Antalet äldre blir idag allt fler och behovet av vård flyttas upp i åldrarna. Det kräver att insatser inom äldrevård och omsorg håller hög kvalité och placerar människan i centrum för att skapa förutsättningar för äldre att leva ett värdigt, meningsfullt liv och känna välbefinnande. Frågan om mat, trygghet, identitet, social interaktion, anpassning och KASAM är faktorer som påverkar äldres tillvaro på äldreboende. Syftet med studien var att få djupare kunskap och förståelse i äldres livsvärld på äldreboende, hur man som boende upplever sin vardag och vilken betydelse äldreboendet som institution har för deras hälsa. Två livsberättelseintervjuer genomfördes under en timme var med två äldre, en man och en kvinna boende på ett äldreboende i Mellansverige. Resultatet tolkades och analyserades utifrån tidigare forskning, salutogent och patogent perspektiv på hälsa och teorier som KASAM, Maslows behovstrappa och immanent pedagogik. Resultatet visade att deltagarna är väldigt nöjda med sin vistelse på äldreboendet och hänvisar till aspekter som uppskattning av hjälp med mat, trygghet och tillit. Tidigare livserfarenheter och livsförhållanden lyfts fram i samband med uppskattningens betydelse. Dock framgår det även att tillvaron består av begränsningar som gör att personernas viktiga, betydelsefulla områden i livet inte fullt tillgodoses, vilket påverkar de äldres möjlighet att uppleva meningsfullhet i tillvaron. De äldres hälsotillstånd, tidsaspekt gällande personalens möjlighet att tillgodose behov, en fråga om mindre spontanitet och de äldres uppfattningar att inte kunna fodra hur mycket hjälp som helst är påverkande faktorer.

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

Streptococcus zooepidemicus (Sz) and Streptococcus equi (Se) share 98% DNA sequence homology, but display different pathogenic properties. Infection by one organism does not cross-protect against the other. To better understand pathogenic differences between these organisms and gain information about which proteins are expressed in horses infected experimentally with Se, intrauterine Sz or naturally with respiratory Sz we compared antibody specificities of convalescent sera using ELISA. These comparisons were based on sets of 8 and 14 immunoreactive recombinant proteins of Se strain CF32 and Sz strain NC78, respectively. Sera from donkeys that were previously naturally affected with strangles and later developed Sz pneumonia secondary to an experimental influenza challenge were also included. Serum antibody responses were quantitatively and qualitatively much greater following recovery from strangles than following respiratory Sz infection. Increased reactions to Se proteins IdeE2, Se75.3, Se46.8, Se18.9 and Se42.0 were observed for the majority of strangles sera but not for sera from respiratory Sz infection cases. Reactions of sera from Sz respiratory disease to Sz proteins varied greatly and were mostly to HylC and ScpC. Interestingly, sera of donkey recovered from Sz bronchopneumonia did not show increased antibody reaction to any of the proteins even though these donkeys had also recovered from clinical strangles 6 months previously. Only 1/5 mare with Sz placentitis presented increased serum antibody responses to MAP. In conclusion, adaptive immune responses to Se of horses with strangles are stronger and involve a greater number of proteins than adaptive immune responses to Sz infection of the lower respiratory tract. In an effort to develop an improved vaccine against Se, modified live strain of EHV-1, RacH was constructed to express three recombinant antigens of Se SeM, IdeE and Se18.9. Two groups of 10 and 2 ponies were vaccinated intramuscularly or intranasally, respectively. Another group (n=6) vaccinated with empty RacH served as controls. Sera from 2/3 ponies from each vaccination groups and 1/2 serum from IN vaccinated ponies showed increased serum neutralizing antibodies to EHV-1. ELISA detected no significant increase in antibodies to proteins. Only one IM and IN vaccinated pony showed serum bactericidal activity post vaccination.

Most bacterial infections can be correlated to contamination of consumables such as food and water. Upon contamination, boil water advisories have been ordered to ensure water is safe to consume, despite the evidence that heat-killed bacteria can induce genomic instability of exposed (intestine) and distal cells (liver and spleen). We hypothesize that exposure to components of heat-killed Escherichia coli O157:H7 will induce genomic instability within animal cells directly and indirectly exposed to these determinants. Mice were exposed to various components of dead bacteria such as DNA, RNA, protein or LPS as well as to whole heat-killed bacteria via drinking water. Here, we report that exposure to whole heat-killed bacteria and LPS resulted in significant alterations in the steady state RNA levels and in the levels of proteins involved in proliferation, DNA repair and DNA methylation. Exposure to whole heat-killed bacteria and their LPS components also leads to increased levels of DNA damage. / xiv, 132 leaves : ill. (chiefly col.) ; 29 cm

The availability of completely sequenced genomes for a number of organisms provides an opportunity to understand the molecular basis of physiology, metabolism, regulation and evolution of these organisms. Significant understanding of the complexity of organisms can be obtained from the functional characterization of repertoire of proteins encoded in their genomes. Computational approaches for recognition of function of proteins of unknown function encoded in genomes often rely on ability to detect well characterized homologues. Homology searches based on pair-wise sequence comparisons can reliably detect homologues with sequence identity more than 30%. However, detecting homologues characterized by sequence identity below 30% is difficult using these methods. Distant homology relationship can be established using profiles or position specific scoring matrices, which encapsulate information about structurally and functionally conserved residues. These conserved residues imply high constraints at a particular amino acid residue site due to their involvement in structural stability, enzymatic activity, ligand binding, protein folding or protein–protein interactions. In addition, information on three dimensional structures of proteins also aid in detection of remote homologues, as tertiary structures of proteins are conserved better than the primary structures of proteins. The gross objective of the work reported in this thesis is to employ various sensitive remote homology detection methods to recognize relevant functional information of proteins encoded mainly in pathogenic organisms. Since proteins do not work in isolation in a cell, it has become essential to understand the in vivo context of functions of proteins. For this purpose, it is essential to have an understanding of all molecules that interact with a particular protein. Thus, another major area of bioinformatics has been to integrate protein-protein interaction information to enable better understanding of context of functional events. Protein-protein interaction analysis for host-pathogen can lead to useful insight into mode of pathogenesis and subsequent consequences in host cell. Chapters 2-6 of the thesis discuss the sequence and structural characteristics along with remote evolutionary relationships and functional implications of uncharacterized proteins encoded in genomes of following pathogens: Helicobacter pylori, Plasmodium falciparum and Leishmania donovani. The Chapters 6-8 discuss mainly various sequence, structural and functional aspects of protein kinases encoded in genomes of various prokaryotes and viruses. Chapter 1 discusses background information and literature survey in the areas of homology detection and prediction of protein-protein interactions. The growth of genomic data and need for processing genomic data to infer context of various functional events have been highlighted. Different approaches to recognize functions of proteins (experimental as well as computational) have been discussed. Various experimental and computational approaches to detect/predict protein-protein interactions have been mentioned. Chapter 2 discusses recognition of non-trivial remote homology relationships involving proteins of Helicobacter pylori and their implications for function recognition. H. pylori is microaerophilic, Gram negative bacterial pathogen. It colonizes human gastric mucosa and is a causative agent of gastroduodenal disease. The pathogen infects about 50% of the human population. It can lead to development of Mucosa-associated lymphoid tissue lymphoma. About 10% of the infected population develop gastric or duodenal ulcer and approximately 1% develop gastric cancer. H. pylori has been classified as class I carcinogen by WHO. Pathogen is characterized by type IV secretion system. The complete genomic sequences of three widely studied strains including 26695, J99 and HPAG1 of Helicobacter pylori are available. According to the genome analysis, the number of predicted open reading frames in strain 26695, J99 and HPAG1 are 1590, 1495 and 1536 respectively. Out of predicted H. pylori proteins from 26695, J99 and HPAG1 strains, numbers of proteins with no functional domain assignments in Pfam database (Protein family database) are 453, 357 and 400 respectively. There are proteins in different strains of H. pylori genomes where one part of the protein is associated with at least one protein domain of known function and hence preliminary indication of their functions is available whereas rest of the region is not associated with any function. There are 772, 803 and 790 such segments in proteins from strains 26695, J99 and HPAG1 respectively with at least 45 residues with no functional assignment currently available. Sensitive remote homology detection methods have been employed to establish relationships for 294 amino acid sequences and results have been grouped into 4 categories. Results of homology detection have been further confirmed by studying conservation of amino acid residues which are important for functioning of the proteins concerned. (i) Remote relationship has been established involving protein domain families for which no bonafide member is currently known in H. pylori. For example: DNA binding protein domain (Kor_B) has been assigned to a H. pylori protein at sequence identity of 20%. Study involving secondary structure prediction and conservation of amino acid residues confirms the results of homology detection methods. (ii) Remote relationship has been established involving H. pylori hypothetical proteins and protein domain families, for which paralogous members are present in Helicobacter pylori. For example, Cytochrome_C, an electron transfer protein domain could be associated with a Helicobacter pylori protein sequence which shows a sequence identity of 14% with sequences of bonafide cytochrome C. (iii) “Missing” metabolic proteins of H. pylori have also been recognized. For example, Aspartoacylase (EC 3.5.1.15) catalyzes deacetylation of N-acetylaspartic acid to produce acetate and L-aspartate. This enzyme in aspartate metabolism pathway has not been reported so far from H. pylori. A remote evolutionary relationship between a H. pylori protein and Aspartoacylase domain has been established at sequence identity of 17% thus filling the gap in this metabolic pathway in the pathogen. (iv) New functional assignments for domains in H. pylori sequences with prior assignment of domains for the rest of the sequences have been made. For example, DNA methylase domain has been assigned to C-terminal region of H. pylori protein which already had Helicase domain assigned to the N-terminal region of the protein. All these information should open avenues for further probing by carrying out experiments which will impact the design of inhibitor against this pathogen and will result in better understanding of pathogenesis of this organism in human. Chapter 3 describes prediction of protein–protein interactions between Helicobacter pylori and the human host. A lack of information on protein-protein interactions at the host-pathogen interface is impeding the understanding of the pathogenesis process. A recently developed, homology search-based method to predict protein-protein interactions is applied to the gastric pathogen, Helicobacter pylori to predict the interactions between proteins of H. pylori and human proteins in vitro. Many of the predicted interactions could potentially occur between the pathogen and its human host during pathogenesis as we focused mainly on the H. pylori proteins that have a transmembrane region or are encoded in the pathogenic island and those which are known to be secreted into the human host. By applying the homology search approach to protein-protein interaction databases DIP and iPfam, in vitro interactions for a total of 623 H. pylori proteins with 6559 human proteins could be predicted. The predicted interactions include 549 hypothetical proteins of as yet unknown function encoded in the H. pylori genome and 13 experimentally verified secreted proteins. A total of 833 interactions involving the extracellular domains of transmembrane proteins of H. pylori could be predicted. Structural analysis of some of the examples reveals that the predicted interactions are consistent with the structural compatibility of binding partners. Various probable interactions with discernible biological relevance are discussed in this chapter. For example, interaction between CFTR protein (NP_000483) and multidrug resistance protein (HP1206) has been predicted. The structure of the CFTR intracellular domain is known in the homomeric form and consists of five AAA transport domains in tandem (PDB code 1XMI). Out of the five identical subunits, two subunits (the B chain and the E chain in the PDB structure) have been selected. The structure of multidrug resistance protein of the pathogen based on the B chain (sequence identity 32%) of the template has been modeled. This exercise suggests that interface residues in the model are congenial for interaction. This makes the structural complex feasible in in vitro conditions and suggests that the pathogen protein may compete for occupancy with the host protein. Chapter 4 describes recognition of Plasmodium-specific protein domain families and their roles in Plasmodium falciparum life cycle. Malaria in humans is caused by the parasites of intracellular, eukaryotic protozoan of apicomplexan nature belonging to the genus Plasmodium. Out of five species of Plasmodium, namely, P. falciparum, P. ovale, P. vivax, P. malariae and P. knowlesi which infects human, P. falciparum causes lethal infection. P. falciparum proteins have diverged extensively during the course of evolution. Pathogen genome is rich in A+T composition which larger than the homologous proteins from other organisms due to presence of low complexity regions. Organism specific families are important as they play roles in peculiar life style of an organism. If the organism is a pathogen, then these family members may play roles in pathogenesis. Inhibiting these specific proteins is unlikely to interfere with host system as no homolog may be present in host. In the present work we identify Plasmodium specific protein families and their role in different stages of life cycle of the pathogen. A total of 5086 amino acid sequences (full length sequences/fragments of proteins) show homology only with amino acid sequences from Plasmodium organisms and hence are Plasmodium-specific. These Plasmodium-specific amino acid sequences cluster into 106 Plasmodium-specific families (≥2 members per family). 14 Plasmodium-specific protein domain families with known physico-chemical properties are observed. These Plasmodium-specific protein domain families are involved in various important functions such as rosetting and sequestering of infected erythrocytes, binding to surface of host cell and invasion process in life cycle of pathogen. Also, 89 new Plasmodium-specific protein domain families have been recognized. Analysis of various aspects of members of Plasmodium-specific proteins domain families such as their potential to target apicoplast, protein-protein interaction, expression profile and domain organization has been performed to derive relevant information about function. New Plasmodium specific domain families for which no function can be associated could provide some insight into much diverged Plasmodium species. These proteins may play role in parasite-specific life style. Experimental work on these Plasmodium-specific proteins might fill the gaps of less understood physiology of this parasite. Chapter 5 presents genome-wide compilation of low complexity regions (LCR) in proteins. An indepth analysis of the nature, structure, and functional role of the proteins containing low complexity regions in Plasmodium falciparum, was undertaken given the high prevalence of LCRs in the proteome of this organism. Low complexity regions and repeat patterns have been recognized in proteins encoded in 986 genomes (68 archaea, 896 prokaryotes and 22 eukaryotes). Low complexity regions have been classified into following three categories: a) Composition of LCRs: (i) LCRs can be stretches of homo amino acid residues (ii) LCRs can be stretches of more than one amino acid residue type b) Periodicity of amino acids in LCRs: Certain amino acid residues can be observed at certain specific periodicity in proteins. c) Repeat patterns: Certain motif of amino acid residues are repeated in protein. 850 Plasmodium falciparum proteins are observed to have at least one repeat pattern where the repeating unit is at least 5 amino acid residues long. Statistical analysis on single amino acid residue repeats indicate that occurrence of stretches of homo amino acid residues is not a random event. Studies on recognition of functions, protein protein interactions and organization of tethered domain(s) in proteins containing LCR suggest that these proteins are part of variety of functional events such as signal transduction, enzymatic processes, cell differentiation, pyrimidine biosynthesis, fatty acid biosynthesis and chromosomal replication. Representations of low complexity regions of Plasmodium falciparum in protein data bank suggest that LCRs can take conformation of regular secondary structure (apart from disordered regions) in 3-D structures of proteins. Chapter 6 describes sequence analysis, structural modeling and evolutionary studies of Leishmania donovani hypusine pathway enzymes. Leishmania is an eukaryotic kinetoplastid protozoan parasite which causes leishmaniasis in humans. Hypusine is a non standard polyaminederived amino acid Nε-(4-amino-2-hydroxybutyl) lysine and is named after its two structural components, hydroxyputrescine and lysine. The eukaryotic translation initiation factor 5A (eIF5A) is the only cellular protein containing hypusine. Synthesis of hypusine is critical for the function of elF5A and is essential for eukaryotic cell proliferation and survival. Formation of hypusine is the result of a two step post-translational modification process involving enzymes (i) deoxyhypusine synthase (DHS) (ii) deoxyhypusine hydroxylase (DOHH). DHS, the first enzyme involved in hypusine pathway catalyzes the NAD-dependent transfer of the butylamino moiety of spermidine (substrate) to the ε-amino group of a specific lysine residue of eIF5A precursor and generates deoxyhypusine containing intermediate. DOHH, the second enzyme in same pathway catalyzes the hydroxylation of deoxyhypusine-containing intermediate, generating hypusine-containing mature eIF5A. Two putative deoxyhypusine synthase (DHS) sequences DHS34 and DHS20 have been identified in Leishmania donovani, by Professor Madhubala and coworkers (Jawaharlal Nehru University, New Delhi) with whom the work embodied in this chapter was done in collaboration. Detailed comparison of DHS34 sequence from Leishmania with human DHS protein indicated conservation of functionally important residues. 3D structural modeling studies of protein suggested that residues around the active site were absolutely conserved. NAD binding regions are located spatially closer, however, one NAD binding region was observed in a large (225 amino acid residues long) insertion. Based on these observations, DHS34 was predicted to have enzymatic activity. Experimental studies done by our collaborators confirmed preliminary results of computational analysis. Based on sequence and structural analysis of DHS20 and DOHH proteins, DHS20 and DOHH were proposed to be catalytically inactive and active respectively. Experimental studies on these proteins supported results of computational analysis. Deoxyhypusine synthase (DHS) and Deoxyhypusine hydroxylase (DOHH) are key proteins conserved in the hypusine synthesis pathways of eukaryotes. Because they are highly conserved, they could be coevolving. Comparison of the genetic distance matrices of DHS and DOHH proteins reveals that their evolutionary rates are better correlated when compared to the rate of an unrelated protein such as Cytochrome C. This indicates that they are coevolving, further serving as an indicator that, even non-interacting proteins that are functionally coupled, experience correlated evolution. However, this correlation does not extend to their tree topologies. Chapter 7 provides a classification scheme for protein kinases encoded in genomes of prokaryotic organisms. Overwhelming majority of the Ser/Thr protein kinases identified by gleaning archaeal and eubacterial genomes could not be classified into any of the well known Hanks and Hunter subfamilies of protein kinases. This is owing to the development of Hanks and Hunter classification scheme based on eukaryotic protein kinases which are highly divergent from their prokaryotic homologues. A large dataset of prokaryotic Ser/Thr protein kinases prokaryotic Ser/Thr protein kinases. Traditional sequence alignment and phylogenetic approaches have been used to identify and classify prokaryotic kinases which represent 72 subfamilies with at least 4 members in each. Such a clustering enables classification of prokaryotic Ser/Thr kinases and it can be used as a framework to classify newly identified prokaryotic Ser/Thr kinases. After series of searches in a comprehensive sequence databases, it is recognized that 38 subfamilies of prokaryotic protein kinases are associated to a specific taxonomic level. For example 4, 6 and 3 subfamilies have been identified that are currently specific to phylum proteobacteria, cyanobacteria and actinobacteria respectively. Similarly, subfamilies which are specific to an order, sub-order, class, family and genus have also been identified. In addition to these, it was also possible to identify organism-diverse subfamilies. Members of these clusters are from organisms of different taxonomic levels, such as archaea, bacteria, eukaryotes and viruses. Interestingly, occurrence of several taxonomic level specific subfamilies of prokaryotic kinases contrasts with classification of eukaryotic protein kinases in which most of the popular subfamilies of eukaryotic protein kinases occur diversely in several eukaryotes. Many prokaryotic Ser/Thr kinases exhibit a wide variety of modular organization which indicates a degree of complexity in protein-protein interactions and the signaling pathways in these microbes. Chapter 8 focuses on recognition, classification of protein kinases encoded in genomes of viruses and their implications in various functions and diseases. Protein kinases encoded by viral genomes play a major role in infection, replication and survival of viruses. Using traditional sequence homology detection tools, sequence alignment methods and phylogenetic approaches, protein kinases were recognized. 646123 protein sequences from 35799 viral genomes (including strains) have been used in this analysis. Protein kinases are identified using a combination of profile-based search methods such as PSI-BLAST, RPS-BLAST and HMMER approaches. Based upon sequence similarity over the length of catalytic kinase domains, 479 protein kinase domains recognized in 244 viral genomes have been clustered into 46 subfamilies with minimum sequence identity of 35% within a subfamily. Viral protein kinases are encoded in genomes of retro-transcribing viruses or viruses which possess double stranded DNA as genetic material. Based on the available functional information present for one or more members of a subfamily, a putative function has been assigned to other members of the subfamily. Information regarding interaction of viral protein kinases with viral/host protein has also been considered for enhancing understanding of function of kinases in a subfamily. Out of 46 subfamilies, 14 subfamilies are characterized by various functions. Kinases belonging to UL97, US69, UL13 and BGLF subfamilies are virus specific. For 7 subfamilies, nearest neighbors are from well characterized eukaryotic protein kinase groups such as AGC, CAMK and CDK. Out of 25 new uncharacterized subfamilies observed in this analysis, 13 subfamilies are virus specific. Different subfamilies have been characterized by various functions which are crucial for viral infection such as synthesis of structural unit, replication of genetic material, modification of cellular components, alteration in host immune system, competing with cellular protein for efficient usage of host machinery. Also, many viral kinases share very high sequence identity (~97%) with their eukaryotic counterpart and represent disease state. For example, a protein kinase encoded in Avian erythroblastosis virus shares 97% sequence identity with catalytic domain of human epidermal growth factor receptor tyrosine kinase. Leucine at position 861 in human protein is substituted by Gln in cancer conditions; the viral protein kinase sequence possesses Gln at corresponding position and thus represents disease state. Chapter 9 provides study of dependency on the ability of 3-D structural features of comparative models and crystal structures of inactive forms of enzymes to predict enzymes by considering protein kinases as case study. With the advent of structural genomics initiatives, there is a surge in the number of proteins with 3-D structural information even before functional features are understood on many of these proteins. One of the useful annotations of a protein is the demarcation of a protein into an enzyme or non-enzyme solely from the knowledge of 3-D structure. This is facilitated by the identification of active sites and ligand binding sites in a protein. In this work, which was carried out in collaboration with Dr Jim Warwicker of Manchester University, UK, an approach developed by Warwicker and coworkers has been used. In the 3D structure of proteins, the largest clefts are generally considered to be ligand binding sites. This feature along with other sequence alignment independent properties such as residue preferences, fraction of surface residues and secondary structure elements have been considered to differentiate enzymes from non-enzymes. Electrostatic potential at the active site is one of the key properties utilized in this respect. Active sites in enzymes are generally associated with ionizable groups which can take part in catalysis. In addition to the feature of large clefts in enzymes, active site residues are in buried environments and show larger deviation in pKa values than surface residues. The method proposed by Warwicker and co-workers distinguish proteins in to enzymes and non-enzymes considering the electrostatic features at clefts along with the sequence profile of the protein concerned. Conformation of the inactive state of an enzyme is not congenial to the catalytic function. In an ideal situation, a method should be capable of predicting an enzyme irrespective of whether determined structure corresponds to active or inactive state. Peak potential values have been calculated by using Warwicker program for a set of 15 protein kinases for which 3-D structures are present in active as well in inactive conformations. Comparison of peak potential values calculated for active and inactive conformations suggests that algorithm can differentiate between active and inactive conformations as value for active conformations are generally higher than corresponding values for inactive conformations. However, the peak potential values are high enough for even the inactive conformations to be predicted as enzyme. Peak potential values calculated for generated homology models of protein kinases (for which crystal structures are already available) at different sequence identities with template sequences predict protein kinases as enzymes and their peak potential values are comparable to corresponding values for X-ray structures. This suggests that proteins for which there are no crystal or NMR structures yet available and no good template with high sequence identity are present, peak potential values for models generated at low sequence identity can still give insight into probable function of protein as an enzyme. The enzyme/non-enzyme prediction algorithm was also found to be useful in confirming enzyme functionality using 3-D models of putative viral kinases. Initially, putative function of kinase has been assigned to these viral proteins based solely upon their sequence characteristics such as presence of residues/motifs which are important for activity of the protein. The enzyme recognition method which is not directly sensitive to these motifs confirmed that all the analyzed putative viral kinases are enzymes. Chapter 10 presents conclusions of work embodied in the entire thesis. Very briefly, various computational approaches have been used to analyze and understand structural and functional properties of repertoire of proteins of pathogenic organisms. Analysis of uncharacterized protein domain families has helped to understand the functional implications of constituent proteins. Experimental validation of these results can further facilitate unraveling of functional aspects of proteins encoded in various pathogenic organisms. Apart from studies embodied in the thesis, author has been involved in two other studies, which are provided as appendices. Appendix 1 describes comparison of substitution pattern of amino acid residues of protein encoded in P. falciparum genome with substitution pattern of corresponding homologous proteins from non-Plasmodium organisms. Salient differences have been highlighted. Appendix 2 discusses study of bacterial tyrosine kinases with an objective of recognition of all putative protein tyrosine kinases in E. coli. Computational study suggests that protein SopA can be a potential tyrosine kinase and this conclusion is being tested experimentally in collaborator’s laboratory.

La surveillance de la santé se définit comme la production et le traitement de données destinées à informer les programmes de mitigation des risques sanitaires. La surveillance des maladies infectieuses animales est généralement considérée comme un bien public, impliquant la responsabilité de l’Etat. La surveillance des maladies émergentes transfrontalières, dont l’influenza aviaire hautement pathogène (IAHP), est même perçue comme un bien public mondial, justifiant un partage d’informations entre Etats. La forme la plus répandue de la surveillance, dite passive ou réactive, repose sur la communication d’acteurs privés ou publics d’informations qu’ils détiennent sur l’état sanitaire des populations animales qu’ils observent aux autorités en charge de la surveillance. La surveillance se trouve donc confrontée à la problématique des biens publics dont la gestion est dépendante de la décision décentralisée d’acteurs privés. Deux questions se posent alors : quels sont les facteurs qui influencent la décision de transmettre une information aux systèmes de surveillance publics ? Ces facteurs sont-ils purement financiers ou impliquent-ils d’autres types d’enjeux, qui font intervenir l’environnement social de l’individu, le territoire dans lequel il s’insère et ses rapports de pouvoirs ? Une autre question est celle de l’existence de réseaux d’information, établis entre acteurs privés et publics permettant d’alerter un maximum d’acteurs de l’apparition d’un risque sanitaire. Comment ces réseaux de constituent-ils ? Dans quelle mesure sont-ils liés aux systèmes de surveillance publics ? Quelles formes de gestion du risque, sous contrôle privé ou public, permettent-ils ? Le cas étudié est celui de l’IAHP due à H5N1 chez les volailles domestiques en Asie du Sud-Est. Une étude a été menée dans quatre zones d’échelle spatiale réduite réparties sur les deux pays, trois au Viet Nam et une en Thaïlande. La théorie des graphs a été appliquée à la diffusion de l’information sur les suspicions d’IAHP entre acteurs privés et publics des territoires avicoles. La structure de ces réseaux d’information est conditionnée par l’organisation politique des territoires ruraux, sous forme de villages, et par les filières dans lesquels s’insèrent les élevages présents dans les territoires. Dans les zones d’étude du Viet Nam présentant un grand nombre d’élevage commerciaux privés, les acteurs amont de la filière avicole commerciale, qui fournissent aliments et produits vétérinaires aux éleveurs, ont un accès privilégié à l’information issue du secteur avicole commercial et villageois. Dans la zone d’étude de Thaïlande, les acteurs impliqués dans les combats de coqs ont un accès privilégié à l’information issue des éleveurs villageois. Ces acteurs centraux dans les réseaux facilitent la diffusion spatiale des informations et l’accès de l’ensemble des éleveurs à ces informations. Les autorités vétérinaires sont présentes dans les réseaux mais la priorité qui leur est accordée est faible en comparaison aux acteurs privés de la filière. En parallèle, des entretiens qualitatifs ou semi-quantitatifs utilisant les outils de l’épidémiologie participative ont été menés afin d’identifier les enjeux associés à la déclaration des suspicions aux autorités vétérinaire. Les enjeux diffèrent selon les territoires et les types de production avicoles qui les composent. Ces enjeux vont au-delà des problématiques purement financières : risques sanitaires et nuisances environnementales pour le voisinage, responsabilité dans les pertes économiques des autres éleveurs et des partenaires commerciaux, et valeur affective et sociale de l’animal sont autant de composantes potentielles de la décision de l’éleveur de déclarer une suspicion aux autorités. Une partie de ces enjeux est liée aux mesures de contrôle mise en place par l’Etat face au risque sanitaire. Cependant, d’autres sont strictement associés à la diffusion de l’information. / Health surveillance is defined as the production and processing of data aimed at informing health risk mitigation programs. Surveillance of infectious animal diseases is usually considered as a public good, involving the responsibility of the state. Surveillance of transboundary emerging diseases, like HPAI, is even perceived as an international public good, justifying information sharing between countries. The most common type of surveillance, i.e. passive or reactive surveillance, is based on communications from private or public actors of the information they hold about the health status of animal populations they observe to authorities in charge of health surveillance. Animal health is therefore confronted with the problematic of public goods whose production depends on decentralized private decision. Two questions may be raised: what are the factors influencing the decision to transmit information to public surveillance systems? Are these factors solely of monetary nature or are they linked with other types of issues, among which the social environment of individuals, the place where they live and their power relationships? Another question relates to the existence of information networks established between private and public actors which enable to a part of the population of sanitary threats. How these are networks constituted? To which extent are they linked with public surveillance systems? Which type of risk management do they allow? The studied case is H5N1 HPAI in domestic poultry in Southeast Asia. A study was conducted in four areas of limited spatial scale distributed in two countries, three in Viet Nam and one in Thailand. Graph theory was applied to the diffusion of information related to HPAI suspicions between actors, private or public. The structure of these networks is shaped by the political organization of rural places, the villages, and by the value chains to which poultry farms belong. In study areas of Viet Nam with widespread commercial poultry farming, upstream actors of the value chain, supplying feed and veterinary products to farmers have better access to information from the commercial and backyard poultry farms. In the Thailand study area, actors participating in cock fighting games have a better access to information from backyard farms. These actors who are central in information networks facilitate the spatial spread of information and access of farmers to information from distant locations. Veterinary authorities are included in the information networks but their attributed priority is week in comparison with private actors of value chains. Besides, qualitative and semi-quantitative interviews were conducted, using tools of participatory epidemiology, in order to identify issues linked with suspicion reporting to veterinary authorities. Those issues differ according to places and types of poultry production. They go beyond purely monetary concerns: sanitary risks and environmental nuisances to the neighborhood, responsibility in economic losses of other farmers and commercial partners and social and affective value of animals are potential components of the decision of farmers to report a suspicion to veterinary authorities. A part of these issues are linked with disease control measures implemented by the state in response to sanitary risks. However, others are strictly associated with information spread. It is the case, for example, of impacts of information on poultry market prices.

Les bactéries pectinolytiques des genres Pectobacterium (ancien nom Erwinia carotovora) et Dickeya (ancien nom Erwinia chrysanthemi) sont les agents des maladies de la jambe noire et de la pourriture molle. Ils provoquent des dommages aux cultures et des pertes économiques élevées. Les pertes causées par les bactéries pectinolytiques sont évaluées à environ 2 à 10% du rendement de pommes de terre, en fonction de l'année. En 2009, les pertes en pommes de terre en Europe ont été estimées à 250 millions d'euros. Au cours des dernières années, des souches de Dickeya ont été de plus en plus souvent isolées de plantes malades en Pologne, en France et d'autres pays européens. Le genre Dickeya est un groupe très diversifié, qui, selon la nomenclature actuelle contient sept espèces: D. aquatica, D. chrysanthemi, D. dadantii, D. dianthicola, D. paradisiaca, D. solani et D. zeae. Les résultats récents, obtenus dans différents pays européens, indiquent qu'un nouveau groupe de souches de Dickeya peut infecter efficacement les plantes de pomme de terre et causer des symptômes de la maladie en climat tempéré. Les souches de D. solani sont considérés comme plus agressives que les autres bactéries causant la jambe noire. Une analyse préliminaire a suggéré qu’elles ont besoin de plus faibles températures optimales pour le développement de la maladie ainsi que de niveaux d'inoculum inférieurs pour la propagation de l'infection. Elles semblent avoir une plus forte capacité à coloniser les racines de plantes de pomme de terre et à se propager à travers le système vasculaire de la plante. Les souches de D. solani produisent une large gamme d’enzymes dégradant de la paroi cellulaire végétale, qui sont les principaux facteurs de virulence. Les objectifs de l'étude étaient les suivants: 1) la caractérisation phénotypique et génotypique des souches de D. solani isolées dans des pays ayant des conditions climatiques différentes: Pologne, Finlande et Israël, 2) l'étude de l’influence d'extraits de pomme de terre sur l'expression de quelques gènes sélectionnés de D. solani: pelD, pelL, tssk, lfaA, 3) la génomique comparative de dix souches de D. solani, basée sur 4 génomes séquencés pour cette étude et 6 séquences génomiques disponibles dans la base de données GenBank. En conclusion, toutes les études génomiques ont montré que les souches de D. solani forment un groupe très homogène. Cependant, leur analyse phénotypique révèle une certaine variabilité entre les souches provenant de différentes conditions climatiques. La raison des variations observées dans les traits phénotypiques peut être liée à la régulation de l'expression des gènes codant les facteurs de virulence qui peuvent être influencés par la température, le pH, la carence en fer ou en oxygène et la disponibilité en azote, ainsi que par la présence de composés spécifiques des tissus végétaux. / Dickeya solani is a species consisting of newly emerged plant pathogenic bacteria that cause blackleg and soft rot diseases. They are responsible for great damages to potato plantations in most of European countries. D. solani strains produce a wide range of plant cell-wall degrading enzymes which are the main virulence factors. The aims of the study were: 1) phenotypic and genotypic characterizations of the D. solani strains isolated in countries with different climatic conditions: Poland, Finland and Israel, 2) study of the potato tuber extract influence on the expression of a few selected D. solani genes : pelD, pelL, tssK, lfaA,3) comparative genomics of ten D. solani strains, performed on 4 genomes sequenced for this study and 6 genome sequences available in the GenBank databases. The results showed that the strains from different climatic conditions have identical profiles in rep-PCR (with three different primers) and in Restriction Fragments Lenght Polymorphism-Pulse Field Gel Electrophoresis. However, they do differ phenotypically, especially in the activity of plant cell-wall degrading enzymes. Polish strains have higher activities of pectinolytic, cellulolytic and proteolytic enzymes than Finnish and Israeli strains. D. solani mutants in the pelD, pelL, tssK, lfaA genes were constructed by site-specific mutagenesis. The highest induction by plant extracts was observed for the lfaA gene. The expression of pelL is also induced by plant derived signal(s), but not that of pelD and tssK. Comparative genomics helped to elucidate the D. solani pangenome. The 10 D. solani strains genomes are coding for a total of 41 947 proteins which were grouped into 5 045 Orthologous Groups, 3 809 belonging to the core genome, 413 to the accessory genome and 823 to the unique genome. Some pathogenicity-related genes as well as their regulators were selected on the basis of the knowledge available for D. dadantii 3937, the most studied Dickeya strain, which belongs to a closely related species. Analysis of their protein sequence showed no difference in the sequence of those genes within the 10 genomes. All the genetic studies proved that D. solani strains form a very homogenous group. On the other hand, the phenotypic analysis showed some variability among strains from different climatic conditions. The observed variations in the phenotypic traits can results from a different regulation of the expression of the genes encoding virulence factors which are influenced by temperature, pH, iron deprivation, oxygen and nitrogen availability, as well as by the presence of plant compounds.

Water is an indispensible and yet a difficult resource to be renewed, thus water scarcity has become one of the major challenges faced worldwide, with the Southern regions of Africa being the most impacted and affected, especially the Eastern Cape Province of South Africa where rural communities depend on receiving waterbodies that are often negatively impacted by wastewater final effluents. This present study was conducted between August and December 2010 to assess the physicochemical and microbial qualities of the final effluents of peri-urban and rural communities based wastewater treatment plants in the Eastern Cape Province. The physicochemical parameters were determined on site and in the laboratory, while bacteriological qualities were determined using culture based techniques. The virological qualities were determined by molecular methods using reverse transcriptase polymerase chain reaction for the target RNA virus and the conventional polymerase chain reaction for the target DNA virus. For both wastewater treatment plants, the physicochemical parameters ranged as follows: chemical oxygen demand (5.95-45 mg/L); total dissolved solids (114.5-187.0 mg/L); salinity (0.12-0.20 psu); temperature (14.2-25.7oC); pH (6.0-7.6); nitrate and nitrites (1.55-6.7 mg/L and 0.023-1.15 mg/L respectively); biological oxygen demand (3.5-7.8 mg/L); turbidity (1.49-6.98 NTU); and chlorine residual (0-2.97 mg/L). Feacal indicator bacteria counts ranged as follows: feacal coliforms (0-1.25×104 cfu/100 ml); total coliforms (0-3.95×104 cfu/100 ml); and enterococci (0-5.0×103 cfu/100 ml). xviii Seventy five percent of the rural community based plant and 80 percent of the peri-urban community based plant were positive for coxsackie A virus, while hepatitis A virus was detected in all the rural community based plant 80 percent of the peri-urban community based plant. This study suggests the need for intervention by appropriate regulatory agencies to ensure regular monitoring of the qualities of final effluents of wastewater treatment facilities in the Eastern Cape Province and ensure compliance to established guidelines.

Black band disease (BBD) of corals is a temperature dependent, highly virulent, polymicrobial disease affecting reef-building corals globally. The microbial consortium of BBD is primarily comprised of functional physiological groups that include photosynthetic cyanobacteria, sulfate reducers, sulfide oxidizers and a vast repertoire of heterotrophic bacteria. Quorum sensing (QS), the cell-density dependent communication phenomenon in bacteria, is known to induce expression of genes for a variety of virulence factors in diseases worldwide. Microbes capable of QS release signals such as acyl homoserine lactones (AHLs) and autoinducer-2 (AI-2), which coordinate microbial interaction. The focus of the present study was to investigate the presence and potential role of QS in BBD pathogenicity, utilizing culture dependent and independent methodologies. Isolates across coral health states including BBD, were screened for production of QS signals, and AHL and AI-2 production capabilities were analyzed via LC-MS/MS. The effect of temperature on AHLs was also examined. Additionally, antimicrobial production capabilities of isolates were tested. BBD metagenomes were utilized to screen for sequences related to QS, antimicrobial synthesis, and antimicrobial resistance genes. BBD isolates represented a significantly higher proportion of isolates capable of producing QS signals in comparison to healthy coral isolates. Several AHLs produced by coral derived bacterial cultures were identified, and three AHLs, specifically 3OHC4, 3OHC5 and 3OHC6, showed a significant increase in production at an elevated temperature of 30 °C, which correlates with increased BBD incidence on reefs with increasing water temperature. Most of the BBD cultured isolates were identified as vibrios. Several sequences related to QS, antimicrobial synthesis and resistance genes were detected in the BBD metagenomes. Based on the findings of this study, a model for potential microbial interactions amongst BBD heterotrophs, centered around QS, is proposed. Taken together, the findings from this study provide a clearer understanding of the potential role of QS in BBD, and serve as the basis for further studies aimed at elucidating the pathogenesis of an intricate coral disease.