.2). Dazu wurde die Expression eines Orthologs des no-on-transientA-Gens (nonA) mit Hilfe der RNA-Interferenz-Methode spezifisch herunterreguliert. Bei nonA handelt es sich um ein vielversprechendes Kandidatengen, da Punktmutationen in der codierenden Region des Gens die Eigenschaften des männlichen Balzgesangs bei Drosophila melanogaster beeinflussen. Zudem belegen Gentransfer-Experimente bei Drosophila, dass dieses Gen artspezifische Informationen des Balzgesangs enthält. Die Analyse der Gesangsdaten ergab, dass sich die Periodenlänge durch das Herunterregulieren von NONA nicht verändert. Außerdem konnte gezeigt werden, dass nonA-dsRNA-injizierte Tiere seltener 3-silbige Chirps produzieren, dafür aber mehr 4- und 5-silbige Chirps. Die Auswertung der tageszeitlichen Gesangsaktivität zeigte, dass alle Tiere signifikant am häufigsten im ersten Nachtquartal (nach Erlöschen der Beleuchtung) zirpten. Ein Effekt durch das Herunterregulieren von NONA konnte statistisch nicht belegt werden. Allerdings schien es einen Trend bei nonA-dsRNA-injizierten Tieren zu geben, gleichmäßiger über den Tag verteilt Gesangsaktivität zu zeigen. Transgene Drosophila melanogaster, deren arteigenes nonA durch das der Grille ersetzt bzw. ergänzt worden war, zeigten durchweg eine verbesserte Überlebensfähigkeit (Steigerungen zwischen 27 und 340%). Auch das positiv phototaktische Verhalten wurde durch das Grillen-NONA bei allen transformanten Fliegen verstärkt; allerdings fiel dieser Effekt eher marginal aus. Dennoch kann durchaus von einer zumindest teilweisen funktionellen Konservierung des nonA-Gens zwischen Gryllus bimaculatus und Drosophila melanogaster ausgegangen werden. / The present thesis aims to widen our understanding of the genetic background of the acoustic communication system of the cricket Gryllus bimaculatus (see also 1.2). Therefore the expression of an ortholog of the no-on-transientA (nonA) gene was specifically inhibited via RNA-interference. The nonA gene is one of the most interesting candidate genes in this context, as point mutations in the coding region of the gene affect the characteristics of the male’s calling song. Furthermore, gene transfer experiments in Drosophila showed that this gene obviously carries species-specific song information. The analysis of the calling song of nonA-RNAi-treated crickets, revealed that the duration of the syllable period was not influenced by the “knock-down” of the gene, but that the inhibition had a certain impact on the maximum number of syllables per chirp, as nonA-dsRNA-injected crickets produced significantly less 3-syllable chirps and significantly more 4- and 5-syllable chirps. Differences in the daytime calling activity between nonA-dsRNA-injected crickets and control groups could not be verified. The calling activity of all groups reached its peak in the first quarter of the night and significantly differed from the low calling activity during the remaining quarters of the day. Although the activity of all animals reached its peak during the first quarter of the night, there seems to be a trend that this rhythmical behaviour was less pronounced in nonA-dsRNA-injected crickets. Drosophila melanogaster mutants, which had been transformed with the nonA ortholog of Gryllus bimaculatus, increased their survival by 27% to 340%. In addition, the positive phototactic behaviour was slightly increased in all tested animals - this effect, however, remained marginal. Nevertheless, the nonA gene seems to be at least partly functionally conserved between Gryllus bimaculatus and Drosophila melanogaster.

Die molekularbiologische Untersuchung der Wechselwirkungen zwischen Pathogenen und ihren Wirtszellen ist ein wertvoller Ansatz zur Erschließung bakterieller Pathogenitätsmechanismen und hilft, unser ständig wachsendes Wissen über fundamentale Prozesse in eukaryotischen Zellen zu erweitern. Das Gram-negative Bakterium Salmonella Typhimurium ist ein gängiger Modellorganismus, um den intrazellulären Lebensstil bakterieller Pathogene und deren Einfluss auf Wirtszellprozesse zu erforschen. In der vorliegenden Arbeit wurde ein FACS-basierter Hochdurchsatz RNA Interferenz Screen etabliert und durchgeführt, um Wirtszellfaktoren zu entschlüsseln, welche in die intrazelluläre Replikation von Salmonella Typhimurium in humanen Epithelzellen involviert sind. Ein Salmonellen-Stamm, der zwei fluoreszierende Reporterproteine exprimiert, wurde konstruiert, um die bakterielle Replikation und die metabolische Aktivität in infizierten Wirtszellen zu detektieren. Der Einsatz einer humanen Kinase-Bibliothek lieferte 48 potentielle Kandidatengene, von denen 15 in einer anschließenden Validierung als relevante Faktoren identifiziert werden konnten. Die Mitogen-aktivierte Protein Kinase MKK7, deren Depletion eine verminderte bakterielle Replikation zur Folge hatte, wurde für eine weitergehende funktionelle Charakterisierung ausgewählt. Es zeigte sich, dass reduzierte MKK7 Proteinmengen eine Verringerung des Proteins zytosolische Phospholipase A2 (cPLA2) durch eine transkriptionelle Regulation zur Folge hatten. Die Bedeutung von cPLA2 für die bakterielle Infektion wurde durch die Salmonellen-induzierte, dauerhafte Phosphorylierung des Faktors deutlich und konnte durch Replikationsvergleiche in cPLA2-depletierten und nicht-depletierten Zellen bestätigt werden. Mikroskopische Ergebnisse deuteten darauf hin, dass die Phospholipase für den fehlerfreien Aufbau von Salmonellen-induzierten Filamenten notwendig ist, welche unerlässlich für die Salmonellenreplikation in Epithelzellen sind. / The study of pathogen-host cell interactions on the molecular level is a valuable tool to reveal bacterial pathogenicity mechanisms and, moreover, contributes to our increasing knowledge of fundamental cellular processes of eukaryotic cells. The Gram negative bacterium Salmonella Typhimurium is a well established model organism to investigate the intracellular lifestyle of bacterial pathogens and their modulation of host cell processes. In this work, a FACS-based high-throughput RNA interference screen was established and performed to elucidate host cell factors involved in the intracellular replication of Salmonella Typhimurium. A Salmonella strain expressing two fluorescent reporter constructs was generated which allowed for monitoring the bacterial replication and metabolic activity within infected cells. A human kinome-wide siRNA library was screened and 48 candidates were chosen for further validation. Among these, 15 host cell genes were identified to influence Salmonella intracellular replication. The mitogen activated protein kinase MKK7, whose depletion caused a decrease in bacterial replication, was selected for a more profound functional characterization. It could be demonstrated that the knock down of MKK7 caused a decrease in phospholipase A2 (cPLA2) protein levels due to a transcriptional regulation. A role for cPLA2 during the bacterial intracellular lifestyle was implicated by the finding that Salmonella induced a permanent phosphorylation of the phospholipase. The necessity of cPLA2 was confirmed with replication assays in cPLA2 depleted cells using siRNA and shRNA mediated knock down strategies. Microscopic experiments indicated that the phospholipase A2 is involved in the accurate generation of Salmonella-induced filaments, structures that were reported to be indispensable for replication.

Os conhecimentos sobre a regulação dos níveis de cálcio e manganês no Aspergillus fumigatus são bastante limitados, sendo que a homeostase destes íons pode ser diretamente controlada pela ação de ATPases específicas, dentre elas as cálcio ATPases da subfamília PMR1. Desta forma, o objetivo do presente estudo foi a expressão, caracterização e validação como alvo quimioterapêutico do gene Afpmr1 de A. fumigatus. Inicialmente, foi realizada a complementação funcional, de uma cepa de S. cerevisiae nocaute para a PMR1, em meios de cultura suplementados com EGTA ou manganês, revertendo o fenótipo da cepa nocute. Além disto, após expressão do gene Afpmr1, foi verificada uma reversão na intensa distribuição de quitina na parede celular da cepa nocaute. Paralelamente, para a RNAi, um fragmento do gene Afpmr1 apresentando baixa identidade com outros genes de cálcio ATPases de diferentes espécies foi clonado em vetor de expressão em A. fumigatus (pALB1). Após indução da expressão, a construção de RNA dupla fita para RNAi silenciou tanto o gene alb1 isoladamente (clone controle), quanto o duplo silenciamento com o gene de interesse Afpmr1, conferindo à ambas construções coloração branca às colônias. Uma vez confirmado o silenciamento gênico, por técnicas de RT-PCR quantitativo, os clones selecionados foram utilizados em ensaios de fagocitose e killing de macrófagos. O clone com o gene Afpmr1 silenciado apresentou diminuição na porcentagem de fagocitose, no número médio de conídios fagocitados e na eficiência de eliminação destes conídios quando comparados com seus controles. Estes resultados mostram que o gene Afpmr1 pode ser expresso funcionalmente em sistemas heterólogos e seu silenciamento, em A. fumigatus, influencia processos celulares que podem estar relacionados à manutenção da estrutura e composição da parede celular, além de desencadear alterações na fagocitose e killing de macrófagos. / The knowledge about the regulation of Aspergillus fumigatus calcium and manganese levels are very limited, while these ions homeostasis could be directly controlled by the function of specific ATPases, like the PMR1 calcium ATPase. In this way, the aim of the present work was the expression, characterization e validation, as chemotherapeutic target, of the A. fumigatus Afpmr1 gene. Initially, the functional complementation of a PMR1 knock-out strain phenotype was analyzed in EGTA or manganese supplemented culture media. Besides, after Afpmr1 expression, an intense distribution of chitin through the cell wall of the knock-out strain was reversed. At the same time, a fragment of the Afpmr1 gene, showing low identity values for another calcium ATPase genes, was cloned in an A. fumigatus expression vector (pALB1) for RNAi. After the induction of gene expression, a double strand RNA construct for RNAi has properly silenced either the alb1 gene alone (control clone), or the double silencing with the gene of interest Afpmr1, leading to both constructions white colored colonies. After confirmation of the gene silencing by quantitative RT-PCR techniques, the selected clones were used in macrophages killing and phagocytosis assays. The Afpmr1 silenced clone showed a decrease in the phagocytosis percentage, in the mean number of internalized conidia and in the killing percentage when compared with control groups. These results show that the Afpmr1 gene can be functionally expressed in eukaryotic heterologous systems and its silencing, in A. fumigatus, alters cellular processes that can be related with the maintenance of the cell wall structure and composition, as well as promote alterations in the macrophages phagocytosis and killing.