Mitochondrial genomes provide a valuable dataset for phylogenetic studies, in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence-based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combine pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts.

7 ABSTRACT Mitochondria of opisthokonts undergo permanent fusion and fission throughout the cell cycle. Keeping these two processes in balance is vital for various aspects of mitochondrial and cellular homeostasis. Both mitochondrial fusion and division mechanisms are controlled by highly conserved dynamin-related GTPases that are present in all kingdoms of life. The aspects of mitochondrial dynamics outside the opisthokonts is, however, almost completely unexplored phenomenon. In our work, we introduced a tool for live imaging of the reduced forms of mitochondria into model organisms Giardia intestinalis and Trichomonas vaginalis, anaerobic protist parasites from the Excavata supergroup of Eukaryotes. Using this technique, we investigated the dynamics of the mitosomes, the simplest forms of mitochondria, of G. intestinalis. The division of mitosomes is restricted to Giardia mitosis and is absolutely synchronized with the process. The synchrony of the nuclear and the mitosomal division persists also during the encystation of the parasite. Surprisingly, the sole dynamin-related protein of the parasite seems not to be involved in mitosomal division. However, throughout the cell cycle mitosomes associate with the...

Oxidative stress is a hallmark of several aging and trauma related neurological disorders, but the precise details of how altered neuronal activity elicits subcellular redox changes have remained difficult to resolve. Current redox sensitive dyes and fluorescent proteins can quantify spatially distinct changes in reactive oxygen species levels, but multicolor probes are needed to accurately analyze compartment-specific redox dynamics in single cells that can be masked by population averaging. Our lab previously engineered a genetically-encoded red-shifted redox-sensitive fluorescent protein sensors using a Förster resonance energy transfer relay strategy. Here, we developed a second-generation excitation ratiometric sensor called rogRFP2 with improved red emission for quantitative live-cell imaging. Using this sensor to measure activity-dependent redox changes in individual cultured neurons, we observed an anticorrelation in which mitochondrial oxidation was accompanied by a concurrent reduction in the cytosol. This behavior was dependent on the activity of Complex I of the mitochondrial electron transport chain and could be modulated by the presence of co-cultured astrocytes. We also demonstrated that the red fluorescent rogRFP2 facilitates ratiometric redox imaging in Drosophila retinas. The proof-of-concept studies reported here demonstrate that this new rogRFP2 redox sensor can be a powerful tool for understanding redox biology both in vitro and in vivo across model organisms. In addition, we have used these tools that monitor cellular redox, to study oxidative stress and ROS changes in Parkinson’s disease models. Here, we have established cellular models for studying Parkinson’s disease causing LRRK2 mutations to create a platform for future work to explore the relationship between PD associated LRRK2 variants and oxidative stress.

No description available.

The lactate level assesment in various body fluids plays an important role in the diagnostics of mitochondrial disorders in children. However, the interpretation of lactate level is often difficult due to its unspecificity and variability even in particular mitochondrial disorders. Three specific aims have been stated in this PhD Thesis: 1. To analyse the role of lactate examination in the differential diagnosis between children with mitochondrial disorders and children with other diseases. 2. To study the lactate level differences in various mitochondrial syndromes. 3. To characterise the clinical and laboratory data of neonates with mitochondrial disorders and to suggest new diagnostic algorhytms. Clinical and laboratory data from patients hospitalized in the Department of Pediatrics were collected. Laboratory methods were provided in the cooperation with the Mitochondrial laboratory of the Department of Pediatrics and Institute of Inherited Metabolic Disorders. The study with lactate levels in 107 patients documented that brief seizures lasting less than 2 minutes did not increase lactate concentration in the CSF. CSF-lactate was a relialable marker in differential diagnosis in the children with mitochondrial disorders against children with epilepsy. 2. The severity of particular phenotype is more...

Polychaetes are among the most abundant and diverse groups in the benthic environment; however, the diversity of marine polychaetes remains underexplored. On coral reef ecosystems, scientists predict 80-90% of species are still undescribed due to low sampling efforts in certain regions and the understudied nature of smaller invertebrates, such as polychaetes. Sabellidae, a prominent family of polychaetes, are known for their widespread distribution and are recognized as an ornamental worm due to their feather-like appendages. Here, we detail the diversity of Sabellidae around the understudied Arabian Peninsula. The Arabian Peninsula is surrounded by diverse marine ecosystems (e.g., coral reefs, seagrass beds) occurring in extreme environmental conditions (e.g., higher seawater temperature and strong seasonal variation). Our samples included 178 sabellids from the Saudi Arabian Red Sea, the Arabian Sea, and the Arabian Gulf. Collected from February 2019 to February 2020, these sabellids were sampled from hard and soft substrate on coral reefs and their associated habitats. We used two molecular markers, the cytochrome c oxidase subunit I (COI) and 16S ribosomal DNA alongside an array of morphological analyses, including widely used characters, meristic counts, and morphometric measurements, to identify seven morphotypes. Environmental and biological information was also recorded to understand more about the ecology of these relatively understudied polychaetes. Our combined morphological and genetic analyses acknowledge the presence of six species from the genera Sabellastarte, Bispira, Branchiomma, and Acromegalomma. Our study identified the existence of potential undescribed species in the region and proposed expanded geographic ranges for three accepted species, Sabellastarte sanctijosephi, Branchiomma luctuosum, and Acromegalomma nechamae. The present work increases the current knowledge about the overall systematics of marine polychaetes in the Arabian Peninsula and ultimately contributes to the reassessment of the family’s biogeography.

>Magister Scientiae - MSc / Silver nanoparticles (AgNPs) apart from being chemically significant, have shown a lot of health benefits, the most studied being their anti-bacterial and anti-inflammatory properties. These biological properties can be further enhanced by adding compounds with known medical properties giving rise to even more desired potent materials. Anti-bacterial and cytotoxicity studies show that these AgNPs can kill bacteria, prevent infections and regenerate skin cells. On the other hand, previous studies have reported dimethyl sulfoxide (DMSO) with attractive wound healing abilities specifically cell growth promotion. It was then envisaged that the combination of DMSO and AgNPs could lead to a potent wound healing agent. It is a well-known fact that non-healing wounds pose a socioeconomic threat to a large population worldwide. / 2023

Cytologic smears of a Warthin's tumor (WT) typically consist of sheets of oncocytic (oxyphilic) cells and scattered lymphocytes. Reparative foci within this neoplasm can occur, which may give rise to exfoliated, malignant‐appearing, squamouslike cells. A false‐positive diagnosis of squamous carcinoma can occur when these atypical cells dominate the cytologic aspirate. Histochemical and immunoperoxidase stains may aid in diagnosing an atypical WT when the usual cytologic features are absent.

Hypoxia-inducible factor- 1α (HIF-1α) is a transcription factor that directs many of the cellular responses to hypoxia. In these studies, we have used a mouse model containing a cardiac-specific, oxygen-stabilized, doxycycline (Dox)-off regulated HIF-1α transgene to probe the role of HIF-1α in cardioprotection. Hearts used in these studies were derived from wild-type (WT), noninduced (Non-I), and 2 day (2D) and 6 day (6D) Dox-deprived mice. Whereas HIF-1α protein is undetectable in WT mice, it is present in heart tissue of "noninduced" transgenic mice, presumably because of leakiness of the promoter construct. In mice denied Dox for 2 or 6 days, HIF-1α is overexpressed to a much greater extent than Non-I or WT animals, as expected. WT and HIF-1α- expressing hearts (Non-I, 2D and 6D induced) were subjected to 30 min of ischemia, and functional recovery was measured upon reperfusion. Recovery of preischemic left ventricular developed pressure was 14% for WT, 67% for Non-I hearts, 64% for 2D-induced, and 62% for 6D-induced hearts. 6D-induced HIF hearts have increased preischemic glycogen reserves, higher glycogen synthase protein levels, and significantly higher lactic acid release during ischemia. 6D-induced HIF hearts were also better able to maintain ATP levels during ischemia compared with WT and Non-I hearts. Interestingly, Non-I hearts showed no significant increase in glycogen reserves, glycolytic flux, or greater ATP preservation during ischemia and yet were protected to a similar extent as the 6D-induced hearts. Finally, the mitochondrial membrane potential of isolated adult myocytes was monitored during anoxia or treatments with cyanide and 2-deoxyglucose. HIF-1α expression was shown to protect mitochondrial polarization during both stress treatments. Taken together these data indicate that, while HIF-1α expression in heart does induce increases in compensatory glycolytic capacity, these changes are not necessarily required for cardioprotection, at least in this model of ischemic stress.

Hypoxia-inducible factor- 1α (HIF-1α) is a transcription factor that directs many of the cellular responses to hypoxia. In these studies, we have used a mouse model containing a cardiac-specific, oxygen-stabilized, doxycycline (Dox)-off regulated HIF-1α transgene to probe the role of HIF-1α in cardioprotection. Hearts used in these studies were derived from wild-type (WT), noninduced (Non-I), and 2 day (2D) and 6 day (6D) Dox-deprived mice. Whereas HIF-1α protein is undetectable in WT mice, it is present in heart tissue of "noninduced" transgenic mice, presumably because of leakiness of the promoter construct. In mice denied Dox for 2 or 6 days, HIF-1α is overexpressed to a much greater extent than Non-I or WT animals, as expected. WT and HIF-1α- expressing hearts (Non-I, 2D and 6D induced) were subjected to 30 min of ischemia, and functional recovery was measured upon reperfusion. Recovery of preischemic left ventricular developed pressure was 14% for WT, 67% for Non-I hearts, 64% for 2D-induced, and 62% for 6D-induced hearts. 6D-induced HIF hearts have increased preischemic glycogen reserves, higher glycogen synthase protein levels, and significantly higher lactic acid release during ischemia. 6D-induced HIF hearts were also better able to maintain ATP levels during ischemia compared with WT and Non-I hearts. Interestingly, Non-I hearts showed no significant increase in glycogen reserves, glycolytic flux, or greater ATP preservation during ischemia and yet were protected to a similar extent as the 6D-induced hearts. Finally, the mitochondrial membrane potential of isolated adult myocytes was monitored during anoxia or treatments with cyanide and 2-deoxyglucose. HIF-1α expression was shown to protect mitochondrial polarization during both stress treatments. Taken together these data indicate that, while HIF-1α expression in heart does induce increases in compensatory glycolytic capacity, these changes are not necessarily required for cardioprotection, at least in this model of ischemic stress.