Après un cycle de la production des protéines, les sous-unités des ribosomes terminés sont dissociés, afin de les rendre disponibles pour de nouveaux cycles de traduction. Si lors de la traduction le ribosome pause, il ne pourra pas terminer la traduction et être recyclé par la voie classique. Un mécanisme de recyclage alternatif a évolué pour dissocier de tels ribosomes arrêtés. Un complexe composé des facteurs Dom34 et Hbs1 induit leur dissociation. Ce complexe est aussi impliqué dans des voies de contrôle qualité qui ciblent des ARN qui causent des arrêts ribosomiques. Dans cette thèse, l'importance de plusieurs sites fonctionnels du complexe Dom34-Hbs1 pour ces voies contrôle qualité des ARNs est étudiée. De plus, la relation entre ces voies et leurs détails sont examiné. Finalement, un nouveau rôle de Dom34-Hbs1, en dissociant des ribosomes inactifs ce qui rend leurs sous-unités disponibles pour de nouveaux cycles de la traduction, est décrit. / Protein production is a cyclic process that consists of four stages: initiation, elongation, termination and recycling. During recycling the subunits of terminated ribosomes are dissociated, to make them available for new rounds of translation. If ribosomes stall during translation, ribosomes cannot terminate properly and canonical recycling cannot occur. Cells have mechanisms to rescue these stalled ribosomes. A complex formed by the factors Dom34 and Hbs1 induces their dissociation. This compex in RNA quality control, targeting RNAs that cause ribosomal stalling. In this thesis the importance of several functional sites of the Dom34-Hbs1 complex for the degradation of these RNA sis investigated. Details of and therelationship between RNA quality control pathways in which the complex functions are further investigated. Finally, a new role of this complex, dissociating inactive ribosomes and there by making their subunits available to re-enter the translation cycle is described.

Les ribosomes sont des macrocomplexes ribonucléoprotéiques sophistiqués, essentiels pour décoder l’information génétique et la traduire en protéines fonctionnelles. Chez les organismes eucaryotes, le ribosome est constitué de deux sous-unités, la petite (40S) et la grande (60S). Leur biogenèse est un processus fondamental, très complexe, qui mène à la synthèse et l’assemblage de 4 ARNr et 80 protéines ribosomiques (79 chez la levure). La biogenèse du ribosome a longtemps été étudiée chez Saccharomyces cerevisiae. Près de 20 ans de recherches ont été nécessaires à la communauté scientifique pour identifier les quelques 200 facteurs de synthèse du ribosome levurien. Alors que le schéma global de cette voie de biosynthèse semble conservé chez les organismes eucaryotes, de nombreux éléments suggèrent qu’elle serait plus élaborée chez l’homme et nécessiterait un plus grand nombre de facteurs que chez la levure. De plus, la caractérisation de nombreuses ribosomopathies, ou maladies du ribosome prédisposant aux cancers, a suscité un intérêt accru pour l’étude de la voie de biosynthèse du ribosome dans le paradigme expérimental le plus approprié, la cellule humaine.<p><p>Au cours de ma thèse de doctorat, j’ai contribué à un projet systématique d’identification de facteurs d’assemblage (FA) du ribosome chez l’homme. Pratiquement, nous avons identifié 286 FA humains, dont beaucoup sont homologues aux facteurs levuriens connus, et 74 sont sans équivalent chez la levure. Par ailleurs, j’ai caractérisé en détail certains facteurs. En particulier, Trm112 pour lequel j’ai montré qu’il agit comme un stabilisateur de la méthyltransférase (MTase) Bud23, spécifique à l’ARNr 18S de la sous-unité levurienne 40S. J’ai également participé à la caractérisation de mutations à l’interface du complexe Bud23-Trm112. Enfin, j’ai contribué à l’étude de trois FA que nous avons identifiés chez l’homme, DIMT1L et WBSCR22-TRMT112. J’ai montré que ces protéines sont les orthologues des MTases levuriennes Dim1 et Bud23-Trm112, qu’elles sont requises pour la synthèse et la modification de l’ARNr mature de la petite sous-unité ribosomique, et qu’elles seraient impliquées dans un mécanisme conservé contrôlant la qualité de la voie de biosynthèse du ribosome.<p><p>La totalité des FA que nous avons identifiés en cellule humaine sont à la disposition de la communauté scientifique dans une base de données en ligne accessible sur la page www.RibosomeSynthesis.com. Nous espérons que cette ressource contribuera à une meilleure compréhension des mécanismes moléculaires sous-jacents au développement des ribosomopathies et à l’élaboration d’agents thérapeutiques efficaces.<p> / Doctorat en sciences, Spécialisation biologie moléculaire / info:eu-repo/semantics/nonPublished

No controle da qualidade da água, parâmetros microbiológicos são avaliados e devem estar de acordo com os limites estipulados em portarias e resoluções. Todas as metodologias de monitoramento microbiano demandam o cultivo dos organismos-alvo. Em muitos casos, as cepas isoladas devem ser analisadas por teses fenotípicos para determinação da espécie. Por meio de inóculos de E. coli, demonstrou-se que a variação na técnica de plaqueamento se deve especialmente à falta de consistência entre as diluições. Além disso, para a análise de réplicas, comarando-se as médias de dois métodos de diluição, foi demonstrado que ser utilizado apenas uma série de diluição derivada de um único inóculo. Utilizando-se culturas puras de E. coli, E. faecalis e P. aeruginosa, a recuperação foi similar entre os meios seletivos respectivos (m-Endo, m-EI, m-PA-C) e meio não seletivo (Tripticase Soy Agar). A utilização da técnica de membrana filtrante resultou em contagens significativamente maiores para E.coli e E. faecalis em comparação ao método de spread plate. A microbiota natural presente na água potável (torneira) não influenciou significativamente as contagens de E. coli, E. faecalis e P. aeruginosa em meios seletivos. Entretanto, na água mineral engarrafada inoculada artificialmente com P. aeruginosa, a contagem foi significativamente maior na réplica estéril. Na análise de água marinha, e na réplica não estéril inoculada com E. faecalis, a contagem foi signifivativamente menor e as células de P. aeruginosa produziram colônias atípicas. Analisando-se amostras do meio ambiente (biofilmes de estação de tratamento de água, lodo de esgoto e água de córrego contaminado), 45 colônias típicas isoladas em meios de cultura seletivos foram identificadas por meio do sequenciamento do gene 16S rRNA, testes bioquímicos e MALDI-TOF. Os resultados de sequenciamento do gene 16SrRNA tiveram baixa correlação com a identificação dos organismos por testes bioquímicos (46,6% em nível de gênero e 20% em nível de espécie) e MALDI-TOF (60% em nível de gênero e 48,8% em nível de espécie). Para as cepas identificadas como E. coli e Enterococcus spp., a correlação entre o sequenciamento e MALDI-TOF foi de 75% e 62%, respectivamente. Uma vez que a quantificação de micro-organismo por membrana filtrante depende do micro-organismo em análise e do tipo de água, é necessário que os laboratórios realizem testes de padronização antes de implementar essa metodologia. Os resultados demonstram que os métodos convencionais utilizados não são adequados e suficientes para a análise da qualidade da água e, portanto, novas metodologias devem ser empregadas. Idealmente devem ser utilizadas técnicas baseadas em características fenotípicas, genômica e proteômica cujos resultados são complementares e fornecem uma identificação mais acurada. / All over the world regulatory agencies specify microbiological water quality parameters to guarantee water safety. Conventional microbiological water quality analysis is based on the cultivation of the target organisms. In many analysis protocols, phenotypic assays of isolated strains are mandated for species determination. Reference samples are required for quality assessment and quality control of analytical protocols. Using E. coli as a model organism, it was demonstrated here that the variability of plate counts of reference cultures is caused mainly by the spread of counts in individual serial dilutions. Besides, comparing the means obtained by two dilution approaches, it was demonstrated that in the analysis of replicates it is possible to use only a set of dilutions derived for a unique inoculum. Recovery of pure cultures of E. coli, E. faecalis and P. aeruginosa was similar on selective culture media (m-Endo, m-EI, m-PA-C) and with the non-selective medium (Tripticase Soy Agar). The membrane filter technique yielded significantly higher counts for E.coli and E. faecalis in comparison to spread plate method. The autochthonous microbiota of potable water (tap water) did not influence the counts of E. coli, E. faecalis and P. aeruginosa on selective culture media. However, the sterile replica of mineral water spiked with P. aeruginosa showed higher counts for these bacteria. For marine water analysis, the non-sterile replica spiked with E. faecalis yielded low counts and P. aeruginosa produced an atypical colony. Both, sample-induced variation in target strain recovery and colony appearance on culture plates indicates the requirement for method evaluation tests on particular sample matrices before implementing routine microbiological analysis by culture-based methods in the laboratory. 45 typical colonies obtained from environmental samples in selective culture media (biofilms from activated sludge, drinking water treatment plants and water from creek contaminated with raw sewage) were analyzed by 16S rRNA gene sequencing, biochemical phenotypic assays and MALDI-TOF. Sequencing showed low correlation with phenotypic assays (46,6% at the genus level and 20% at the species level) and MALDI-TOF (60% at the genus level and 48,8% at the species level). On the other hand, the strains identified as E. coli an Enterococcus spp. by 16S rDNA gene sequencing demonstrated a high correlation with MALDI-TOF (75% and 62%, respectively). Since the results showed that conventional methods aren´t suitable and sufficient to assess water quality, new technologies should be employed. Ideally, techniques should be based on phenotypic, genomic and proteomic features since the results are complementary and provide a more accurate identification.

Microbial enzymes implicated in plant cell hydrolysis may have several potential aplications such as biomass degradation biocatalysts or with biofuel production. Bark beetles establish symbiosis with several microbial strains which play different roles benifitting the beetle, as the production of hydrolytic enzymes to degrade the ingested wood, the protection against mirobial antagonist or the detoxification of the environment. Fungal symbionts have been traditionally the best studied, but several recent research with bacterial symbionts of several bark beetle species show that bacterial also display important functions for the host. In this study, the bacterial communities of the bark beetle species Cryphalus piceae and Pithophtorus pithophtorus, collected in the Czech Republic from pine and fir trees, respectively, were isolated and 55 out of 89 samples were identified by 16S rRNA gene amplification and sequencing. Members of the genera Erwinia, Pantoea, Curtobacterium, Yersinia, Pseudomonas and Staphylococcus were detected. The isolates were object of study for their possible biotechnological potential in (ligno)cellulose materials degradation by screening several enzymes implicated in plant cell hydrolysis, as cellulases, xylanases, amylases, laccases, as well as their capability for colorant...

Lactic acid bacteria were isolated from 10 samples of the traditionally fermented foods (5 samples of Vietnamese fermented pork roll and 5 samples of the salted field cabbage) and 5 samples of fresh cow milks collected from households in Vietnam. 22 strains of lactic acid bacteria were isolated for inhibition to Lactobacillus plantarum JCM 1149. Of these, only 2 strains including DC1.8 and NC1.2 have rod shape, the others have coccus shape. 7 strains showing higher antibacterial activity were selected for checking spectrum of antibacteria with indicator bacteria consistting of Bacillus subtilis ATCC 6633, Enterococcus faecium JCM 5804 and Staphylococcus aureus TLU. By which, 3 strains including NC3.5 (from Vietnamese fermented pork roll), DC1.8 (from salted field cabbage) and MC3.19 (from fresh cow milk) were selected because of their higher antibacterial ability. However, the antibacterial activity of the lactic acid bacteria can be based on their disposable compounds and some other antibacterial compounds produced during their growth (such as lactic acid, H2O2, bacteriocins, etc.). For seeking lactic acid bacteria with capability of producing bacteriocins, antibacterial compounds with protein nature, 3 above strains were checked sensitiveness to proteases (including protease K, papain, α – chymotrypsin and trypsin). Because bacteriocins are proteinaceous antibacterial compounds, so their antibacterial activity will be reduced if proteases are added. The result showed DC1.8 and MC3.19 were capable of producing bacteriocin during culture process. They were identified as Lactobacillus acidophilus and Lactococcus lactis and classified, respectively, based on analysis chemical characterisitcs by standard API 50 CHL kit and phylogeny relationship by 16s rRNA sequences. / Các chủng vi khuẩn lactic được phân lập từ 10 mẫu thực phẩm lên men truyền thống (5 mẫu nem chua, 5 mẫu dưa cải bẹ muối) và 5 mẫu sữa bò tươi được thu thập từ các hộ gia đình ở Việt Nam. 22 chủng vi khuẩn lactic đã được phân lập với tiêu chí có khả năng kháng lại vi khuẩn kiểm định Lactobacillus plantarum JCM 1149. Trong số đó, 2 chủng DC1.8 và NC1.2 có tế bào hình que, các chủng còn lại có tế bào hình cầu. 7 chủng thể hiện hoạt tính kháng khuẩn cao được lựa chọn để xác định phổ kháng khuẩn rộng hơn với ba loài vi khuẩn kiểm định Bacillus subtilis ATCC 6633, Enterococcus faecium JCM 5804 và Staphylococcus aureus TLU. Từ đó lựa chọn được 3 chủng có hoạt tính kháng khuẩn cao hơn hẳn. Các chủng này gồm NC3.5 phân lập từ nem chua, DC1.8 phân lập từ dưa cải bẹ muối và MC3.19 phân lập từ sữa bò tươi. Tuy nhiên, hoạt tính kháng khuẩn của vi khuẩn lactic bao gồm những hợp chất nội tại có trong nó và cả những hợp chất được sinh ra trong quá trình phát triển của nó (như axit lactic, H2O2, bacteriocin, …). Với định hướng tìm chủng vi khuẩn lactic có khả năng sinh bacteriocin, chất kháng khuẩn có bản chất protein, 3 chủng trên được kiểm tra độ nhạy cảm với các protease (gồm protease K, papain, α – chymotrypsin và trypsin). Do bacteriocin là chất kháng khuẩn có bản chất protein nên hoạt tính kháng khuẩn của chúng sẽ bị giảm nếu protease được bổ xung vào. Kết quả lựa chọn được chủng DC1.8 và MC3.19 có khả năng sinh bacteriocin. Hai chủng này được phân loại đến loài nhờ vào phân tích đặc điểm sinh hóa bằng kit API 50 CHL và mối quan hệ di truyền thông qua trình tự gen 16s rRNA. Kết quả phân loại đã xác định chủng DC1.8 thuộc loài Lactobacillus acidophilus và chủng MC3.19 thuộc loài Lactococcus lactis.

Marginale Parodontitis, die multikausale Erkrankung des Parodonts ist eine Infektionskrankheit, modifiziert durch Wirtsfaktoren und äußere Einflüße. Die als pathogene Mischflora bezeichnete Kombination kommensaler Mikroorganismen spielt die primäre Rolle in der Ätiopathogenese der Parodontitis. In der Aufstellung des Studienziels wurden einzelne Bakterienarten (T. forsythensis, P. gingivalis, A. actinomycetemcomitans, C. rectus, F. nucleatum, Fusobacterium spp., P. intermedia, E. corrodens, V. parvula und C. ochracea) ausgewählt, die eventuell als "Markerkeime" in der aggressiven Form der Parodontitis betrachtet werden können. Dazu wurde eine Kontrollgruppe untersucht, die eine gesunde parodontale Flora besitzt. Die angewandte Nachweismethode basiert auf der PCR-Amplifikation von 16S rDNA und darauffolgender dot-blot Hybridisierung mit Oligonukleotidsonden. Die entsprechenden Sonden wurden hergestellt, optimiert und evaluiert. Für die epidemiologische Untersuchung wurde subgingivale Plaque von vier Parodontaltaschen und einer Kontrollstelle von 45 Patienten mit aggressiver Parodontitis, sowie an fünf Stellen von 21 Senioren entnommen. Die Prävalenz der einzelnen Bakterienarten wurde mit Hilfe des Chi-Quadrat Test verglichen. Obgleich eine hohe interindividuelle Variabilität der Kolonisationsmuster zu beobachten war, konnten T. forsythensis, P. gingivalis, C. rectus und F. nucleatum signifikant häufiger in den Parodontaltaschen als an den gesunden Stellen nachgewiesen werden und können deswegen als "Leitkeime" der aggressiven Parodontitis angesehen werden. A. actinomycetemcomitans konnte nur bei einzelnen Patienten mit aggressiver Parodontitis festgestellt werden. Die Ergebnisse für P. intermedia und E. corrodens ließen keine eindeutige Assoziation sowohl mit der aggressiven Parodontitis als auch mit dem gesunden Parodontalzustand zu. Bei Senioren wurde C. ochracea besonders häufig nachgewiesen. Die Ergebnisse dieser Studie bewiesen die erfolgreiche Einsetzbarkeit der hergestellten Oligonukleotidsonden. / A multifactorial risk pattern of periodontitis has been recognized, where in addition to host and environmental factors, a pathogenic microbiota plays a primary role. The purpose of the current research was to analyze the prevalence of periodontitis-associated microorganisms in patients with aggressive periodontitis and periodontally healthy elders by using molecular-biologic detection methods like eubacterial PCR-amplification of 16S rDNA in combination with dot-blot hybridization. The oligonucleotide probes for the detection of T. forsythensis, P. gingivalis, A. actinomycetemcomitans, C. rectus, F. nucleatum, Fusobacterium spp., P. intermedia, E. corrodens, V. parvula and C. ochracea were designed and evaluated. The PCR products of 42 cultivated target and closely related bacteria were used for the optimization of hybridization conditions. For the epidemiological study, subgingival plaque was sampled from four pockets and one healthy site of 45 aggressive periodontitis patients as well as from five sites of 21 elderly. The differences in the prevalence of bacterial species were analyzed by the chi-square test. The data revealed frequent colonization by T. forsythensis, P. gingivalis, F. nucleatum and C. rectus in patients with aggressive periodontitis, however individual variations were obvious. These species could be predominantly identified in periodontal pockets, but were significantly less common in the healthy sites of the periodontitis patients and in the elderly. These putative pathogens can be conclusively determined as the key-bacteria in patients with aggressive periodontitis. No direct association for P. intermedia and E. corrodens with aggressive periodontitis or periodontal health could be seen. A. actinomycetemcomitans could be detected in only a few patients, reducing its suspected importance in the etiology of aggressive periodontitis. C. ochracea was highly prevalent in the well-maintained elderly, suggesting its association with healthy flora. The results of the study confirmed the reliability of the oligonucleotide probes in a specific and sensitive detection of the respective oral species.

Several yeast species had previously been isolated from water systems in the North West Province, South Africa. Some of the identified species had, in other studies, been associated with superficial mucosal infections to life threatening diseases. Antifungal drugs are used to treat such yeast infections. However, due to prophylactic usage and continuous exposure some yeast species have developed resistance to some antifungal agents. The aim of this study was to determine the diversity and antifungal susceptibility of yeasts in selected rivers, Mooi River and Harts River in the North West Province, South Africa. Waters samples were collected from the rivers in summer and winter seasons. Physico-chemical parameters such as pH, temperature, total dissolved solids, chemical oxygen demand, nitrates and phosphates were measured to determine the water quality. Yeast colonies were enumerated at room temperature and 37°C using yeast-malt-extract agar (containing 100 ppm chloramphenicol). Pure isolates from 37°C were identified by biochemical tests and 26S rRNA gene sequencing. Yeast sequences of isolated yeasts were sent to Genbank. Phylogenetic tree was conducted to determine phylogenetic relationship between the yeast isolates. Disk diffusion antifungal susceptibility tests were conducted on the yeast species. Physico-chemical parameters of the water were within target water quality range for livestock farming but in most sampling sites out of range for irrigation use. pH, Nitrates, phosphates and chemical oxygen demand levels ranged from 7.40 to 8.64, 0 to 5.4 mg/L, 0 to 7.14 mg/L and 31 to 43 mg/L, respectively. Elevated levels of total dissolved solids were measured in all the sampling sites. Total yeast counts ranged between 320-4200 cfu/L and 27-2573 cfu/L for room temperature and 37˚C. All the yeast colonies isolated were non-pigmented. Diazonium Blue B tests determined the yeasts isolates as ascomycetes. Haemolysin and extracellular enzyme production tests were negative on all the isolates. Yeasts isolates were identified and belonged to the genera Arxiozyma, Candida, Clavispora, Cyberlindnera, Lecythophora, Pichia, Saccharomyces, and Wickerhamomyces. Saccharomyces cerevisiae and Candida glabrata were mostly isolated species. Furthermore, the results indicated that levels of yeast could be correlated to physico-chemical quality of water. A large number of isolates were resistant to azoles, especially fluconazole as well as other antifungal classes. Most of the Candida species were resistant to almost all the antifungals. Several of the isolated yeast species are opportunistic pathogens. They could cause infections in sensitive individuals during occasional direct contact especially immune compromised people. Resistance of these yeast species to antifungal agents is a major health concern. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Several yeast species had previously been isolated from water systems in the North West Province, South Africa. Some of the identified species had, in other studies, been associated with superficial mucosal infections to life threatening diseases. Antifungal drugs are used to treat such yeast infections. However, due to prophylactic usage and continuous exposure some yeast species have developed resistance to some antifungal agents. The aim of this study was to determine the diversity and antifungal susceptibility of yeasts in selected rivers, Mooi River and Harts River in the North West Province, South Africa. Waters samples were collected from the rivers in summer and winter seasons. Physico-chemical parameters such as pH, temperature, total dissolved solids, chemical oxygen demand, nitrates and phosphates were measured to determine the water quality. Yeast colonies were enumerated at room temperature and 37°C using yeast-malt-extract agar (containing 100 ppm chloramphenicol). Pure isolates from 37°C were identified by biochemical tests and 26S rRNA gene sequencing. Yeast sequences of isolated yeasts were sent to Genbank. Phylogenetic tree was conducted to determine phylogenetic relationship between the yeast isolates. Disk diffusion antifungal susceptibility tests were conducted on the yeast species. Physico-chemical parameters of the water were within target water quality range for livestock farming but in most sampling sites out of range for irrigation use. pH, Nitrates, phosphates and chemical oxygen demand levels ranged from 7.40 to 8.64, 0 to 5.4 mg/L, 0 to 7.14 mg/L and 31 to 43 mg/L, respectively. Elevated levels of total dissolved solids were measured in all the sampling sites. Total yeast counts ranged between 320-4200 cfu/L and 27-2573 cfu/L for room temperature and 37˚C. All the yeast colonies isolated were non-pigmented. Diazonium Blue B tests determined the yeasts isolates as ascomycetes. Haemolysin and extracellular enzyme production tests were negative on all the isolates. Yeasts isolates were identified and belonged to the genera Arxiozyma, Candida, Clavispora, Cyberlindnera, Lecythophora, Pichia, Saccharomyces, and Wickerhamomyces. Saccharomyces cerevisiae and Candida glabrata were mostly isolated species. Furthermore, the results indicated that levels of yeast could be correlated to physico-chemical quality of water. A large number of isolates were resistant to azoles, especially fluconazole as well as other antifungal classes. Most of the Candida species were resistant to almost all the antifungals. Several of the isolated yeast species are opportunistic pathogens. They could cause infections in sensitive individuals during occasional direct contact especially immune compromised people. Resistance of these yeast species to antifungal agents is a major health concern. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Treatment of lower respiratory tract infection (pneumonia and pleural infection) relies on the use of empirical broad spectrum antibiotics, primarily because reliable pathogen identification occurs infrequently. Another consequence of poor rates of pathogen identification is that our understanding of the microbiology of these infections is incomplete. This thesis addresses some of these issues by combining the acquisition of high quality lower respiratory tract samples, free from nasooropharyngeal contamination, with novel molecular microbiological techniques in an attempt to increase rates of pathogen identification. Four main areas are examined: (i) The role of so-called ‘atypical pneumonia’ bacteria in causing pleural infection. These pathogens have been previously identified in the pleural space infrequently and routine culture usually fails to isolate such bacteria. High sensitivity nested polymerase chain reaction (PCR) is a culture-independent technique which is used to undertake a systematic evaluation for these pathogens in pleural infection samples. (ii) The role of Pneumocystis jirovecii in pleural infection, either as a co-infecting pathogen or in monomicrobial infection. This fungus causes severe pneumonia, particularly in the immunosuppressed, but is increasingly recognised as a co-pathogen in community-acquired pneumonia, and is frequently isolated in the upper and lower respiratory tract in health. A high sensitivity real-time PCR assay is used to examine for this fungus. (iii) Ultra-deep sequencing of the 16S rRNA gene is used to perform a comprehensive microbial survey in samples taken from the multi-centre MIST2 study of pleural infection. The techniques employed allow analysis of polymicrobial samples and give very high taxonomic resolution, whilst incorporating methods to control for potential contamination. Further, these techniques provide confirmation of the results from the ‘atypical’ bacteria nested PCR study. (iv) Bedside ultrasound-guided percutaneous transthoracic needle aspiration (TNA) of consolidated lung is undertaken in patients with pneumonia, as part of the PIPAP study. An evaluation is undertaken of the efficacy and acceptability of TNA. Aspirate samples acquired are also processed using ultra-deep sequencing of the 16S rRNA gene. Other samples obtained as part of the PIPAP study, such as ‘control’ lung aspirates and ‘control’ pleural fluid samples, are similarly processed to enable calculation of sensitivity and specificity of the sequencing methodology.

Disertacijos darbo tikslas – aptikti ir identifikuoti Lietuvoje paplitusias fitoplazmas vabzdžiuose, surinktuose nuo įvairių augalų su fitoplazminiais simptomais ir nustatyti fitoplazmų vabzdžius pernešėjus bei atskleisti identifikuotų ir kitų fitoplazmų filogenetinius giminingumus. Lietuvoje jau žinomos keletas labiausiai paplitusių fitoplazmų grupių bei pogrupių, taip pat aptikta nemažai jų augalų-šeimininkų. Duomenų apie galimus šių bakterijų pernešėjus Lietuvoje beveik nėra. Pernešėjų identifikavimas ir tyrimas padės kurti veiksmingesnes strategijas bei sistemas kovai su fitoplazminėmis infekcijomis. Fitoplazmų ir jų pernešėjų identifikavimas suteiks svarbių duomenų tiriant šių patogenų ekologiją, paplitimą, kilmę, epidemiologiją, plitimo kelius. Informacija bus naudinga Lietuvos ir kaimyninių šalių augalų apsaugai. Taip pat galės padėti nustatant galimų invazinių vabzdžių rūšių bei fitoplazmų kamienų atsiradimą Lietuvoje dėl klimato kaitos. Šio darbo metu pirmą kartą Lietuvoje molekuliniais metodais buvo išaiškinti fitoplazmų vabzdžiai pernešėjai. Daugelis aptiktų fitoplazmų pogrupių nustatytos identifikotuose vabzdžiuose pirmą kartą, kaip Lietuvoje taip ir pasaulyje. Penkiose augalų rūšyse fitoplazmos aptiktos pirmą kartą Lietuvoje. Darbo metu nustatytas vienas visiškai naujas Lietuvai ir pasauliui ir vienas naujas Lietuvai fitoplazmų pogrupiai bei jų augalai šeimininkai, kas prisideda prie Lietuvoje bei pasaulyje aptinkamų fitoplazmų paplitimo ir bioįvairovės tyrimo... [toliau žr. visą tekstą] / The aim of the research was to identify the phytoplasmas detected in insects that were found on various phytoplasma-infected plants, and to reveal phytoplasma insect-vectors as well as phytogenetical relationships of identified phytoplasmas. From previous research, we already know a few mostly widespread phytoplasma groups, subgroups, and many of their host plants in Lithuania. The data on potential vectors of these bacteria are very scarce in Lithuania. The identification and research of insect vectors will help to create more effective strategies and systems to fight with phytoplasmal infections. Identification of phytoplasmas and their vectors will provide important data for research of ecology, distribution, origin, epidemiology, and ways of spreading of these pathogens. Such information is beneficial for plant protection institutions and plant growers in Lithuania and neighbouring countries. It will help to ascertain possible invasive insect species and phytoplasma strains in Lithuania. During this research for the first time in Lithuania, we determined possible phytoplasma insect vectors using molecular biology methods. Most of the detected phytoplasma subgroups were found in the identified insect species for the first time in Lithuania and worldwide. Our data on new potential insect vector species extend the spectrum of phytoplasma vectors in our region. Phytoplasmas were detected for the first time in five plant species in Lithuania. We identified in this work one... [to full text]