Refine
Has Fulltext
- yes (84)
Is part of the Bibliography
- yes (84)
Year of publication
- 2018 (84) (remove)
Document Type
- Journal article (61)
- Doctoral Thesis (22)
- Preprint (1)
Language
- English (84) (remove)
Keywords
- Fluoreszenzmikroskopie (3)
- super-resolution microscopy (3)
- Apis mellifera (2)
- Biene (2)
- Camponotus floridanus (2)
- Drosophila melanogaster (2)
- Genom (2)
- Phänologie (2)
- Tagesrhythmus (2)
- Timing (2)
- Trypanosomen (2)
- Virulenzfaktor (2)
- X-ray crystallography (2)
- bioinformatics (2)
- circadian clock (2)
- division of labor (2)
- evolution (2)
- fitness (2)
- foraging (2)
- genomics (2)
- honeybee (2)
- land use (2)
- melanoma (2)
- neuroblastoma (2)
- proteins (2)
- symbiosis (2)
- 16S metabarcoding (1)
- 3D modeling (1)
- 4TH-Corner Problem (1)
- AMP-activated protein kinase (AMPK) (1)
- Acyrthosiphon pisum (1)
- Adhäsion (1)
- African trypanosomes (1)
- Alkaloide (1)
- Ameise (1)
- Ameisen (1)
- American foulbrood (1)
- Aneuploidy (1)
- Ant (1)
- Antibody clearance (1)
- Ants (1)
- Articular-Cartilage (1)
- Aspergillus (1)
- AstA (1)
- Atta vollenweideri (1)
- Aurora-A (1)
- BRAF (1)
- Beauveria bassiana (1)
- Beige adipocytes (1)
- Biodiversity (1)
- Biodiversity Exploratories (1)
- Biodiversitätsexploratorien (1)
- Biokinetics (1)
- Biologie (1)
- Biomarkers (1)
- Biomechanical Properties (1)
- Body size (1)
- Body weight (1)
- Bottom-up (1)
- Bärtierchen (1)
- C/EBP (1)
- CCHamide1 (1)
- CIR aerial imagery (1)
- CNG channel (1)
- COPD (1)
- CPAF activation (1)
- Caenorhabditis elegans (1)
- Camponotus (1)
- CarO (1)
- Cellular imaging (1)
- Chromatin and Epigenetics (1)
- Chronobiologie (1)
- Circadian Clock (1)
- Circadiane Uhr (1)
- Circadianer Rhythmus (1)
- Circular dichroism (1)
- Climate change (1)
- Coffin–Lowry syndrome (1)
- Cohesin complex (1)
- Collagen (1)
- Community ecology (1)
- Comparative genomics (1)
- Compressive Properties (1)
- DFNB68 (1)
- DNA (1)
- DNA complex (1)
- Dmrt1bY (1)
- Drosophila (1)
- Drosophila melanogaster motoneuron (1)
- Ecological Networks (1)
- Ecological networks (1)
- Ecology (1)
- Ecosystem ecology (1)
- Endogenous clock (1)
- Endophytische Pilze (1)
- Enzymes (1)
- Epichloe (1)
- Epichloë (1)
- Erythrozyt (1)
- Erythrozytenadhärenz (1)
- European foulbrood (1)
- Exacerbation (1)
- Exazerbation (1)
- F-actin (1)
- Fagus sylvatica (1)
- Fitness (1)
- Fluorescence spectroscopy (1)
- Fungal cell-walls (1)
- Fusarium fujikuroi (1)
- Galectin-1 (1)
- Gene Regulation (1)
- Gene-prediction (1)
- Genregulation (1)
- Geruchssinn (1)
- Glutamin (1)
- Glykoproteine (1)
- Gräser (1)
- HECT (1)
- HUWE1 (1)
- Hibernation (1)
- Hochauflösende Mikroskopie (1)
- Host-endosymbiont interactions (1)
- Host-pathogen interactions (1)
- Human Knee (1)
- Human Medial Meniscus (1)
- Hymenoptera (1)
- Immun-Transkriptom (1)
- Immunreaktion (1)
- Influenza (1)
- Injuries (1)
- Innate immunity (1)
- Innere Uhr (1)
- Insect (1)
- Insekt (1)
- Interactome (1)
- JNK (1)
- Jmjd6 (1)
- Klima (1)
- Kohlendioxid (1)
- Kommunikation (1)
- Korrelative Mikroskopie (1)
- Landnutzung (1)
- Latimeria menadoensis (1)
- Leaf cutting ants (1)
- Lolium perenne (1)
- ME/CFS (1)
- MIPs (1)
- MYC (1)
- Maus (1)
- Mechanistic model (1)
- Meiose (1)
- Meiosis (1)
- Merogone experiments (1)
- Metabolismus (1)
- Metarhizium anisopliae (1)
- Model (1)
- Models (1)
- Molecular biophysics (1)
- Molecular neuroscience (1)
- Motiliät (1)
- Multiple Traits (1)
- Multipolar mitosis (1)
- Muscidifurax (1)
- Mutagenese (1)
- Myc (1)
- N-MYC (1)
- NTHi (1)
- Nahrungsaufnahme (1)
- Nasonia (1)
- Nestbau (1)
- Neuroanatomie (1)
- Neurobiology (1)
- Obstruktive Ventilationsstörung (1)
- Olfaction (1)
- Onkogen (1)
- OpsA (1)
- Oryza sativa (1)
- Osmia (1)
- Osteoarthritis (1)
- PABPs (1)
- PKCζ, (1)
- Paenibacterin (1)
- Parasite development (1)
- Peptide (1)
- Period (1)
- Pollinators (1)
- Polyspermy (1)
- Preclinical (1)
- Protein (1)
- Protein kinase D1 (PKD1) (1)
- Proteom (1)
- Protopterus annectens (1)
- Pteromalidae (1)
- RSK (1)
- Re-Annotation (1)
- Re-annotation (1)
- Repair (1)
- Röntgen-Kleinwinkelstreuung (1)
- Röntgenstrukturanalyse (1)
- S1PR2 (1)
- SIM (1)
- Schlaf (1)
- Science history (1)
- Sea urchin development (1)
- Shaggy kinase (1)
- Single-molecule fluorescence microscopy (1)
- Sox5 (1)
- Soziale Insekten (1)
- Species Traits (1)
- Staphylococcus aureus (1)
- Stress (1)
- Stressresistenz (1)
- Super-resolution microscopy (1)
- Synaptische Proteine (1)
- Synaptonemal complex (1)
- T cells (1)
- T. brucei (1)
- TFIIIC (1)
- Tagesrhythmik (1)
- Taufliege (1)
- Timeless (1)
- Tiotropium (1)
- Tn1549 transposon (1)
- Tn916-like transposon family (1)
- Traits-Environment Relationships (1)
- Transcriptome (1)
- Transkription <Genetik> (1)
- Transkriptionsfaktor (1)
- Transkriptom (1)
- Transposon (1)
- Treatment (1)
- Trichomalopsis (1)
- Trypanosoma (1)
- Trypanosoma brucei (1)
- Trypanosoma brucei brucei (1)
- Trypanosomes (1)
- VSG (1)
- Variables Oberflächen Glycoprotein (1)
- Variant surface glycoprotein (1)
- Venusfliegenfalle (1)
- Verhalten (1)
- Viral infections (1)
- Voltage-Clamp-Methode (1)
- Wild bees (1)
- Zellbiologie (1)
- Zelloberfläche (1)
- Zellteilung (1)
- Zika virus (1)
- action potentials (1)
- activity rhythms (1)
- ageing (1)
- agricultural intensity (1)
- agroecology (1)
- airborne laser scanning (ALS) (1)
- airflow (1)
- alkaloids (1)
- animal behaviour (1)
- anti-microbial activit (1)
- antibiotic resistance (1)
- apoptosis (1)
- artificial diet (1)
- assortative mating (1)
- autosomal recessive non-synstromic hearing loss (1)
- bPAC (1)
- bacterial genomics (1)
- bacterial transcription (1)
- bakanae (1)
- bee disease (1)
- beech forests (1)
- bees (1)
- behavioral conditioning (1)
- behavioral rhythms (1)
- behavioral transition (1)
- bioassays (1)
- biodiversity (1)
- biodiversity estimation (1)
- biological pest control (1)
- bird diversity (1)
- black woodpecker (1)
- breast cancer (1)
- brood rearing (1)
- building behavior (1)
- cAMP (1)
- calcium (1)
- cancer (1)
- cancer genomics (1)
- cancer models (1)
- carabid beetles (1)
- carbon dioxide (1)
- cell growth (1)
- cell wall synthesis (1)
- cellular neuroscience (1)
- cellular waveform (1)
- ceramides (1)
- chemical communication (1)
- chemical ecology (1)
- chemotherapy (1)
- chlamydia (1)
- chlamydia serine proteases (1)
- chlamydial inclusion (1)
- circadian clocks (1)
- circadian rhythm (1)
- climate change (1)
- climate control (1)
- climate-change (1)
- cognition (1)
- cohesin (1)
- colon cancer (1)
- coloration (1)
- computational modelling (1)
- conditional sex allocation (1)
- conditioned response (1)
- conjugative transposition (1)
- correlative methods (1)
- crop (1)
- crop diversity (1)
- cryptochrome (1)
- crystallography (1)
- cylic GMP (1)
- dMyc (1)
- dSTORM (1)
- dead tree (1)
- deadwood (1)
- defense (1)
- diet (1)
- dispersal (1)
- dmP53 (1)
- dog microbiome (1)
- drug design (1)
- ecological intensification (1)
- ecology (1)
- ecosystem services (1)
- emergence (1)
- endophytic fungi (1)
- endophytische Pilze (1)
- endoreplication (1)
- erythrocyte adherence (1)
- evolutionary genetics (1)
- exaptation (1)
- experimental evolution (1)
- feral honey bees (1)
- flagellate (1)
- fluorescence (1)
- flupyradifurone (1)
- flytrap (1)
- foliar fungal community (1)
- free energy (1)
- fungal biology (1)
- fungal endophytes (1)
- fungal rhodopsins (1)
- fungus-farming insects (1)
- fungus-plant interaction (1)
- gametogenesis (1)
- gene transfer (1)
- genome evolution (1)
- green light perception (1)
- ground dwelling predators (1)
- guanylyl cyclase-A (1)
- habitat requirements (1)
- habitat suitability model (HSM) (1)
- haematopoietic stem cells (1)
- hibernation (1)
- hollow tree (1)
- honey bees (1)
- host screening (1)
- human microbiome (1)
- hypothalamus (1)
- imaging and sensing (1)
- indole-3-acetic acid (IAA) (1)
- infection (1)
- inflammation mediators (1)
- insect vision (1)
- insect-fungus mutualism (1)
- insecticides (1)
- insertion-site deep sequencing (1)
- insulin (1)
- inventory (1)
- ion channels in the nervous system (1)
- ionizing radiation (1)
- jasmonate (1)
- ketogenic diet (1)
- ketone bodies (1)
- landscape heterogeneity (1)
- laparoscopic right colectomy (1)
- leaf-cutting ants (1)
- localization microscopy (1)
- lymph nodes (1)
- mRNA (1)
- machine learning (1)
- macrophages immunobiology (1)
- marine biology (1)
- mass spectrometry (1)
- master sex-determining gene (1)
- mate recognition (1)
- medaka (1)
- meiosis (1)
- mesenchymal stem cells (1)
- metabolic pathways (1)
- metabolic profile (1)
- metabolism (1)
- metagenomics (1)
- miR-146a (1)
- miR-193a (1)
- microRNA (1)
- microbial ecology (1)
- microbiome (1)
- microbot (1)
- microenvironment (1)
- microscopy (1)
- microswimmer (1)
- mitigation strategies (1)
- mixed hearing loss (1)
- molecular docking (1)
- molecular dynamics (1)
- motility (1)
- mouse microbiome (1)
- multidrug-resistant bacteria (1)
- mutualism (1)
- natriuretic peptides (1)
- nest climate (1)
- neural circuits (1)
- neuropeptide (1)
- neurotransmitters (1)
- neutral sphingomyelinase 2 (1)
- nutrients (1)
- obesity (1)
- olfaction (1)
- oncogenesis (1)
- optogenetics (1)
- ovary (1)
- pacemaker neuron (1)
- paediatric cancer (1)
- parasite (1)
- patch-clamp (1)
- pathogen vector (1)
- pathogens (1)
- pea aphid (1)
- peptidase inhibitor PI15 (1)
- peripheral nervous system (1)
- pesticide (1)
- pharmacology (1)
- phenological response (1)
- phenological shift (1)
- photoreceptor (1)
- phototransduction (1)
- phylogenomics (1)
- pig microbiome (1)
- pigment pattern (1)
- pigment-dispersing factor (1)
- plant-insect-microbe interactions (1)
- polarization (1)
- pollen (1)
- pollination (1)
- pollinator interactions (1)
- potassium (1)
- predictive markers (1)
- prezygotic reproductive isolation (1)
- radiation response (1)
- ras (1)
- rat hippocampal neurons (1)
- research software (1)
- rice–plant infection (1)
- salivary gland (1)
- sampling method (1)
- seahorse (1)
- secretion (1)
- senescence (1)
- sensory cues (1)
- sex chromosomes (1)
- sex differentiation (1)
- sexual conflict (1)
- sexually antagonistic genes (1)
- simulation (1)
- snags (1)
- social bees (1)
- speciation (1)
- species interactions (1)
- species richness (1)
- spectral sensitivity (1)
- spiders (1)
- standing deadwood (1)
- staphylinid beetles (1)
- structure-activity relationship (1)
- study system (1)
- swarming (1)
- synapse (1)
- synaptic development (1)
- synaptic proteins (1)
- synaptic vesicles (1)
- taste (1)
- teleost fish (1)
- temperate zones (1)
- temporal organization (1)
- testis (1)
- the microtubule-organizing center (1)
- three-toed woodpecker (Picoides tridactylus) (1)
- timing (1)
- transcriptional rewiring (1)
- transcriptome (1)
- translational research (1)
- tree cavity (1)
- trypanobot (1)
- trypanosoma (1)
- tsetse (1)
- tumor (1)
- two-color microscopy (1)
- tyrosine recombinase (1)
- ubiquitin (1)
- vancomycin (1)
- varroa (1)
- venus (1)
- viruses (1)
- visual pigments (1)
- waggle dance (1)
- water microbiology (1)
- whole exome sequencing (1)
- wild bees (1)
- wild honey bees (1)
- zebrafish (1)
- zeitgeber (1)
- zeitliche Organisation (1)
- β-Hydroxybutyrate (1)
- β-cells (1)
- β3 adrenergic receptor (ADRB3) (1)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (84) (remove)
Sonstige beteiligte Institutionen
ResearcherID
- J-8841-2015 (1)
Genetic foundation of unrivaled survival strategies - Of water bears and carnivorous plants -
(2018)
All living organisms leverage mechanisms and response systems to optimize reproduction, defense, survival, and competitiveness within their natural habitat. Evolutionary theories such as the universal adaptive strategy theory (UAST) developed by John Philip Grime (1979) attempt to describe how these systems are limited by the trade-off between growth, maintenance and regeneration; known as the universal three-way trade-off. Grime introduced three adaptive strategies that enable organisms to coop with either high or low intensities of stress (e.g., nutrient deficiency) and environmental disturbance (e.g., seasons). The competitor is able to outcompete other organisms by efficiently tapping available resources in environments of low intensity stress and disturbance (e.g., rapid growers). A ruderal specism is able to rapidly complete the life cycle especially during high intensity disturbance and low intensity stress (e.g., annual colonizers). The stress tolerator is able to respond to high intensity stress with physiological variability but is limited to low intensity disturbance environments. Carnivorous plants like D. muscipula and tardigrades like M. tardigradum are two extreme examples for such stress tolerators. D. muscipula traps insects in its native habitat (green swamps in North and South Carolina) with specialized leaves and thereby is able to tolerate nutrient deficient soils. M. tardigradum on the other side, is able to escape desiccation of its terrestrial habitat like mosses and lichens which are usually covered by a water film but regularly fall completely dry. The stress tolerance of the two species is the central study object of this thesis. In both cases, high througput sequencing data and methods were used to test for transcriptomic (D. muscipula) or genomic adaptations (M. tardigradum) which underly the stress tolerance. A new hardware resource including computing cluster and high availability storage system was implemented in the first months of the thesis work to effectively analyze the vast amounts of data generated for both projects. Side-by-side, the data management resource TBro [14] was established together with students to intuitively approach complex biological questions and enhance collaboration between researchers of several different disciplines. Thereafter, the unique trapping abilities of D. muscipula were studied using a whole transcriptome approach. Prey-dependent changes of the transcriptional landscape as well as individual tissue-specific aspects of the whole plant were studied. The analysis revealed that non-stimulated traps of D. muscipula exhibit the expected hallmarks of any typical leaf but operates evolutionary conserved stress-related pathways including defense-associated responses when digesting prey. An integrative approach, combining proteome and transcriptome data further enabled the detailed description of the digestive cocktail and the potential nutrient uptake machinery of the plant. The published work [25] as well as a accompanying video material (https://www.eurekalert.org/pub_releases/ 2016-05/cshl-fgr042816.php; Video credit: Sönke Scherzer) gained global press coverage and successfully underlined the advantages of D. muscipula as experimental system to understand the carnivorous syndrome. The analysis of the peculiar stress tolerance of M. tardigradum during cryptobiosis was carried out using a genomic approach. First, the genome size of M. tardigradum was estimated, the genome sequenced, assembled and annotated. The first draft of M. tardigradum and the workflow used to established its genome draft helped scrutinizing the first ever released tardigrade genome (Hypsibius dujardini) and demonstrated how (bacterial) contamination can influence whole genome analysis efforts [27]. Finally, the
M. tardigradum genome was compared to two other tardigrades and all species present in the current release of the Ensembl Metazoa database. The analysis revealed that tardigrade genomes are not that different from those of other Ecdysozoa. The availability of the three genomes allowed the delineation of their phylogenetic position within the Ecdysozoa and placed them as sister taxa to the nematodes. Thereby, the comparative analysis helped to identify evolutionary trends within this metazoan lineage. Surprisingly, the analysis did not reveal general mechanisms (shared by all available tardigrade genomes) behind the arguably most peculiar feature of tardigrades; their enormous stress tolerance. The lack of molecular evidence for individual tardigrade species (e.g., gene expression data for M. tardigradum) and the non-existence of a universal experimental framework which enables hypothesis testing withing the whole phylum Tardigrada, made it nearly impossible to link footprints of genomic adaptations to the unusual physiological capabilities. Nevertheless, the (comparative) genomic framework established during this project will help to understand how evolution tinkered, rewired and modified existing molecular systems to shape the remarkable phenotypic features of tardigrades.
Staphylococcus aureus asymptomatically colonises one third of the healthy human population, finding its niche in the nose and on skin. Apart from being a commensal, it is also an important opportunistic human pathogen capable of destructing tissue, invading host cells and killing them from within. This eventually contributes to severe hospital- and community-acquired infections. Methicillin-resistant Staphylococcus aureus (MRSA), resistant to commonly used antibiotics are protected when residing within the host cell.
This doctoral thesis is focused on the investigation of staphylococcal factors governing intracellular virulence and subsequent host cell death. To initiate an unbiased approach to conduct this study, complex S. aureus mutant pools were generated using transposon insertional mutagenesis. Genome-wide infection screens were performed using these S. aureus transposon mutant pools in vitro and in vivo, followed by analysis using Transposon insertion site deep sequencing (Tn-seq) technology.
Amongst several other factors, this study identified a novel regulatory system in S. aureus that controls pathogen-induced host cytotoxicity and intra-host survival. The primary components of this system are an AraC-family transcription regulator called Repressor of surface proteins (Rsp) and a virulence associated non-coding RNA, SSR42. Mutants within rsp exhibit enhanced intra-host survival in human epithelial cells and delayed host cytotoxicity. Global gene-expression profiling by RNA-seq demonstrated that Rsp controls the expression of SSR42, several cytotoxins and other bacterial factors directed against the host immune system. Rsp enhances S. aureus toxin response when triggered by hydrogen peroxide, an antimicrobial substance employed by neutrophils to destroy pathogens. Absence of rsp reduces S. aureus-induced neutrophil damage and early lethality during mouse pneumonia, but still permits blood stream infection. Intriguingly, S. aureus lacking rsp exhibited enhanced survival in human macrophages, which hints towards a Trojan horse-like phenomenon and could facilitate dissemination within the host.
Hence, Rsp emerged as a global regulator of bacterial virulence, which has an impact on disease progression with prolonged intra-cellular survival, delayed-lethality but allows disseminated manifestation of disease. Moreover, this study exemplifies the use of genome-wide approaches as useful resources for identifying bacterial factors and deduction of its pathogenesis.
Neuropeptides and peptide hormones carrying neural or physiological information are intercellular signalling substances. They control most if not all biological processes in vertebrates and invertebrates by acting on specific receptors on the target cell. In mammals, many different neuropeptides and peptide hormones are involved in the regulation of feeding and sleep. In \textit{Drosophila}, allatostatin A (AstA) and myoinhibitory peptides (MIPs) are brain-gut peptides. The AstA receptors are homologues of the mammalian galanin receptors and the amino acid sequences of MIPs are similar to a part of galanin, which has an orexigenic effect and is implicated in the control of sleep behaviour in mammals. I am interested in dissecting pleiotropic functions of AstA and MIPs in the regulation of food intake and sleep in \textit{Drosophila}. \par
In the first part of the dissertation the roles of brain-gut peptide allatostatin A are analysed. Due to the genetic and molecular tools available, the fruit fly \textit{Drosophila melanogaster} is chosen to investigate functions of AstA. The aims in this part are to identify pleiotropic functions of AstA and assign specific effects to the activity of certain subsets of AstA expressing cells in \textit{Drosophila} adults. A new and restricted \textit{AstA\textsuperscript{34}-Gal4} line was generated. The confocal imaging result showed that AstA neurons are located in the posterior lateral protocerebrum (PLP), the gnathal ganglia (GNG), the medullae, and thoracic-abdominal ganglion (TAG). AstA producing DLAa neurons in the TAG innervate hindgut and the poterior part of midgut. In addition, AstA are detected in the enteroendocrine cells (EECs).\par
Thermogenetic activation and neurogenetic silencing tools with the aid of the \textit{UAS/Gal4} system were employed to manipulate the activity of all or individual subsets of AstA cells and investigate the effects on food intake, locomotor activity and sleep. Our experimental results showed that thermogenetic activation of two pairs of PLP neurons and/or AstA expressing EECs reduced food intake, which can be traced to AstA signalling by using \textit{AstA} mutants. In the locomotor activity, thermogenetic activation of two pairs of PLP neurons and/or AstA expressing EECs resulted in strongly inhibited locomotor activity and promoted sleep without sexual difference, which was most apparent during the morning and evening activity peaks. The experimental and control flies were not impaired in climbing ability. In contrast, conditional silencing of the PLP neurons and/or AstA expressing EECs reduced sleep specifically in the siesta. The arousal experiment was employed to test for the sleep intensity. Thermogenetically activated flies walked significantly slower and a shorter distance than controls for all arousal stimulus intensities. Furthermore, PDF receptor was detected in the PLP neurons and the PLP neurons reacted with an intracellular increase of cAMP upon PDF, only when PDF receptor was present. Constitutive activation of AstA cells by tethered PDF increased sleep and thermogenetic activation of the PDF producing sLNvs promoted sleep specifically in the morning and evening. \par
The study shows that the PLP neurons and/or EECs vis AstA signalling subserve an anorexigenic and sleep-regulating function in \textit{Drosophila}. The PLP neurons arborise in the posterior superior protocerebrum, where the sleep relevant dopaminergic neurons are located, and EECs extend themselves to reach the gut lumen. Thus, the PLP neurons are well positioned to regulate sleep and EECs potentially modulate feeding and possibly locomotor activity and sleep during sending the nutritional information from the gut to the brain. The results of imaging, activation of the PDF signalling pathway by tethered PDF and thermoactivation of PDF expressing sLNvs suggest that the PLP neurons are modulated by PDF from sLNv clock neurons and AstA in PLP neurons is the downstream target of the central clock to modulate locomotor activity and sleep. AstA receptors are homologues of galanin receptors and both of them are involved in the regulation of feeding and sleep, which appears to be conserved in evolutionary aspect.\par
In the second part of the dissertation, I analysed the role of myoinhibitory peptides. MIPs are brain-gut peptides in insects and polychaeta. Also in \textit{Drosophila}, MIPs are expressed in the CNS and EECs in the gut. Previous studies have demonstrated the functions of MIPs in the regulation of food intake, gut motility and ecdysis in moths and crickets. Yet, the functions of MIPs in the fruit fly are little known. To dissect effects of MIPs regarding feeding, locomotor activity and sleep in \textit{Drosophila melanogater}, I manipulated the activity of MIP\textsuperscript{WÜ} cells by using newly generated \textit{Mip\textsuperscript{WÜ}-Gal4} lines. Thermogenetical activation or genetical silencing of MIP\textsuperscript{WÜ} celles did not affect feeding behaviour and resulted in changes in the sleep status. \par
My results are in contradiction to a recent research of Min Soohong and colleagues who demonstrated a role of MIPs in the regulation of food intake and body weight in \textit{Drosophila}. They showed that constitutive silencing of MIP\textsuperscript{KR} cells increased food intake and body weight, whereas thermogenetic activation of MIP\textsuperscript{KR} cells decreased food intake and body weight by using \textit{Mip\textsuperscript{KR}-Gal4} driver. Then I repeated the experiments with the \textit{Mip\textsuperscript{KR}-Gal4} driver, but could not reproduce the results. Interestingly, I just observed the opposite phenotype. When MIP\textsuperscript{KR} cells were silenced by expressing UAS-tetanus toxin (\textit{UAS-TNT}), the \textit{Mip\textsuperscript{KR}$>$TNT} flies showed reduced food intake. The thermogenetic activation of MIP\textsuperscript{KR} cells did not affect food intake. Furthermore, I observed that the thermogenetic activation of MIP\textsuperscript{KR} cells strongly reduced the sleep duration.\par
In the third part of the dissertation, I adapted and improved a method for metabolic labelling for \textit{Drosophila} peptides to quantify the relative amount of peptides and the released peptides by mass spectrometry under different physiological and behavioural conditions. qRT-PCR is a practical technique to measure the transcription and the corresponding mRNA level of a given peptide. However, this is not the only way to measure the translation and production of peptides. Although the amount of peptides can be quantified by mass spectrometry, it is not possible to distinguish between peptides stored in vesicles and released peptides in CNS extracts. I construct an approach to assess the released peptides, which can be calculated by comparing the relative amount of peptides between two timepoints in combination with the mRNA levels which can be used as semiquantitative proxy reflecting the production of peptides during this period. \par
After optimizing the protocol for metabolic labelling, I carried out a quantitative analysis of peptides before and after eclosion as a test. I was able to show that the EH- and SIFa-related peptides were strongly reduced after eclosion. This is in line with the known function and release of EH during eclosion. Since this test was positive, I next used the metabolic labelling in \textit{Drosophila} adult, which were either fed \textit{ad libitum} or starved for 24 hrs, and analysed the effects on the amount of AstA and MIPs. In the mRNA level, my results showed that in the brain \textit{AstA} mRNA level in the 24 hrs starved flies was increased compared to in the \textit{ad libitum} fed flies, whereas in the gut the \textit{AstA} mRNA level was decreased. Starvation induced the reduction of \textit{Mip} mRNA level in the brain and gut. Unfortunately, due to technical problems I was unable to analyse the metabolic labelled peptides during the course of this thesis.\par
N-MYC is a member of the human MYC proto-oncogene family, which comprises three transcription factors (C-, N- and L-MYC) that function in multiple biological processes. Deregulated expression of MYC proteins is linked to tumour initiation, maintenance and progression. For example, a large fraction of neuroblastoma displays high N-MYC levels due to an amplification of the N-MYC encoding gene. MYCN-amplified neuroblastoma depend on high N-MYC protein levels, which are maintained by Aurora-A kinase. Aurora-A interaction with N-MYC interferes with degradation of N-MYC via the E3 ubiquitin ligase SCFFBXW7. However, the underlying mechanism of Aurora-A-mediated stabilisation of N-MYC remains to be elucidated.
To identify novel N-MYC interacting proteins, which could be involved in N-MYC stabilisation by Aurora-A, a proteomic analysis of purified N-MYC protein complexes was conducted. Since two alanine mutations in MBI of N-MYC, T58A and S62A (N-MYC mut), disable Aurora-A-mediated stabilisation of N-MYC, N-MYC protein complexes from cells expressing either N-MYC wt or mut were analysed. Proteomic analysis revealed that N-MYC interacts with two deubiquitinating enzymes, USP7 and USP11, which catalyse the removal of ubiquitin chains from target proteins, preventing recognition by the proteasome and subsequent degradation. Although N-MYC interaction with USP7 and USP11 was confirmed in subsequent immunoprecipitation experiments, neither USP7, nor USP11 was shown to be involved in the regulation of N-MYC stability. Besides USP7/11, proteomic analyses identified numerous additional N-MYC interacting proteins that were not described to interact with MYC transcription factors previously. Interestingly, many of the identified N-MYC interaction partners displayed a preference for the interaction with N-MYC wt, suggesting a MBI-dependent interaction. Among these were several proteins, which are involved in three-dimensional organisation of chromatin domains and transcriptional elongation by POL II. Not only the interaction of N-MYC with proteins functioning in elongation, such as the DSIF component SPT5 and the PAF1C components CDC73 and CTR9, was validated in immunoprecipitation experiments, but also with the POL III transcription factor TFIIIC and topoisomerases TOP2A/B. ChIP-sequencing analysis of N-MYC and TFIIIC subunit 5 (TFIIIC5) revealed a large number of joint binding sites in POL II promoters and intergenic regions, which are characterised by the presence of a specific motif that is highly similar to the CTCF motif. Additionally, N-MYC was shown to interact with the ring-shaped cohesin complex that is known to bind to CTCF motifs and to assist the insulator protein CTCF. Importantly, individual ChIP experiments demonstrated that N-MYC, TFIIIC5 and cohesin subunit RAD21 occupy joint binding sites comprising a CTCF motif.
Collectively, the results indicate that N-MYC functions in two biological processes that have not been linked to MYC biology previously. Furthermore, the identification of joint binding sites of N-MYC, TFIIIC and cohesin and the confirmation of their interaction with each other suggests a novel function of MYC transcription factors in three-dimensional organisation of chromatin.
New experimental methods have drastically accelerated the pace and quantity at which biological data is generated. High-throughput DNA sequencing is one of the pivotal new technologies. It offers a number of novel applications in various fields of biology, including ecology, evolution, and genomics. However, together with those opportunities many new challenges arise. Specialized algorithms and software are required to cope with the amount of data, often requiring substantial training in bioinformatic methods. Another way to make those data accessible to non-bioinformaticians is the development of programs with intuitive user interfaces.
In my thesis I developed analyses and programs to tackle current problems with high-throughput data in biology. In the field of ecology this covers the establishment of the bioinformatic workflow for pollen DNA meta-barcoding. Furthermore, I developed an application that facilitates the analysis of ecological communities in the context of their traits. Information from multiple public databases have been aggregated and can now be mapped automatically to existing community tables for interactive inspection. In evolution the new data are used to reconstruct phylogenetic trees from multiple genes. I developed the tool bcgTree to automate this process for bacteria. Many plant genomes have been sequenced in current years. Sequencing reads of those projects also contain data from the chloroplasts. The tool chloroExtractor supports the targeted extraction and analysis of the chloroplast genome. To compare the structure of multiple genomes specialized software is required for calculation and visualization of the relationships. I developed AliTV to address this. In contrast to existing programs for this task it allows interactive adjustments of produced graphics. Thus, facilitating the discovery of biologically relevant information. Another application I developed helps to analyze transcriptomes even if no reference genome is present. This is achieved by aggregating the different pieces of information, like functional annotation and expression level, for each transcript in a web platform. Scientists can then search, filter, subset, and visualize the transcriptome.
Together the methods and tools expedite insights into biological systems that were not possible before.
The sequencing of several ant genomes within the last six years open new research avenues for understanding not only the genetic basis of social species but also the complex systems such as immune responses in general. Similar to other social insects, ants live in cooperative colonies, often in high densities and with genetically identical or closely related individuals. The contact behaviours and crowd living conditions allow the disease to spread rapidly through colonies. Nevertheless, ants can efficiently combat infections by using diverse and effective immune mechanisms. However, the components of the immune system of carpenter ant Camponotus floridanus and also the factors in bacteria that facilitate infection are not well understood.
To form a better view of the immune repository and study the C. floridanus immune responses against the bacteria, experimental data from Illumina sequencing and mass-spectrometry (MS) data of haemolymph in normal and infectious conditions were analysed and integrated with the several bioinformatics approaches. Briefly, the tasks were accomplished in three levels. First, the C. floridanus genome was re-annotated for the improvement of the existing annotation using the computational methods and transcriptomics data. Using the homology based methods, the extensive survey of literature, and mRNA expression profiles, the immune repository of C. floridanus were established. Second, large-scale protein-protein interactions (PPIs) and signalling network of C. floridanus were reconstructed and analysed and further the infection induced functional modules in the networks were detected by mapping of the expression data over the networks. In addition, the interactions of the immune components with the bacteria were identified by reconstructing inter-species PPIs networks and the interactions were validated by literature. Third, the stage-specific MS data of larvae and worker ants were analysed and the differences in the immune response were reported.
Concisely, all the three omics levels resulted to multiple findings, for instance, re-annotation and transcriptome profiling resulted in the overall improvement of structural and functional annotation and detection of alternative splicing events, network analysis revealed the differentially expressed topologically important proteins and the active functional modules, MS data analysis revealed the stage specific differences in C. floridanus immune responses against bacterial pathogens.
Taken together, starting from re-annotation of C. floridanus genome, this thesis provides a transcriptome and proteome level characterization of ant C. floridanus, particularly focusing on the immune system responses to pathogenic bacteria from a biological and a bioinformatics point of view. This work can serve as a model for the integration of omics data focusing on the immuno-transcriptome of insects.