Metabolism of host-derived carbohydrates by Bifidobacterium breve UCC2003

Bifidobacteria are Gram positive, anaerobic, typically Y-shaped bacteria which are naturally found in the digestive tract of certain mammals, birds and insects. Bifidobacterium breve strains are numerically prevalent among the gut microbiota of many healthy breast-fed infants. The prototypical B. breve strain UCC2003 has previously been shown to utilise numerous carbohydrates of plant origin. Various aspects of host-derived carbohydrate metabolism occurring in this bacterium will be described in this thesis. Chapter II describes B. breve UCC2003 utilisation of sialic acid, a nine-carbon monosaccharide, which is found in human milk oligosaccharides (HMOs) and the mucin glycoprotein. B. breve UCC2003 was also shown to cross-feed on sialic acid released from 3’ sialyllactose, a prominent HMO, by the extracellular sialidase activity of Bifidobacterium bifidum PRL2010. Chapter III reports on the transcriptional regulation of sialic acid metabolism in B. breve UCC2003 by a transcriptional repressor encoded by the nanR gene. NanR belongs to the GntR-family of transcriptional regulators and represents the first bifidobacterial member of this family to be characterised. Chapter IV investigates B. breve UCC2003 utilisation of mucin. B. breve UCC2003 was shown to be incapable of degrading mucin; however when grown in co-culture with B. bifidum PRL2010 it exhibits enhanced growth and survival properties. A number of methods were used to investigate and identify the mucin components supporting this enhanced growth/viability phenotype. Chapter V describes the characterisation of two sulfatase-encoding gene clusters from B. breve UCC2003. The transcriptional regulation of both sulfatase-encoding gene clusters was also investigated. The work presented in this thesis represents new information on the metabolism of host-derived carbohydrates in bifidobacteria, thus increasing our understanding of how these gut commensals are able to colonise and persist in the gastrointestinal tract.

Host-derived biomarkers at teeth and implants in partially edentulous patients. A 10-year retrospective study.

OBJECTIVES To assess a selection of host-derived biomarkers in peri-implant sulcus fluid (PISF) and gingival crevicular fluid (GCF) from adjacent teeth 10 years following implant placement. MATERIAL AND METHODS Peri-implant sulcus fluid and GCF samples obtained from the deepest sites of 504 implants and 493 adjacent teeth were analysed for levels of interleukin (IL)-1β, matrix metalloproteinase (MMP)-3, MMP-8, MMP-1, and MMP-1 bound to tissue inhibitor of MMP (TIMP)-1 (MMP-1/TIMP-1) by enzyme-linked immunosorbent assay (ELISA) technique. RESULTS Overall, MMP-8 was detected in 90% of the sites. In more than 50% of the sites, IL-1β was identified while in 30% of the sites MMP-1, MMP-1/TIMP-1 and MMP-3 were found over the detection level. Increased biomarkers levels from PISF and GCF were positively correlated (r = 0.375-0.702; P < 0.001). However, no qualitative and quantitative differences were found between PISF and GCF. The levels of MMP-1 were negatively correlated with those of MMP-1/TIMP-1 at implants (r = -0.644; P < 0.001). Median MMP-1 levels at implants were high (5.17 pg/site) in subjects with severe chronic periodontitis and low in patients with mild-to-moderate chronic periodontitis (0 pg/site; P = 0.026) or gingivitis (0 pg/site; P = 0.034). Levels of IL-1β were found to be different in GCF according to the periodontal conditions (P = 0.001) with the highest level found in mild-to-moderate periodontitis (6.2 pg/site). Clinical attachment levels at implants demonstrated an inverse correlation with MMP-1/TIMP-1 (r = -0.147; P = 0.001). CONCLUSIONS Increased levels of MMP-8 and IL-1β in PISF or GCF may be associated with inflammation around teeth and implants while lower levels of MMP-1/TIMP-1 may be an indicator of disease progression around implants.

Feeding specialization and host-derived chemical defense in Chrysomeline leaf beetles did not lead to an evolutionary dead end

Combination of molecular phylogenetic analyses of Chrysomelina beetles and chemical data of their defensive secretions indicate that two lineages independently developed, from an ancestral autogenous metabolism, an energetically efficient strategy that made the insect tightly dependent on the chemistry of the host plant. However, a lineage (the interrupta group) escaped this subordination through the development of a yet more derived mixed metabolism potentially compatible with a large number of new host-plant associations. Hence, these analyses on leaf beetles document a mechanism that can explain why high levels of specialization do not necessarily lead to “evolutionary dead ends.”

Identification and characterization of a glycosulfatase-encoding gene cluster in Bifidobacterium breve UCC2003

Bifidobacteria constitute a specific group of commensal bacteria, typically found in the gastrointestinal tract (GIT) of humans and other mammals. Bifidobacterium breve strains are numerically prevalent among the gut microbiota of many healthy breast-fed infants. In the current study, we investigated glycosulfatase activity in a bacterial nursling stool isolate, B. breve UCC2003. Two putative sulfatases were identified on the genome of B. breve UCC2003. The sulfated monosaccharide N-acetylglucosamine-6-sulfate (GlcNAc-6-S) was shown to support growth of B. breve UCC2003, while, N-acetylglucosamine-3-sulfate, N-acetylgalactosamine-3-sulfate and N-acetylgalactosamine-6-sulfate, did not support appreciable growth. Using a combination of transcriptomic and functional genomic approaches, a gene cluster, designated ats2, was shown to be specifically required for GlcNAc-6-S metabolism. Transcription of the ats2 cluster is regulated by a ROK-family transcriptional repressor. This study represents the first description of glycosulfatase activity within the Bifidobacterium genus. Bifidobacteria are saccharolytic organisms naturally found in the digestive tract of mammals and insects. Bifidobacterium breve strains utilize a variety of plant and host-derived carbohydrates which allow them to be present as prominent members of the infant gut microbiota as well as being present in the gastrointestinal tract of adults. In this study, we introduce a previously unexplored area of carbohydrate metabolism in bifidobacteria, namely the metabolism of sulfated carbohydrates. B. breve UCC2003 was shown to metabolize N-acetylglucosamine-6-sulfate (GlcNAc-6-S) through one of two sulfatase-encoding gene clusters identified on its genome. GlcNAc-6-S can be found in terminal or branched positions of mucin oligosaccharides, the glycoprotein component of the mucous layer that covers the digestive tract. The results of this study provide further evidence of this species' ability to utilize mucin-derived sugars, a trait which may provide a competitive advantage in both the infant and adult gut.

Antiproteases as therapeutics to target inflammation in cystic fibrosis.

Cystic Fibrosis (CF) is the most common fatal inherited disease of Caucasians, affecting about 1 in 3000 births. Patients with CF have a recessive mutation in the gene encoding the CF transmembrane conductance regulator (CFTR). CFTR is expressed in the epithelium of many organs throughout the exocrine system, however, inflammation and damage of the airways as a result of persistent progressive endobronchial infection is a central feature of CF. The inflammatory response to infection brings about a sustained recruitment of neutrophils to the site of infection. These neutrophils release various pro-inflammatory compounds including proteases, which when expressed at aberrant levels can overcome the endogenous antiprotease defence mechanisms of the lung. Unregulated, these proteases can exacerbate inflammation and result in the degradation of structural proteins and tissue damage leading to bronchiectasis and loss of respiratory function. Other host-derived and bacterial proteases may also contribute to the inflammation and lung destruction observed in the CF lung. Antiprotease strategies to dampen the excessive inflammatory response and concomitant damage to the airways remains an attractive therapeutic option for CF patients.

Catalytic routes to convert saccharides to furanic aldehydes

The conversion of plant biomass-derived carbohydrates (preferably non-edible) into added-value products is envisaged to be at the core of the future biorefineries. Carbohydrates are the most abundant natural organic polymers on Earth. This work deals with the chemical valorisation of plant biomass, focusing on the acid-catalysed conversion of carbohydrates (mono and polysaccharides) to furanic aldehydes, namely 2-furaldehyde (Fur) and 5-hydroxymethyl-2-furaldehyde (Hmf), which are valuable platform chemicals that have the potential to replace a variety of oil derived chemicals and materials. The investigated reaction systems can be divided into two types depending on the solvent used to dissolve the carbohydrates in the reaction medium: water or ionic liquid-based systems. The reaction temperatures were greater than 150 ºC when the solvent was water, and lower than 150 º C in the cases of the ionic liquid-based catalytic systems. As alternatives to liquid acids (typically used in the industrial production of Fur), solid acid catalysts were investigated in these reaction systems. Aiming at the identification of (soluble and insoluble) reaction products, complementary characterisation techniques were used namely, FT-IR spectroscopy, liquid and solid state NMR spectroscopy, TGA, DSC and GC´GC-ToFMS analyses. Complex mixtures of soluble reaction products were obtained and different types of side reactions may occur. The requirements to be put on the catalysts for these reaction systems partly depend on the type of carbohydrates to be converted and the reaction conditions used. The thermal stability is important due to the fact that formation of humins and catalyst coking phenomena are characteristically inherent to these types of reactions systems leading to the need to regenerate the catalyst which can be effectively accomplished by calcination. Special attention was given to fully inorganic nanoporous solid acids, amorphous or crystalline, and consisting of nano to micro-size particles. The investigated catalysts were silicoaluminophosphates, aluminosilicates and zirconium-tungsten mixed oxides which are versatile catalysts in that their physicochemical properties can be fine-tuned to improve the catalytic performances in the conversion of different substrates (e.g. introduction of mesoporosity and modification of the acid properties). The catalytic systems consisting of aluminosilicates as solid acids and water as solvent seem to be more effective in converting pentoses and related polysaccharides into Fur, than hexoses and related polysaccharides into Hmf. The investigated solid acids exhibited fairly good hydrothermal stabilities. On the other hand, ionic liquid-based catalytic systems can allow reaching simultaneously high Fur and Hmf yields, particularly when Hmf is obtained from D-fructose and related polysaccharides; however, catalyst deactivation occurs and the catalytic reactions take place in homogeneous phase. As pointed out in a review of the state of the art on this topic, the development of truly heterogeneous ionic liquid-based catalytic systems for producing Fur and Hmf in high yields remains a challenge.

Caractérisation de la migration du virus Herpès simplex de type 1 (HSV-1) par protéomique

Le virus Herpès simplex de type 1 (HSV-1), agent étiologique des feux sauvages, possède une structure multicouche comprenant une capside icosaédrale qui protège le génome viral d’ADN, une couche protéique très structurée appelée tégument et une enveloppe lipidique dérivant de la cellule hôte et parsemée de glycoprotéines virales. Tous ces constituants sont acquis séquentiellement à partir du noyau, du cytoplasme et du réseau trans-golgien. Cette structure multicouche confère à HSV-1 un potentiel considérable pour incorporer des protéines virales et cellulaires. Toutefois, l’ensemble des protéines qui composent ce virus n’a pas encore été élucidé. De plus, malgré son rôle critique à différentes étapes de l’infection, le tégument demeure encore mal défini et ce, tant dans sa composition que dans la séquence d’addition des protéines qui le composent. Toutes ces incertitudes quant aux mécanismes impliqués dans la morphogenèse du virus nous amènent à l’objectif de ce projet, soit la caractérisation du processus de maturation d’HSV-1. Le premier article présenté dans cette thèse et publié dans Journal of Virology s’attarde à la caractérisation protéique des virus extracellulaires matures. Grâce à l’élaboration d’un protocole d’isolation et de purification de ces virions, une étude protéomique a pu être effectuée. Celle-ci nous a permis de réaliser une cartographie de la composition globale en protéines virales des virus matures (8 protéines de la capside, 23 protéines du tégument et 13 glycoprotéines) qui a fait la page couverture de Journal of Virology. De plus, l’incorporation potentielle de 49 protéines cellulaires différentes a été révélée. Lors de cette étude protéomique, nous avons aussi relevé la présence de nouveaux composants du virion dont UL7, UL23, ICP0 et ICP4. Le deuxième article publié dans Journal of General Virology focalise sur ces protéines via une analyse biochimique afin de mieux comprendre les interactions et la dynamique du tégument. Ces résultats nous révèlent que, contrairement aux protéines ICP0 et ICP4, UL7 et UL23 peuvent être relâchées de la capside en présence de sels et que les cystéines libres jouent un rôle dans cette relâche. De plus, cet article met en évidence la présence d’ICP0 et d’ICP4 sur les capsides nucléaires suggérant une acquisition possible du tégument au noyau. La complexité du processus de morphogenèse du virus ainsi que la mise en évidence d’acquisition de protéines du tégument au noyau nous ont incités à poursuivre nos recherches sur la composition du virus à un stade précoce de son cycle viral. Les capsides C matures, prémisses des virus extracellulaires, ont donc été isolées et purifiées grâce à un protocole innovateur basé sur le tri par cytométrie en flux. L’analyse préliminaire de ces capsides par protéomique a permis d’identifier 28 protéines virales et 39 protéines cellulaires. Les données recueilles, comparées à celles obtenues avec les virus extracellulaires, suggèrent clairement un processus séquentiel d’acquisition des protéines du tégument débutant dans le noyau, site d’assemblage des capsides. Finalement, tous ces résultats contribuent à une meilleure compréhension du processus complexe de maturation d’HSV-1 via l’utilisation de techniques variées et innovatrices, telles que la protéomique et la cytométrie en flux, pouvant être appliquées à d’autres virus mais aussi permettre le développement de meilleurs traitements pour vaincre l’HSV-1.

Carbohydrate Composition and Water-Stable Aggregation of an Oxisol as Affected by Crop Sequence under No-Till

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Actinobacillus actinomycetemcomitans lipopolysaccharide-mediated experimental bone loss model for aggressive periodontitis

Background: Bacterial constituents, such as Gram-negative derived lipopolysaccharide (LPS), can initiate inflammatory bone loss through induction of host-derived inflammatory cytokines. The aim of this study was to establish a model of aggressive inflammatory alveolar bone loss in rats using LPS derived from the periodontal pathogen Actinobacillus actinomycetemcomitans.Methods: Eighteen female Sprague-Dawley rats were divided into LPS test (N = 12) and saline control (N = 6) groups. All artimals received injections to the palatal molar gingiva three times per week for 8 weeks. At 8 weeks, linear and volumetric alveolar bone loss was measured by micro-computed tomography (mu CT). The prevalence of inflammatory infiltrate, proinflammatory cytokines, and osteoclasts was assessed from hematoxylin and eosin, immunohistochemical, or tartrate-resistant acid phosphatase (TRAP)-stained sections. Statistical analysis was performed.Results: A. actinomycetemcomitans LPS induced severe bone loss over 8 weeks, whereas control groups were unchanged. Linear and volumetric analysis of maxillae by mu CT indicated significant loss of bone with LPS, administration. Histologic examination revealed increased inflammatory infiltrate, significantly increased immunostaining for interleukin IL-6 and -1 beta and tumor necrosis factor-alpha, and more TRAP-positive osteoclasts in the LPS group compared to controls.Conclusion: Oral injections of LPS derived from the periodontal pathogen A. actinomycetemcomitans can induce severe alveolar bone loss and proinflammatory cytokine production in rats by 8 weeks.

In vivo preservation of the hybrid layer by chlorhexidine

Host-derived proteases have been reported to degrade the collagen matrix of incompletely-resin-infiltrated dentin. This study tested the hypothesis that interfacial degradation of resin-dentin bonds may be prevented or delayed by the application of chlorhexidine (CHX), a matrix metalloproteinase inhibitor, to dentin after phosphoric acid-etching. Contralateral pairs of resin-bonded Class I restorations in non-carious third molars were kept under intra-oral function for 14 months. Preservation of resin-dentin bonds was assessed by microtensile bond strength tests and TEM examination. In vivo bond strength remained stable in the CHX-treated specimens, while bond strength decreased significantly in control teeth. Resin-infiltrated dentin in CHX-treated specimens exhibited normal structural integrity of the collagen network. Conversely, progressive disintegration of the fibrillar network was identified in control specimens. Auto-degradation of collagen matrices can occur in resin-infiltrated dentin, but may be prevented by the application of a synthetic protease inhibitor, such as chlorhexidine.

Expressão de MMP-13 e ativação de vias de sinalização intracelular em dois modelos de doença periodontal induzida experimentalmente em ratos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Charakterisierung der Apolipoprotein J-Genregulation in Fibroblasten und glatten Gefäßmuskelzellen durch nekrotische Zellen und Toll-like Rezeptoren

Apolipoprotein J (ApoJ) ist ein sezerniertes heterodimeres 80kDa Glykoprotein mit zytoprotektiven und antiinflammatorischen Eigenschaften, das ein nahezu ubiquitäres Expressionsmuster aufweist. Eine stark erhöhte ApoJ-Expression ist mit neurodegenerativen Erkrankungen, Atherosklerose, myokardialem Infarkt sowie einer Vielzahl anderer pathophysiologischer Bedingungen assoziiert. Die potentielle Bedeutung von ApoJ umfasst eine Funktion als extrazelluläres Chaperon, Komplementinhibitor, NF-kB-Inhibitor sowie eine Beteiligung an der Endozytose von nekrotischen Zellfragmenten. Unter Bedingungen, die zu einer massiven Akkumulation von absterbenden Zellen führen, ist eine vermehrte Expression von ApoJ auf die überlebenden Nachbarzellen in den betroffenen Geweben beschränkt. Die molekularen Mechanismen, die dieser gesteigerten ApoJ-Genexpression zugrunde liegen, sind jedoch unbekannt. Untersuchungen unserer Arbeitsgruppe konnten zeigen, dass eine Inkubation mit nekrotischem Zellmaterial in vitro eine Akkumulation von ApoJ-mRNA in Fibroblasten der Zelllinie Rat1 induziert, was darauf hindeutet, dass unter pathophysiologischen Bedingungen von nekrotischen Zellen exponierte bzw. freigesetzte Faktoren zu einer gesteigerten ApoJ-Genexpression in umliegenden vitalen Zellen beitragen können. Die im Rahmen der vorliegenden Arbeit durchgeführten Untersuchungen zeigen eine Korrelation zwischen der Expression von Toll-like Rezeptoren (TLRs) in Fibroblasten (Rat1), glatten Gefäßmuskelzellen (CRL2018) sowie embryonalen Dottersackzellen (10A) und einer durch nekrotische Zellen induzierten ApoJ-mRNA-Expression in diesen Zelllinien. Es wird angenommen, dass TLRs neben pathogenassoziierten Strukturen (PAMPs) auch durch körpereigene Agonisten wie Hitzeschockproteine und Nukleinsäuren aktiviert werden. In weiterführenden Experimenten stellte sich unter anderem heraus, dass neben nekrotischen Zellen auch der TLR3-spezifische Agonist Poly(I:C), eine synthetische doppelsträngige RNA, ausschließlich in den beiden TLR3-exprimierenden Zelllinien CRL2018 und Rat1, nicht jedoch in TLR3-defizienten 10A-Zellen, die ApoJ-mRNA-Expression induziert. Darüber hinaus führt auch die Inkubation mit eukaryotischer RNA (Gesamt-RNA, t-RNA) zu einer Akkumulation von ApoJ-mRNA in CRL2018-Zellen. Die Ergebnisse dieser Arbeit zeigen erstmals, dass die Expression von ApoJ-mRNA durch extrazelluläre Ribonukleinsäuren in TLR3-abhängiger Weise induziert wird, was darauf hindeutet, dass in verletzten Geweben aus post-apoptotischen oder nekrotischen Zellen freigesetzte Ribonukleinsäuren zu einer vermehrten ApoJ-Genexpression in vitalen Nachbarzellen beitragen.

Reversibility of experimental peri-implant mucositis compared with experimental gingivitis in humans

To monitor clinical, microbiological and host-derived alterations occurring around teeth and titanium implants during the development of experimental gingivitis/mucositis and their respective healing sequence in humans.

Bacterial and inflammatory behavior of implants in the early healing phase of chronic periodontitis

To assess the pattern of early bacterial colonization at implants and teeth in patients with a history of chronic periodontitis compared with a group of healthy subjects. Furthermore, the presence of host-derived markers at teeth and implants in the two subject groups was determined.

Periodontal pathogens affect the level of protease inhibitors in gingival crevicular fluid

In periodontitis, an effective host-response is primarily related to neutrophils loaded with serine proteases, including elastase (NE) and protease 3 (PR3), the extracellular activity of which is tightly controlled by endogenous inhibitors. In vitro these inhibitors are degraded by gingipains, cysteine proteases produced by Porphyromonas gingivalis. The purpose of this study was to determine the level of selected protease inhibitors in gingival crevicular fluid (GCF) in relation to periodontal infection. The GCF collected from 31 subjects (nine healthy controls, seven with gingivitis, five with aggressive periodontitis and 10 with chronic periodontitis) was analyzed for the levels of elafin and secretory leukocyte protease inhibitor (SLPI), two main tissue-derived inhibitors of neutrophil serine proteases. In parallel, activity of NE, PR3 and arginine-specific gingipains (Rgps) in GCF was measured. Finally loads of P. gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia and Treponema denticola were determined. The highest values of elafin were found in aggressive periodontitis and the lowest in controls. The quantity of elafin correlated positively with the load of P. gingivalis, Ta. forsythia and Tr. denticola, as well as with Rgps activity. In addition, NE activity was positively associated with the counts of those bacterial species, but not with the amount of elafin. In contrast, the highest concentrations of SLPI were found in periodontally healthy subjects whereas amounts of this inhibitor were significantly decreased in patients infected with P. gingivalis. Periodontopathogenic bacteria stimulate the release of NE and PR3, which activities escape the control through degradation of locally produced inhibitors (SLPI and elafin) by host-derived and bacteria-derived proteases.