published_or_final_version / Biochemistry / Master / Master of Philosophy

published_or_final_version / Biochemistry / Doctoral / Doctor of Philosophy

Η αποικοδόμηση των ενδοκυτταρικών πρωτεϊνών μέσω του μονοπατιού ουβικιτίνης-πρωτεοσώματος αποτελεί βασική διαδικασία που εξυπηρετεί σημαντικές ομοιοστατικές λειτουργίες του κυττάρου. Η ουβικιτίνη δεσμεύεται ομοιοπολικά στις πρωτεΐνες-στόχους μέσω ενός καταρράκτη ενζυμικών αντιδράσεων, στον οποίο καθοριστικό ρόλο παίζουν τα Ε3 ένζυμα, οι Ε3 λιγάσες ουβικιτίνης. Η πρωτεΐνη Arkadia είναι μια Ε3 λιγάση με έναν χαρακτηριστικό RING τομέα 69 αμινοξικών καταλοίπων στο C-τελικό άκρο της, μέσω του οποίου ασκεί την δράση της. Εμπλέκεται στο TGF-β σηματοδοτικό μονοπάτι το οποίο ρυθμίζει θετικά, ουβικιτινιλιώνοντας και στοχεύοντας για αποικοδόμηση πρωτεΐνες που αποτελούν αρνητικούς ρυθμιστές του. Κύριο χαρακτηριστικό του RING τομέα της Arkadia, ο οποίος έχει μελετηθεί και χαρακτηριστεί δομικά μέσω πολυπυρηνικής και πολυδιάστατης NMR φασματοσκοπίας, είναι η δέσμευση δύο ιόντων Zn2+ με χαρακτηριστικό διασταυρώμενο τρόπο (cross brace). Γνωρίζοντας τον πολύ σημαντικό ρόλο του Zn στην δομή και κατ’επέκταση στην δραστικότητα των RING τομέων, πραγματοποιήθηκαν μεταλλάξεις σε δύο αμινοξέα που συμμετέχουν στα μοτίβα δέσμευσης των δύο ιόντων Zn2+, οι H962C και H965C. Το μετάλλαγμα της H962C, στο οποίο εστιάζει η παρούσα εργασία, παρήχθη με βάση τις κλασσικές τεχνικές κλωνοποίησης DNA. Κατάλληλα δείγματα πρωτεΐνης εμπλουτισμένα σε πυρήνες ενεργούς στην φασματοσκοπία NMR, 15N και 13C, προετοιμάστηκαν ώστε να διεξαχθούν τα απαραίτητα πειράματα για τον προσδιορισμό της δομής. Το σύνολο των NMR φασμάτων απέδειξε ότι πρόκειται για ένα καλά δομημένο και σταθερό πολυπεπτίδιο. Τα δεδομένα από τις μετρήσεις ατομικής απορρόφησης και την επεξεργασία των φασμάτων επιβεβαίωσαν την διατήρηση της δέσμευσης δύο ιόντων Zn2+ ανά πολυπεπτίδιο, όπως στον RING τομέα του φυσικού τύπου της Arkadia. Ταυτόχρονα, πραγματοποιούνται περαιτέρω NMR μελέτες και αναλύσεις των φασμάτων με χρήση των κατάλληλων υπολογιστικών προγραμμάτων για την διερεύνηση της δομής και ικανότητας αλληλεπίδρασης με το Ε2 ένζυμο. / The degradation of the intracellular proteins through the ubiquitin-proteasome pathway is a crucial procedure that serves the cellular homeostasis. Ubiquitin is covalently attached to the target proteins through an enzymatic cascade, in which the E3 enzymes (E3 ubiquitin ligases) play a determinant role. Arkadia is an E3 ubiquitin ligase containing a characteristic RING domain in its C-terminus, comprised of 69 amino acids, which is responsible for its function. It is involved in TFG-β signaling pathway, where it ubiquitinates and subsequently leads negative regulators to proteasomal degradation. The most important characteristic of Arkadia’s RING domain, which has been studied and structurally characterized through multinuclear and multidimensional NMR spectroscopy, is that it bounds to zinc ions in a cross-brace manner. As the role of the zinc binding is critical for the structure and subsequently the activity of RING domains, His962 and His965, which participate in the zinc binding motifs, were mutated to cysteines. The Arkadia H962C mutant, on which the present work is focused, was produced through the classical techniques of DNA cloning. Protein samples were uniformly labeled in 15N and 13C nuclei in order for all the necessary NMR experiments to be carried out. The total of the NMR spectra demonstrated that Arkadia RING mutant H962C is a well structured and stable polypeptide. Furthermore, the information that came from the atomic absorption data and the analysis of the NMR spectra confirmed that the RING mutant maintains the RING wild type ability to bind two zinc ions. At the same time, further NMR studies are being carried out in order to investigate its structure and ability to interact with the E2 enzyme.

No description available.

The aim of this study was to describe how elderly’s sexuality can be expressed and to describe factors that affect older people's sexuality. The aim was also to describe the opportunities and barriers to health care providers to promote older people's sexuality and to describe the articles quality based on the methodological aspect of selection. A literature review with a descriptive approach was conducted on four qualitative and ten quantitative articles. The included articles were published between 2003 and 2013. Databases used for article search was PubMed, Cinahl and PsychInfo with the following keywords: Sexuality, Nurses, Aged, Geriatrics, Attitude Of Health Personnel, Residential Facilities, Quality Of Life, Older Adults. The Main results showed that elderly’s sexuality manifested itself in many different ways. The intimacy was to some extent more important than the actual intercourse. In general, poor health, diagnosed diseases, medical treatments and advanced aged had a negative impact on older people's sexuality. A clear policy with guidelines, education and guidance for staff were alternative ways to promote older people's sexuality. Caregiver’s uncertainty and negative attitude about the management and treatment of older people's sexuality was barriers to promoting older people's sexuality. Finally, inadequate or completely lack of guidance on the subject elderly and sexuality was barriers to promoting elderlies sexuality. Older people's sexuality is expressed highly individual and influenced by individual circumstances and situation. Few studies have been conducted on the subject elderly and sexuality, which is why further research in the area is necessary for further evidence. For proper care to be able to be performed more training and research is required in the subject elderly and sexuality.

Every human being in close contact with his family, friends and society. Ties with these people are based on personal qualities and social habits which have been started since early childhood. The formation of social habits is especially important to children growing in partronage institutions. Social skills are an ability: - to get on well with other people and groups, to make and develop interpersonal ties, to look for compromises, to find the rational ways of solving conflicts; - to learn, to work and create together with the others, to achieve the common goals; - to participate in cultural, civil and political life of the community, to respect democratic principles and values of the society, to take care of the environment. Social upbringing is a process, the aim of which is to form important personal qualities of a child: responsibility, independence, tolerance, dutifulness and others which play a great role in their socialization. Sociological researches and practical works show that inmates of Children‘s Home form poor social skills due to objective and subjective reasons. That is why the expression of social shills in the Children‘s Home was chosen as the object of the research. The main purpose of this work is to give the light to the expression of social skills and possibilities of their formation in the children growing in orphanages. The hypothesis has been confirmed: the formation and development of social skills guarantees further independent life of a child.

Understanding the mechanisms plants utilize for seed storage protein (SSP) synthesis, transport and deposition have the potential rewards of enabling high yields of modified or foreign proteins. Hayashi et al. (1999) indicated that the machinery devoted to the synthesis of protein storage vacuoles in cotyledon cells can be induced in vegetative tissue by the constitutive expression of a pumpkin 2S albumin phosphinothricin-acetyl-transferase gene fusion (pumpkin 2S-PAT) resulting in the biogenesis of precursor-accumulating (PAC) vesicles in Arabidopsis leaves. This discovery was the impetus behind the work described which sought to examine this phenomenon further by ectopically evoking SSP trafficking and vesicle biogenesis machinery in leaves. With the aim of elucidating the mechanisms necessary to evoke PAC vesicle biogenesis, a suite of constructs including the pumpkin 2S-PAT and analogous napin-PAT and napin-GFP variants were synthesized. Analysis of these transgenes in Arabidopsis revealed that the pumpkin 2S albumin has a capacity unique from napin peptides to result in fusion protein accumulation. Further, the truncated pumpkin 2S albumin peptide and the pumpkin 2S albumin C-terminus were found to direct deposition to vesicles; however, the C-terminus alone was not enough to direct deposition to vesicles unless combined with a significantly shortened napin peptide. An increased ER protein throughput was correlated to trafficking of the fusion protein by Golgi-independent mechanisms resulting in stable accumulation of the unprocessed protein whereas less ER throughput indicated passage through the Golgi-dependent pathway resulting in accumulation of a processed variant. At the level of gene expression, as examined by a microarray study, both inducible and constitutive ectopic expression of pumpkin 2S-PAT resulted in substantial perturbations of the endomembrane system affecting protein folding, flowering time and ER-associated biosynthetic functions which indicated that modulation of flowering time and photoperiodism are highly dependent on protein trafficking and vacuolar biogenesis mechanisms and that high ER protein throughput occurs at the expense of biosynthesis and cessation of ER functioning.

The establishment of neuronal polarity constitutes a central phase in neuronal development and synaptogenesis. In my thesis, I study factors that regulate the development of neuronal polarity and its relationship with neurotransmitter receptor expression. For my experiments, I have investigated the development of sensory neurons from neonatal rat nodose ganglia in culture. Sensory neurons have a pseudo-unipolar morphology, do not extend dendrites, and are devoid of synaptic connections on their somata. However, nodose neurons form synapses de novo in cultures, and I show that the neurons have retained the ability to extend dendrites. Extrinsic factors control dendrite extension by these neurons: the ganglionic satellite cells inhibit the growth of dendrites and induce the neurons to develop a unipolar morphology. In the absence of satellite cells, nodose neurons establish a new multipolar morphology and, in response to nerve growth factor (NGF), extend several dendrites. However, brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) do not induce the neurons to extend dendrites, but promote the expression of properties typical of nodose neurons in vivo. / As nodose neurons acquire a new dendrite-axonal polarity in the presence of NGF, they increase the density of functional neuronal nicotinic acetylcholine receptors (nAChRs) on their somato-dendritic domains. To learn more about the relationship between dendrites extension and nAChR gene expression, I have examined the changes in transcript levels of nAChR subunits in neonatal rat sympathetic neurons developing in culture. I show that the developmental pattern of nAChR subunit expression in the cultured neurons follows closely that of sympathetic neurons developing in vivo, with the exception of one specific subunit $ alpha sb7$. I show that the increase in $ alpha sb3$ mRNA levels correlates well with an increase in the density of functional nAChRs on the neurons. In addition, my results suggest that these increases are regulated by mechanisms intrinsic to neonatal sympathetic neurons. On the other hand, the changes in $ alpha sb7$ gene expression, which correlate with changes in $ alpha$-bungarotoxin binding, are activity-dependent and regulated by a calcium/calmodulin-dependent protein kinase pathway. The results presented in this thesis provide insights on how neurons are influenced in their extension of dendrites and how this extension affects neurotransmitter receptor expression.

Programmed Cell death (PCD) is a highly conserved and genetically controlled event that plays important roles in animal development, homeostasis and disease. Our first objective was to discover and characterize new genes involved in PCD. Since many PCD genes are conserved in Drosophila, and steroid-induced PCD of larval salivary glands (SGs) is transcriptionally regulated with features of both apoptosis and autophagy, we used this exceptionally well-suited in vivo system and performed Serial Analysis of Gene Expression (SAGE) in three pre-death stages. SAGE identified 1244 expressed transcripts, including genes involved in autophagy, apoptosis, immunity, cytoskeleton remodeling, and proteolysis. Of the 1244 transcripts, 463 transcripts belonged to knownlpredicted genes and were 5-fold differentially expressed prior to cell death. Next, we investigated the role of differentially expressed genes from SAGE, in cell death or cell survival, by RNA interference (RNAi ) in l(2)mbn haemocyte Drosophila cells. l(2)mbn cells undergo morphological changes in response to ecdysone treatment, and ultimately undergo PCD. We used cell viability, cell morphology, and apoptosis assays to identify the death-related genes and determined their ecdysone dependency and function in cell death regulation. Our RNAi screen identified six new pro-death related genes, including SH3PXJ and Soxl4, and 21 new pro-survival genes including SoxN. Identification of Soxl4 as pro-death and SoxN as pro-survival suggests that these Sox box proteins may have opposing roles in ecdysone-mediated cell death. Our final objective was to elucidate the function of CG409], a Drosophila homologue of human TNF-alpha induced proteins 8 (TNFAIP8) we identified from SAGE. We created loss-of-function and overexpression mutants of CG4091 to study gene function in vivo and employed immunoprecipitation and mass-spectrometry assays to identify proteins interacting with CG409] in vitro. We identified two proteins that are involved in n-fatty acid oxidation and several cytoskeletal proteins as interaction partners. Immunofluorescence based assays in vivo and in vitro revealed that CG409] is necessary for cytoskeletal remodeling. Further, defects in CG4091 expression affect cellular functions such as autophagy and lipid metabolism/trafficking that require an intact cytoskeleton. Together, our studies provided new insights into the molecular mechanisms involved in Drosophila SG cell death.

Candidate virulence genes were sought through the genetic analyses of two strains of Mycobacterium tuberculosis, one virulent, H37Rv, one attenuated, H37Ra. Derived from the same parent, H37, genomic differences between strains were first examined via two-dimensional DNA technologies: two-dimensional bacterial genome display, and bacterial comparative genomic hybridisation. The two-dimensional technologies were optimised for mycobacterial use, but failed to yield reproducible genomic differences between the two strains. Expression differences between strains during their infection of murine bone-marrow-derived macrophages were then assessed using Bacterial Artificial Chromosome Fingerprint Arrays. This technique successfully identified expression differences between intracellular M. tuberculosis H37Ra and H37Rv, and six candidate genes were confirmed via quantitative real-time PCR for their differential expression at 168 hours post-infection. Genes identified to be upregulated in the attenuated H37Ra were frdB, frdC, and frdD. Genes upregulated in the virulent H37Rv were pks2, aceE, and Rv1571. Further qPCR analysis of these genes at 4 and 96h post-infection revealed that the frd operon (encoding for the fumarate reductase enzyme complex or FRD) was expressed at higher levels in the virulent H37Rv at earlier time points while the expression of aceE and pks2 was higher in the virulent strain throughout the course of infection. Assessment of frd transcripts in oxygen-limited cultures of M. tuberculosis H37Ra and H37Rv showed that the attenuated strain displayed a lag in frdA and frdB expression at the onset of culture when compared to microaerophilic cultures of H37Rv and aerated cultures of H37Ra. Furthermore, inhibition of the fumarate reductase complex in intracellular bacteria resulted in a significant reduction of intracellular growth. Microarray technology was also applied in the expression analysis of intracellular bacteria at 168h post-infection. Forty-eight genes were revealed to be differentially expressed between the H37Ra and H37Rv strains, and a subset were further analysed via qPCR to confirm and validate the microarray data. phoP was expressed at a lower level in the attenuated M. tuberculosis H37Ra, whereas members of the phoPR regulon were up-regulated in the virulent H37Rv. Additionally, a group of genes (Rv3616c-Rv3613c) that may associate with the region of difference 1 were also up-regulated in the virulent H37Rv.