This work presents a novel approach for the design of a predictive model of music that can be used to analyze and generate musical material that is highly context dependent. The system is based on an approach known as n-gram modeling, often used in language processing and speech recognition algorithms, implemented initially upon a framework of Variable-Length Markov Models (VLMMs) and then extended to Variable-Length Hidden Markov Models (VLHMMs). The system brings together various principles like escape probabilities, smoothing schemes and uses multiple representations of the data stream to construct a multiple viewpoints system that enables it to draw complex relationships between the different input n-grams, and use this information to provide a stronger prediction scheme. It is implemented as a MAX/MSP external in C++ and is intended to be a predictive framework that can be used to create generative music systems and educational and compositional tools for music. A formal quantitative evaluation scheme based on entropy of the predictions is used to evaluate the model in sequence prediction tasks on a database of tabla compositions. The results show good model performance for both the VLMM and the VLHMM while highlighting the expensive computational cost of higher-order VLHMMs.

<p>The engineering of bacterial surfaces has in recent yearsattracted a lot of attention with applications in manydifferent areas of bioscience. Here we describe the use of twodifferent surface display systems for the gram-positivebacteria Staphylococcus carnosus and Staphylococcus xylosus invarious biotechnological applications.</p><p>Environmental microbiology currently attracts a lot ofattention since genetically engineered plants and bacteriamight be used as bioadsorbents for sequestration of toxicmetals. Bacterial surface display of metal-binding peptidesmight enable recycling of the biomass by desorption ofaccumulated heavymetals. In an attempt to recruitstaphylococcal display systems for bioremediation purposes,polyhistidyl peptides were successfullly displayed on thesurface of recombinant S. carnosus and S. xylosus cells.Whole-cell Ni2+-binding assays demonstrated that therecombinant cells had gained metal-binding capacity compared towild-type cells.</p><p>Tailor-made, metal-binding staphylococci was created using apreviously constructed phage-display combinatorial proteinlibrary based on a fungal cellulose-binding domain (CBD)derived from the cellobiohydrolase Cel7A of Trichoderma reseii.Novel metal-binding CBDs were generated through a phagemediated selection procedure. Selected CBD variants, now devoidof cellulose binding, were randomly selected and sequenceanalysis of selected variants revealed a marked preference forhistidine residues at the randomized positions. Surface displayof these novel CBD variants resulted in recombinantstaphylococci with increased metal-binding capacity compared tocontrol strains, indicating that this could become a generalstrategy to engineer bacteria for improved binding to specificmetal ions.</p><p>Directed immobilization of cells with surface displayedheterologous proteins have widespread use in modernbiotechnology. Among other things they could provide aconvenient way of generating biofilters, biocatalysts orwhole-cell diagnostic devices. It was therefore investigatedwhether directed immobilization of recombinant staphylococci oncotton fibers could be achieved by functional display of afungal cellulose-binding domain (CBD). Recombinant S. carnosuscells with surface anchored CBDs from Trichoderma reseii Cel6Awere found to efficiently bind to cotton fibers creating almosta monolayer on the fibrous support. The co-expression of thisCBD together with previously described metal-binding proteinson the surface of our staphylococci would create means fordeveloping effective bioadsorbents for remediationpurposes.</p><p>The original plasmid vector, designed for heterologoussurface display on recombinant S. carnosus cells has exhibitedproblems related to structural instability, possibly due to thepresence of a phage f1 origin of replication in the vectorsequence. This would be a problem if using the vector systemfor library display applications. Therefore, novel surfacedisplay vectors, lacking the phage ori were constructed andevaluated by enzymatic and flow cytometric whole-cell assays.One such novel vector, pSCXm, exhibited dramatically increasedplasmid stability with the retained high surface density ofexpressed heterologous proteins characteristic for the originalS. carnosus display vector, thus making it potentially moresuitable for library display applications.</p><p>The successful engineering of our staphylococcal displaysystem encouraged us to further evaluate the potential to usethe staphylococcal system for display of combinatorial proteinlibraries and subsequent affinity based selections using flowcytometric cell sorting. A model system of recombinant S.carnosus cells with surface displayed engineered protein Adomains was constructed. It was demonstrated that target cellscould be sorted essentially quantitatively from a moderateexcess of background cells in a single sorting-step.Furthermore, the possibility of using staphylococcal surfacedisplay and flow cytometric cell sorting also for specificenrichment of very rare target cells by multiple rounds ofcell-sorting and in between amplification was demonstrated.</p><p><b>Key words:</b>affibody, albumin binding protein, bacterialsurface display, cell immobilization, bioremediation,combinatorial protein engineering, flow cytometry,Gram-positive, metal binding, staphylococcal protein A,Staphylococcus carnosus, Staphylococcus xylosus, whole-celldevices</p>

Gram-negative infection has been linked to hospital water although few studies have examined whether water systems are reservoirs of nosocomial pathogens. This study investigated longitudinal recovery of the opportunistic pathogens Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Acinetobacter baumannii from water outlets of a haematology unit and evaluated Point-Of-Use Filtration (POU-F) as a control measure. In a two-year double cross-over trial, water samples and swabs were taken weekly from 39 showers/taps on the unit. Four study phases alternated between non-filtered (Phases 1 &amp; 3), and filtered outlets (Phases 2 &amp; 4) using Pall AquasafeTM 14-day filters. In Phases 1 &amp; 3; 99% of 1396 samples yielded bacterial growth, with colonies generally too numerous to count. Target species were isolated from 22% of water samples (P. aeruginosa 14%; S. maltophilia 10%) and 10% of swabs. P. aeruginosa was particularly associated with handwash stations and S. maltophilia with showers. A. baumannii was not isolated. With POU-F; 22% of 1242 samples yielded bacterial growth (mean CFU/100ml ,4.6). S. maltophilia was isolated only once from water but never from outlet swabs. PCR typing identified clusters of isolates colonizing different outlets over time but no clear association between water and patient isolates was identified. The incidence of Gram negative infections remained low throughout the study. Without POU-F, water from taps/showers represented a source of bacteria including the target species. POU-F substantially reduced the frequency and number of target species from every outlet, and merits further investigation as an intervention to protect immunocompromised patients from opportunistic pathogens.

No description available.

No description available.

Les premières souches bactériennes résistantes aux antibiotiques sont connues depuis 70 ans et se sont multipliées ces dernières années posant un grave problème de santé publique. Parmi les nombreux types d'infections induites par ces bactéries, nous nous sommes intéressés aux infections intestinales qui peuvent dégénérer en maladies inflammatoires de l'intestin et cancers. Notre travail de thèse a consisté à proposer des outils thérapeutiques dans le traitement des pathologies intestinales infectieuses : des peptides antimicrobiens dérivés de la chromogranine A et des extraits de plantes de la médecine traditionnelle béninoise. La chromogranine A est une protéine libérée par les cellules nerveuses, neuroendocrines et immunitaires au cours d'un stress et maturée en peptides. Des peptides actifs contre quatre souches bactériennes pathogènes (Klebsiella oxytoca, Salmonella enterica, Shigella sonnei et Vibrio cholera non O1) ont été identifiés et l'interaction bactérie-peptide analysée. L'étude de la combinaison peptide-antibiotique montre que la cateslytine permet de réduire les doses d'antibiotiques nécessaires. Ensuite, nous avons étudié l'implication de deux peptides sur un modèle de cellules neuroendocrines, les cellules BON. La chromofungine provoque la stimulation des cellules BON en induisant un influx de calcium extracellulaire, tandis que la catestatine est capable de bloquer l'activité de la chromofungine.Après un screening des extraits de 14 plantes du Bénin, nous avons isolé deux molécules, la sinensétine et l'O-tétraméthyléther scutellaréine, responsables de l'activité antibactérienne de Chromolaena odorata contre les pathogènes étudiés.

Streptococcus equi is the causative agent of strangles, a prevalent and highly contagious disease of horses. Despite the animal suffering and economic burden associated with strangles, little is known about the molecular basis of S. equi virulence. Here we have investigated the contributions of a specific lipoprotein and the general lipoprotein processing pathway to the abilities of S. equi to colonize equine epithelial tissues in vitro and to cause disease in both a mouse model and the natural host in vivo. Colonization of air interface organ cultures after they were inoculated with a mutant strain deficient in the maturase lipoprotein (prtM138-213, with a deletion of nucleotides 138 to 213) was significantly less than that for cultures infected with wild-type S. equi strain 4047 or a mutant strain that was unable to lipidate preprolipoproteins (lgt190-685). Moreover, mucus production was significantly greater in both wild-type-infected and lgt190-685-infected organ cultures. Both mutants were significantly attenuated compared with the wild-type strain in a mouse model of strangles, although 2 of 30 mice infected with the lgt190-685 mutant did still exhibit signs of disease. In contrast, only the prtM138-213 mutant was significantly attenuated in a pony infection study, with 0 of 5 infected ponies exhibiting pathological signs of strangles compared with 4 of 4 infected with the wild-type and 3 of 5 infected with the lgt190-685 mutant. We believe that this is the first study to evaluate the contribution of lipoproteins to the virulence of a gram-positive pathogen in its natural host. These data suggest that the PrtM lipoprotein is a potential vaccine candidate, and further investigation of its activity and its substrate(s) are warranted.

Gram-positive bacteria are part of the normal flora of fish from different aquatic environments. They are mesophilic bacteria and demonstrate optimum growth at ambient temperature. In the sub-tropics, marine fish are caught from seas at temperatures of 16 to 34C, they are usually not iced and are handled at ambient temperature. It was hypothesized that under these conditions Gram-positive bacteria will be abundant in sub-tropical marine fish and will have roles in the spoilage of fish. A review of literature showed that there is a gap in understanding the Gram-positive bacterial populations in sub-tropical marine fish. This is partly due to the fact that the selective media used for isolating Gram-positive bacteria have limitations. Ecological and speciation studies have revealed that the ecology and speciation of many Gram-positive bacteria have not been clearly elucidated. The effect of ambient storage on the individual genera and species of Gram-positive bacteria in fish has been rarely studied. The spoilage potential of Gram-positive bacteria of marine fish origin has not been clearly determined. Therefore, the main aims of this study were to isolate Gram-positive bacteria from fresh and ambient-temperature-stored sub-tropical marine fish, speciate the isolates and study the spoilage potential of the isolates. The practical components of this study were conducted in four parts. The first part dealt with validation of tryptone soya agar with 0.25% phenylethyl alcohol (PEA-TSA) to enumerate Gram-positive bacteria. The second part enumerated Gram-positive bacteria from the muscles, gills and gut of Pseudocaranx dentex (Silver Trevally), Pagrus auratus (Snapper) and Mugil cephalus (Sea Mullet) stored at 25C for 15 hours using PEA-TSA. The third part dealt with the speciation of the isolates using appropriate methods such as polymerase chain reaction, 16S rRNA gene sequence, the VITEK JR system and conventional biochemical methods. In the fourth part, the isolates were assayed qualitatively for their ability to produce volatile sulphur compounds (VSC), reduce trimethylamine oxide and decarboxylate histidine, lysine and ornithine at mesophilic temperature, 32C. Initial studies indicated that PEA-TSA significantly (P< 0.05) reduced the total aerobic bacterial count of fish whereas control Gram-positive bacteria were not affected (P> 0.05). Gram-positive aerobic bacterial counts (GABC) significantly (P< 0.05) increased in the muscles and gills during ambient storage for 15 hours. Within each species, no significant (P> 0.05) differences were found in GABC between muscles and gills. Moreover, there were no significant differences (P> 0.05) in GABC between fish species during storage. In total, 390 bacteria were isolated from the fresh and stored fish; 339 isolates (87%) were found to be Gram-positive. Two hundred and sixty-six isolates (78%) of Gram-positive bacteria were identified to fall into 13 genera, namely Staphylococcus, Micrococcus, Bacillus, Virgibacillus, Brevibacillus, Corynebacterium, Streptococcus, Enterococcus, Aerococcus, Exiguobacterium, Carnobacterium, Vagococcus and Sporosarcina and 30 species. In fresh fish, Staphylococcus epidermidis and Micrococcus luteus were the most frequent isolates. The effect of storage at 25C for 15 hours resulted in a change of Gram-positive bacterial populations; while S. epidermidis, S. xylosus and Bacillus megaterium were no longer present, S. warneri, B. sphaericus, Brevibacillus borstelensis, Enterococcus faecium and Streptococcus uberis increased. Three species, E. faecium, Str. uberis and B. sphaericus, were the most prevalent at the end of storage. Micrococcus luteus and S. warneri were the most prevalent isolates from Pseudocaranx dentex, but E. faecium and Str. uberis were the most frequently isolated from Pagrus auratus and Mugil cephalus. With respect to different parts of the fish body, E. faecium, Str. uberis and B. sphaericus were the most frequent isolates from the muscles, E. faecium, Str. uberis from the gills and M. luteus from the gut. Among the 228 isolates examined, Br. borstelensis 73, Br. borstelensis 291, Str. uberis 339, Vagococcus fluvialis 31 and Vag. fluvialis 132 produced VSC from sodium thiosulphate, cysteine and methionine. However, strains varied in sulphur source utilization. Exiguobacterium acetylicum 5, Exiguobacterium spp. 191, Carnobacterium spp. 338, Br. borstelensis 73, Br. borstelensis 291, Str. uberis 30, Str. uberis 339, Vag. fluvialis 31 and Vag. fluvialis 132 reduced TMAO. No histidine decarboxylase activity was found in the Gram-positive bacterial species tested. Lysine and ornithine were decarboxylated mainly by different strains of S. warneri, S. epidermidis and M. luteus. During ambient storage of fish, the frequency of lysine-decarboxylating bacteria increased and became more diverse after 5 hours of storage. Among fish species examined, the frequencies of lysine- and ornithine-decarboxylating bacteria were higher and more diverse in Pseudocaranx dentex than in Pagrus auratus and Mugil cephalus. This study found that Gram-positive bacteria were abundant and diverse in sub-tropical marine fish; however, their frequencies were affected by fish habitat and fish body part. Ambient temperature storage determined which Gram-positive bacterial species were dominant. With the exception of one isolate of S. aureus, Gram-positive bacteria isolated from sub-tropical marine fish caught from unpolluted water were not potential pathogens. The study also showed that Gram-positive bacteria had greater ability to decarboxylate lysine and ornithine than to produce VSC or reduce TMAO, and the spoilage potential of a bacterial species was a strain-dependent behaviour. This is a significant study as it is the first study on this aspect sub-tropical marine fish. It validated a selective medium that can be used to enumerate most Gram-positive bacteria from a marine environment. Most of the Gram-positive bacterial species from sub-tropical marine fish identified in this study were documented for the first time. The effects of ambient storage and the spoilage potential of Gram-positive bacteria from sub-tropical marine were clearly elucidated.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2005. / Härtill 4 uppsatser.

Os aminoglicosídeos permanecem sendo um dos principais antibióticos no tratamento de infecções causadas por bactérias gram-negativas, apesar do surgimento de novos antibióticos. Na Unidade de Endoscopia Digestiva do Hospital de Clínicas de Porto Alegre os aminoglicosídeos, combinados com antibióticos ß-lactâmicos, têm sido utilizados no tratamento de infecções das vias biliares e como antibiótico profilático em procedimento como a colangiopancreatografia endoscópica retrógrada. O objetivo do presente estudo foi comparar a eficácia terapêutica da dose única total diária com dose fracionada diária de gentamicina no tratamento da infecção das vias biliares, baseando-se na concentração biliar de gentamicina obtida nesses dois regimes terapêuticos e sua relação com a concentração inibitória mínima das principais bactérias isoladas na bile de pacientes com infecção do trato biliar. Os pacientes selecionados foram randomizados para tratamento com gentamicina na dose de 4mg/kg de peso por meio intravenoso sendo divididos em 2 grupos: grupo 1 recebeu dose única diária dividida em 3 horários (8 / 8 horas) e o grupo 2 recebeu o fármaco como dose única total diária. Os resultados do estudo evidenciaram que os níveis biliares de gentamicina nos pacientes tratados com dose única diária de gentamicina (grupo 2) ultrapassaram de 3 a 6 vezes as concentrações inibitórias mínimas das bactérias gram-negativas isoladas, enquanto que os níveis de gentamicina à nível biliar nos pacientes tratados com dose fracionada de gentamicina (grupo 1) conseguiram igualar ou ultrapassar no máximo e 3 vezes, dependendo da bactéria gram-negativa testada, as concentrações inibitórias. Além disto, os níveis biliares de gentamicina dos pacientes tratados com dose única diária permaneceram por intervalo superior a 14 horas acima das concentrações inibitórias mínimas destas bactérias, reforçando ainda mais o efeito pós-antibiótico obtido no intervalo de tempo onde não são detectados mais níveis de gentamicina na bile. Baseado nos efeitos bactericida dependente da concentração e efeito pós-antibiótico dos aminoglicosídeos,os resultados deste estudo sugerem que a dosagem única diária de gentamicina apresenta maior eficácia terapêutica que a dosagem fracionada diária no tratamento da infecção das vias biliares.