Στα πλαίσια αυτής της διδακτορικής εργασίας μελετήθηκαν οι εμπορικά σημαντικότερες περιοχές καλλιέργειας και συγκομιδής οστρακοειδών του Ελλαδικού χώρου. Κατά τη διάρκεια περιόδου 18 μηνών πραγματοποιήθηκε μηνιαία συλλογή δειγμάτων στρειδιών (Οstrea edulis) και μυδιών (Mytilus galloprovincialis), τα οποία συλλέχθηκαν από έξι (6) διαφορετικά σημεία του Ελλαδικού χώρου και αναλύθηκαν για τους εντεροϊούς (EV), τους αδενοϊούς (Adv), τον ιό της ηπατίτιδας Α (HAV), τους ιούς Noro I και II (NLVI και NLVII), για το βακτήριο Ε. coli, καθώς και για σωματικούς κολιφάγους, τους F-sperific RNA βακτηριοφάγους και τους βακτηριοφάγους του Β. fragilis. Επιπλέον αναπτύχθηκαν μέθοδοι τόσο για την ανίχνευση παθογόνων ιών ανθρώπινης προέλευσης στα οστρακοειδή, όσο και για την ανίχνευση των "πιθανών δεικτών" αυτών των ιών. Οι μέθοδοι εξετάστηκαν προκειμένου να αξιολογηθεί η απόδοση καλής ποιότητας από όλα τα εργαστήρια μέσω διεργαστηριακών αναλύσεων. Η μέθοδος που εφαρμόστηκε σε αυτή τη μελέτη για την ανίχνευση των ιών στα οστρακοειδή βασίζεται στην εξαγωγή και την ομογενοποίηση του πεπτικού αδένα με χρήση διαλύματος γλυκίνης, pH 10, απομόνωση των νουκλεϊνικών οξέων και ενίσχυση του γονιδιώματος των ιών που αναλύονται. Για την ανίχνευση του βακτηρίου E. coli χρησιμοποιήθηκε η μέθοδος των πολλαπλών σωλήνων, ενώ για την ανίχνευση των βακτηριοφάγων χρησιμοποιήθηκε η μέθοδος καλλιέργειας διπλοστιβάδας. Για το βακτήριο E. coli, σε σύνολο 138 δειγμάτων, 110 δείγματα (ποσοστό 79,7%) βρέθηκαν να ανήκουν στην κατηγορία Α (MPN/100g σάρκας = <20 έως 220), δηλαδή χαρακτηρίζονται σαν δείγματα χαμηλής μόλυνσης, 25 δείγματα (ποσοστό 18,1%) βρέθηκαν να ανήκουν στην κατηγορία Β (MPN/100g σάρκας = 220 έως 3500), οπότε χαρακτηρίζονται σαν δείγματα μεσαίας μόλυνσης, ακατάλληλα προς κατανάλωση χωρίς να προηγηθεί διαδικασία εξυγίανσης, ενώ μόνο 3 δείγματα (ποσοστό 2,2%) βρέθηκαν να ανήκουν στη κατηγορία C (MPN/100g σάρκας =3500 έως >18000), δηλαδή είναι δείγματα υψηλής μόλυνσης. Οι ιοί που εμφανίζονται με μεγαλύτερη συχνότητα στα οστρακοειδή της Ανατολικής Μεσογείου είναι οι αδενοϊοί (34% των δειγμάτων βρέθηκαν θετικά για τους αδενοϊούς) και ακολουθούν οι εντεροϊοί (16,7% των δειγμάτων βρέθηκαν θετικά για τους εντεροϊούς). Αντίθετα, ο ιός της ηπατίτιδας Α (ποσοστό θετικών δειγμάτων = 4,34%), καθώς και οι ιοί Noro I (ποσοστό θετικών δειγμάτων = 2,1%) και Noro II (ποσοστό θετικών δειγμάτων = 1,47%%) εμφανίζονται σε μικρό ποσοστό δειγμάτων. Τέλος, 80 δείγματα (58%) βρέθηκαν θετικά (παρουσία πλακών βακτηριοφάγων) για τους σωματικούς κολιφάγους, με τον αριθμό των πλακών να κυμαίνεται από 71,4 έως 584800 pfp/100g, 52 δείγματα (37,7%) βρέθηκαν θετικά για τους F-specific RNA βακτηριοφάγους (αριθμός των πλακών από 76,2 έως 17051 p100g) και 33 δείγματα (24%) βρέθηκαν θετικά για τους βακτηριοφάγους του Bacteroides fragilis (αριθμός των πλακών από 194.5 έως 5266,25 pfp/100g). Τόσο για το βακτήριο E. coli όσο και για τους βακτηριοφάγους πραγματοποιήθηκαν διεργαστηριακές αναλύσεις προτύπων, οι οποίες οδήγησαν στο συμπέρασμα ότι οι αντίστοιχες μέθοδοι χαρακτηρίζονται ως αξιόπιστες. Η στατιστική ανάλυση έδειξε ότι το βακτήριο E. coli παρουσιάζει θετική συσχέτιση με τους σωματικούς κολιφάγους, αλλά δεν δείχνει στατιστικά σημαντική συσχέτιση ούτε με τους F-specific RNA βακτηριοφάγους, ούτε με κανέναν από τους ιούς εντερικής προέλευσης. Επίσης, θετική συσχέτιση παρουσίασαν οι αδενοϊοί με τους εντεροϊούς, καθώς και οι σωματικοί κολιφάγοι με τους βακτηριοφάγους του B. fragilis. Η μοναδική συσχέτιση μεταξύ ιών εντερικής προέλευσης και βακτηριοφάγων βρέθηκε για τους αδενοϊούς και τους βακτηριοφάγους του B. fragilis. Εάν αυτό επιβεβαιωθεί σε περαιτέρω μελέτες, τότε η συγκεκριμένη κατηγορία βακτηριοφάγων θα μπορούσε να αποτελέσει έναν καλό δείκτη πρόβλεψης της παρουσίας αδενοϊών σε δείγματα οστρακοειδών. Επιπλέον μελετήθηκε η σχέση που μπορεί να υπάρχει μεταξύ των φυσικοχημικών παραμέτρων και των μικροοργανισμών που εξετάστηκαν. Η επεξεργασία αυτή οδήγησε στο συμπέρασμα ότι το βακτήριο E. coli ανιχνεύεται σε μεγαλύτερα ποσά όταν το διαλυμένο οξυγόνο και η περιεκτικότητα σε άλας του ύδατος είναι αυξημένα. Αντίθετα, αύξηση της θερμοκρασίας οδηγεί σε μείωση της ανίχνευσης του βακτηρίου. Επίσης, η περιεκτικότητα σε άλας φαίνεται να επηρεάζει θετικά και τον ιό της ηπατίτιδας Α, αν και ο μικρός αριθμός θετικών δειγμάτων γι’αυτόν τον ιό δεν μπορεί να επιτρέψει την εξαγωγή ασφαλών συμπερασμάτων. Το pH και το διαλυμένο οξυγόνο των υδάτων οδηγεί σε αύξηση της ανίχνευσης των βακτηριοφάγων του B. fragilis, χωρίς όμως να μπορούμε να ισχυριστούμε ότι κάτι τέτοιο ισχύει, λόγω του μικρού αριθμού θετικών δειγμάτων γι’αυτούς τους βακτηριοφάγους. Τέλος, η αύξηση της θερμοκρασίας των υδάτων φαίνεται να οδηγεί και σε αύξηση της παρουσίας των F-specific RNA βακτηριοφάγων, και το ίδιο παρατηρήθηκε και με την αύξηση του διαλυμένου οξυγόνου στο νερό. Η παρούσα μελέτη αποτελεί την πρώτη διεξοδική έρευνα για την ιογενή κοπρανώδη μόλυνση τον οστρακοειδών στην Ελλάδα. Επιπλέον, αντιπροσωπεύει την πρώτη μελέτη σχετικά με τη αποτελεσματικότητα των οργανισμών - δεικτών ιϊκής μόλυνσης, καθώς και για τη συσχέτιση της μικροβιολογικής επιβάρυνσης των οστρακοειδών με τις φυσικοχημικές παραμέτρους του περιβάλλοντος ύδατος. Η μελέτη κατάλληλων δεικτών που σχετίζονται με την παρουσία εντερικών ιών στα οστρακοειδή οδήγησε σε χρήσιμα συμπεράσματα για τη χρήση της ανίχνευσης των βακτηριοφάγων ως δεικτών ιϊκής μόλυνσης. Εντούτοις, απαιτείται περαιτέρω μελέτη προκειμένου να προσδιοριστεί και η χρήση των βακτηριοφάγων ως δεικτών που θα μαρτυρούν την προέλευση (ανθρώπινη ή ζωική) των εντερικών ιών που ανιχνεύονται στα οστρακοειδή. / In this doctorate investigation, important shellfish growing areas of Greece have been defined and studied. Oysters (Ostrea edulis) and mussels (Mytilus galloprovincialis) were obtained on a monthly basis over an 18 month sampling period. These samples were collected by six (6) different points of Greece and were analyzed for enteroviruses (EV), adenoviruses (Adv), virus of hepatitis A (HAV), Noro viruses I and II (NLVI and NLVII ), bacterium E. coli, as well as for somatic coliphages, F-sperific RNA bacteriophages and bacteriophages of B. fragilis. Moreover, methods were developed for the detection of pathogenic viruses of human origin in the shellfish, as well as for the detection of potential "viral indicators". The methods were examined in order to validate the good quality performance from all the laboratories via interlaboratory analyses. The method that used in this study for the detection of human enteric viruses in the shellfish is based on the export and homogenisation of digestive gland with glycine buffer at pH 10, viral nucleic acid extraction and amplification of the genomes of the analysed human viruses. The procedure applied for detection of E. coli consists on a five tube, three dilution most probable number (MPN) method, while the method for the detection of bacteriophages was the double-agar-layer method. For E. coli analysis, in a total number of 138 samples, 110 samples (79,7%) were found to belong in category A (MPN / 100 g of flesh = < 20 until 220), that it means these samples are characterized as samples of low pollution, 25 samples (18,1%) were found to belong in category B (MPN / 100 g of flesh = 220 until 3500), therefore are characterized as samples of intermediate pollution, inadequate to consumption without precedes process of cleansing, while only 3 samples (2,2%) were found to belong in category C (MPN / 100 g of flesh = 3500 until > 18000), that it means they are samples of high pollution. The viruses that are presented with higher frequency in the shellfish of Eastern Mediterranean are the adenoviruses (34% of samples were found positive for adenoviruses) and follow enteroviruses (16,7% samples they were found positive for enteroviruses). On the contrary, virus of hepatitis A (percentage of positive samples = 4,34%), as well as the Noro I viruses (percentage of positive samples = 2,1%) and Noro II viruses (percentage of positive samples = 1,47%%) are presented in small number of samples. Finally, 80 samples (58%) were found positive (presence of plaques of bacteriophages) for somatic coliphages, with the number of plaques between 71,4 and 584800 pfp / 100 g, 52 samples (37,7%) were found positive for F - specific RNA bacteriophages (number of plaques from 76,2 to 17051 pfp/ 100 g) and 33 samples (24 %) were found positive for the bacteriophages of B. fragilis (number of plaques from 194,5 to 5266,25 pfp / 100 g). Interlaboratory studies involved the testing of reference materials of E. coli and bacteriophages were used as part of the good quality performance assessment program to be applied all over the study, and led to the conclusion that the corresponding methods are characterized by good reliability. According to the statistical analysis of the results, the presence of E. coli seems to be significantly related with the presence of somatic coliphages. However, E. coli do not present significant statistical relation neither with F - specific RNA bacteriophages, nor with all of the viruses of intestinal origin. Also, adenoviruses were significantly related with enteroviruses, as well as somatic coliphages with the bacteriophages of B. fragilis. The unique significant relation between viruses of intestinal origin and bacteriophages was found for the adenoviruses and bacteriophages of B. fragilis. If this is confirmed in further studies, then this category of bacteriophages could constitute a good indicator of forecast of presence adenoviruses in samples of shellfish. Moreover, we studied the relation that can exist between the physic-chemical parameters and the micro-organisms that were examined. This analysis led to the conclusion that E. coli is detected in higher levels when the dissolved oxygen and the salinity of water are increased. On the contrary, increase of temperature leads to reduction of detection of E. coli. Also, the salinity appears to influence positively also virus of hepatitis A, even if the small number of positive samples of this virus cannot allow the export of sure conclusions. The pH and the dissolved oxygen of waters lead to increase of detection of bacteriophages of B. fragilis, but the small number of positive samples for these bacteriophages can’t give safe conclusions. Finally, the increase of temperature of waters appears to lead also to increase of presence of F - specific RNA of bacteriophages, and the same was also observed with the increase of dissolved oxygen in water. This study constitutes the first extensive research for the fecal viral pollution of shellfish in Greece. Moreover, it represents the first study with regard to the effectiveness viral indicators, as well as for the correlation of microbiological parameters of shellfish with the physical-chemical parameters of water. The study of suitable indicators that are related with the presence of enteric viruses in the shellfish led to useful conclusions on the use of detection of bacteriophages as indicators of viral pollution. Nevertheless, further study is required in order to determine also the use of bacteriophages as indicators that will testify the origin (human or animal) of the enteric viruses that are detected in the shellfish.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

This study focuses on the isolation and characterization of bacteria from lignocellulosic biomass obtained from the sediments of the Tyume River in Alice, Eastern Cape and to determine those bacterial isolates with good potential for modification and decomposition of lignocellulosic biomass for industrial application. Several bacterial isolates were recovered and screened for ability to degrade various lignocellulosic materials. Nine of the isolates were positive for lignocellulolytic activity. Four isolates were cellulase positive and six were xylanase positive. Moreover, one isolate (SB1) was positive for both xylanase and cellulase activities and showed the best hydrolysis zone on solid media. This isolate was then chosen as the best and identified molecularly. The 16S rDNA sequence analysis indicated that SB1 was a Bacillus cereus species. Factors affecting the cellulose and xylanase enzyme production by the organisms were studied. The organisms produced the enzymes maximally at earlier hours of incubation (12-30 hr) and optimally at acidic pH (3-5) and at moderate temperatures (35-45ºC). SB1 appears to hold promise in the decomposition of lignocellulosic wastes.

Introdução: Apesar dos avanços nas técnicas de diagnóstico e tratamento, o câncer de próstata avançado ainda é uma condição letal. Terapêuticas mais eficazes são necessárias para reduzir as taxas de morbi-mortalidade associadas à doença. A Proteína-78 regulada pela glicose (GRP78), uma proteína de choque térmico envolvida na apresentação de antígenos, foi recentemente descrita como sendo um possível marcador molecular para o câncer de próstata. Ainda mais, a resposta imune a essa proteína mostrou correlação com o desenvolvimento de doença hormônio-independente e com pior sobrevida para a doença. Objetivos: Neste estudo, avaliou-se a hipótese de que a GRP78 poderia ser usada como marcador molecular em câncer de próstata no desenvolvimento de um sistema de receptor-ligante, através do uso da tecnologia de apresentação de fagos. Casuística e métodos: Inicialmente, foram clonados dois peptídeos que apresentam afinidade à proteína regulada pela GRP78 (os peptídeos WIFPWIQL e WDLAWMFRLPVG) no vetor fUSE5, criando-se fagos com capacidade teórica de ligação à mesma proteína. Posteriormente foi testada a capacidade de ligação desses fagos à GRP78 na membrana de células prostáticas malignas em solução, em xeno-tumores in vivo e em metástases ósseas de câncer de próstata humano. Resultados: Demonstrou-se que ambos os fagos se ligam especificamente à GRP78 in vitro, em comparação à proteínas com seqüência semelhante (proteínas de choque térmico 70 e 90) e não semelhante (albumina sérica bovina). Em seguida, mostrou-se que esses fagos se ligam com afinidade pelo menos 30 vezes maior à células de câncer de próstata que o fago controle, e que os fagos são internalizados por essas células. Posteriormente, mostrou-se que os fagos rastrearam xeno-tumores prostáticos quando injetados in vivo num modelo animal de câncer de próstata. Finalmente, mostrou-se que os fagos ligam-se especificamente à GRP78 expressa em metástases ósseas de adenocarcinoma prostático humano. Conclusões: Os fagos criados apresentam capacidade de ligação específica à GRP78 in vitro, em células em suspensão e in vivo. A estratégia e o sistema de receptor-ligante definidos no presente estudo podem ter implicacões relevantes no desenvolvimento de terapias dirigidas para o tratamento do câncer de próstata. / Introduction: Despite the advances in diagnosis and treatment, advanced prostate cancer remains a lethal condition. Improved methods of therapy are needed to reduce the morbidity and mortality rates associated with this disease. The Glucose-regulated protein-78 (GRP78), a stress-responsive heat-shock protein involved in antigen presentation, was recently described as a possible molecular marker for prostate cancer. Moreover, immune response against this protein was shown to have correlation with the development of androgen-independent prostate cancer and shorter overall survival. Objectives: We hipothesized that GRP78 could be used as a molecular marker for prostate cancer in the development of a receptor-ligand system, by using phage display technology. Patients and methods: We initially cloned two GRP78-targeting peptides (WIFPWIQL and WDLAWMFRLPVG) into a fUSE5-based phage. We then tested binding capacity of the phage to GRP78 in vitro, to GRP78 expressed in intact prostate cancer cell membranes, to a prostate cancer xenograft and to human bone metastases. Results: We showed that both phage created bound specifically to GRP78 in vitro, in comparison to related (Heat-shock proteins 70 and 90) and unrelated control proteins (bovine serum albumin). Next, we showed that these phage bound at least 30 times more to prostate cancer cells than the control phage, and were also internalized into these cells. Both GRP78-binding phage showed a strong homing in vivo to a human prostate cancer xenograft in a mouse model. Finally, we showed that both phage bound specifically to GRP78 expressed in human prostate cancer bone metastases. Conclusions: Both phage are capable of binding specifically to GRP78 in vitro, in the context of intact prostate cancer cells and in vivo. The strategy and the ligand-receptor system we have defined in this study may have relevant implications in the development of targeted therapies for the treatment of prostate cancer.

Introdução: Apesar dos avanços nas técnicas de diagnóstico e tratamento, o câncer de próstata avançado ainda é uma condição letal. Terapêuticas mais eficazes são necessárias para reduzir as taxas de morbi-mortalidade associadas à doença. A Proteína-78 regulada pela glicose (GRP78), uma proteína de choque térmico envolvida na apresentação de antígenos, foi recentemente descrita como sendo um possível marcador molecular para o câncer de próstata. Ainda mais, a resposta imune a essa proteína mostrou correlação com o desenvolvimento de doença hormônio-independente e com pior sobrevida para a doença. Objetivos: Neste estudo, avaliou-se a hipótese de que a GRP78 poderia ser usada como marcador molecular em câncer de próstata no desenvolvimento de um sistema de receptor-ligante, através do uso da tecnologia de apresentação de fagos. Casuística e métodos: Inicialmente, foram clonados dois peptídeos que apresentam afinidade à proteína regulada pela GRP78 (os peptídeos WIFPWIQL e WDLAWMFRLPVG) no vetor fUSE5, criando-se fagos com capacidade teórica de ligação à mesma proteína. Posteriormente foi testada a capacidade de ligação desses fagos à GRP78 na membrana de células prostáticas malignas em solução, em xeno-tumores in vivo e em metástases ósseas de câncer de próstata humano. Resultados: Demonstrou-se que ambos os fagos se ligam especificamente à GRP78 in vitro, em comparação à proteínas com seqüência semelhante (proteínas de choque térmico 70 e 90) e não semelhante (albumina sérica bovina). Em seguida, mostrou-se que esses fagos se ligam com afinidade pelo menos 30 vezes maior à células de câncer de próstata que o fago controle, e que os fagos são internalizados por essas células. Posteriormente, mostrou-se que os fagos rastrearam xeno-tumores prostáticos quando injetados in vivo num modelo animal de câncer de próstata. Finalmente, mostrou-se que os fagos ligam-se especificamente à GRP78 expressa em metástases ósseas de adenocarcinoma prostático humano. Conclusões: Os fagos criados apresentam capacidade de ligação específica à GRP78 in vitro, em células em suspensão e in vivo. A estratégia e o sistema de receptor-ligante definidos no presente estudo podem ter implicacões relevantes no desenvolvimento de terapias dirigidas para o tratamento do câncer de próstata. / Introduction: Despite the advances in diagnosis and treatment, advanced prostate cancer remains a lethal condition. Improved methods of therapy are needed to reduce the morbidity and mortality rates associated with this disease. The Glucose-regulated protein-78 (GRP78), a stress-responsive heat-shock protein involved in antigen presentation, was recently described as a possible molecular marker for prostate cancer. Moreover, immune response against this protein was shown to have correlation with the development of androgen-independent prostate cancer and shorter overall survival. Objectives: We hipothesized that GRP78 could be used as a molecular marker for prostate cancer in the development of a receptor-ligand system, by using phage display technology. Patients and methods: We initially cloned two GRP78-targeting peptides (WIFPWIQL and WDLAWMFRLPVG) into a fUSE5-based phage. We then tested binding capacity of the phage to GRP78 in vitro, to GRP78 expressed in intact prostate cancer cell membranes, to a prostate cancer xenograft and to human bone metastases. Results: We showed that both phage created bound specifically to GRP78 in vitro, in comparison to related (Heat-shock proteins 70 and 90) and unrelated control proteins (bovine serum albumin). Next, we showed that these phage bound at least 30 times more to prostate cancer cells than the control phage, and were also internalized into these cells. Both GRP78-binding phage showed a strong homing in vivo to a human prostate cancer xenograft in a mouse model. Finally, we showed that both phage bound specifically to GRP78 expressed in human prostate cancer bone metastases. Conclusions: Both phage are capable of binding specifically to GRP78 in vitro, in the context of intact prostate cancer cells and in vivo. The strategy and the ligand-receptor system we have defined in this study may have relevant implications in the development of targeted therapies for the treatment of prostate cancer.