Fastidiosipila sanguinis gen. nov., sp nov., a new Gram-positive, coccus-shaped organism from human blood

Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6% O-2. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al, Int J Syst Bacteriol 44 (1994), 812-826]. Sequence divergence values of 15% or more were observed between the unidentified bacterium and all other recognized species within this and related rRINIA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp, nov. The type strain of Fastidiosipila sanguinis is CCUG 47711(T) (= CIP 108292(T)).

Atopococcus tabaci gen. nov., sp nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium isolated from tobacco

A novel Gram-positive, aerobic, catalase-negative, coccus-shaped organism originating from tobacco was characterized using phenotypic and molecular taxonomic methods. The organism contained a cell wall murein based on L-lysine (variation A4 alpha, type L-lysine-L-glutamic acid), synthesized long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types (with C(16:1)omega 9, C-16:0 and C(18:1)omega 9 predominating) and possessed a DNA G+C content of 46 mol%. Based on morphological, biochemical and chemical characteristics, the coccus-shaped organism did not conform to any presently recognized taxon. Comparative 16S rRNA gene sequencing studies confirmed the distinctiveness of the unknown coccus, with the bacterium displaying sequence divergence values of greater than 7% with other recognized Gram-positive taxa. Treeing analysis reinforced its distinctiveness, with the unidentified organism forming a relatively long subline branching at the periphery of an rRNA gene sequence cluster which encompasses the genera Alloiococcus, Allolustis, Alkalibacterium, Atopostipes, Dolosigranulum and Marinilactibacillus. Based on phenotypic and molecular phylogenetic evidence, it is proposed that the unknown organism from tobacco be classified as a new genus and species, Atopococcus tabaci gen. nov., sp. nov. The type strain of Atopococcus tabaci is CCUG 48253(T) (= CIP 108502(T)).

Allofustis seminis gen. nov., sp. nov., a novel Gram-positive, catalase-negative, rod-shaped bacterium from pig semen

An unknown Gram-positive, catalase-negative, facultatively anaerobic, non-spore-forming, rod-shaped bacterium originating from semen of a pig was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a directly cross-linked cell wall murein based on L-lysine and a DNA G + C content of 39 mol%. Comparative 16S rRNA gene sequencing showed that the unidentified rod-shaped organism formed a hitherto unknown subline related, albeit loosely, to Alkalibacterium olivapovliticus, Alloiococcus otitis, Dolosigranulum pigrum and related organisms, in the low-G + C-content Gram-positive bacteria. However, sequence divergence values of > 11 % from these recognized taxa. clearly indicated that the novel bacterium represents a separate genus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig semen be classified as a new genus and species, Allofustis seminis gen. nov., sp. nov. The type strain is strain 01-570-1(T) (=CCUG 45438(T)=CIP 107425(T)).

A neurofuzzy network knowledge extraction and extended gram-Schmidt algorithm for model subspace decomposition

This paper introduces a new neurofuzzy model construction and parameter estimation algorithm from observed finite data sets, based on a Takagi and Sugeno (T-S) inference mechanism and a new extended Gram-Schmidt orthogonal decomposition algorithm, for the modeling of a priori unknown dynamical systems in the form of a set of fuzzy rules. The first contribution of the paper is the introduction of a one to one mapping between a fuzzy rule-base and a model matrix feature subspace using the T-S inference mechanism. This link enables the numerical properties associated with a rule-based matrix subspace, the relationships amongst these matrix subspaces, and the correlation between the output vector and a rule-base matrix subspace, to be investigated and extracted as rule-based knowledge to enhance model transparency. The matrix subspace spanned by a fuzzy rule is initially derived as the input regression matrix multiplied by a weighting matrix that consists of the corresponding fuzzy membership functions over the training data set. Model transparency is explored by the derivation of an equivalence between an A-optimality experimental design criterion of the weighting matrix and the average model output sensitivity to the fuzzy rule, so that rule-bases can be effectively measured by their identifiability via the A-optimality experimental design criterion. The A-optimality experimental design criterion of the weighting matrices of fuzzy rules is used to construct an initial model rule-base. An extended Gram-Schmidt algorithm is then developed to estimate the parameter vector for each rule. This new algorithm decomposes the model rule-bases via an orthogonal subspace decomposition approach, so as to enhance model transparency with the capability of interpreting the derived rule-base energy level. This new approach is computationally simpler than the conventional Gram-Schmidt algorithm for resolving high dimensional regression problems, whereby it is computationally desirable to decompose complex models into a few submodels rather than a single model with large number of input variables and the associated curse of dimensionality problem. Numerical examples are included to demonstrate the effectiveness of the proposed new algorithm.

Development of a miniaturised microarray-based assay for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria

We describe the development of a miniaturised microarray for the detection of antimicrobial resistance genes in Gram-negative bacteria. Included on the array are genes encoding resistance to aminoglycosides, trimethoprim, sulphonamides, tetracyclines and beta-lactams, including extended-spectrum beta-lactamases. Validation of the array with control strains demonstrated a 99% correlation between polymerase chain reaction and array results. There was also good correlation between phenotypic and genotypic results for a large panel of Escherichia coli and Salmonella isolates. Some differences were also seen in the number and type of resistance genes harboured by E. coli and Salmonella strains. The array provides an effective, fast and simple method for detection of resistance genes in clinical isolates suitable for use in diagnostic laboratories, which in future will help to understand the epidemiology of isolates and to detect gene linkage in bacterial populations. (C) 2008 Published by Elsevier B.V. and the International Society of Chemotherapy.

Array based detection of antibiotic resistance genes in Gram negative bacteria isolated from retail poultry meat in the UK and Ireland

The use of antibiotics in birds and animals intended for human consumption within the European Union (EU) and elsewhere has been subject to regulation prohibiting the use of antimicrobials as growth promoters and the use of last resort antibiotics in an attempt to reduce the spread of multi-resistant Gram negative bacteria. Given the inexorable spread of antibiotic resistance there is an increasing need for improved monitoring of our food. Using selective media, Gram negative bacteria were isolated from retail chicken of UK-Intensively reared (n = 27), Irish-Intensively reared (n = 19) and UK-Free range (n = 30) origin and subjected to an oligonucleotide based array system for the detection of 47 clinically relevant antibiotic resistance genes (ARGs) and two integrase genes. High incidences of β-lactamase genes were noted in all sample types, acc (67%), cmy (80%), fox (55%) and tem (40%) while chloramphenicol resistant determinants were detected in bacteria from the UK poultry portions and were absent in bacteria from the Irish samples. Denaturing Gradient Gel Electrophoresis (DGGE) was used to qualitatively analyse the Gram negative population in the samples and showed the expected diversity based on band stabbing and DNA sequencing. The array system proved to be a quick method for the detection of antibiotic resistance gene (ARG) burden within a mixed Gram negative bacterial population.

A Metal-Repressed Promoter From Gram-Positive Bacillus subtilis Is Highly Active and Metal-Induced in Gram-Negative Cupriavidus metallidurans

A synthetic version of the metal-regulated gene A (mrgA) promoter from Bacillus subtilis, which in this Gram-positive bacterium is negatively regulated by manganese, iron, cobalt, or copper turned out to promote high level of basal gene expression that is further enhanced by Co(II), Cd(II), Mn(II), Zn(II), Cu(II), or Ni(II), when cloned in the Gram-negative bacterium Cupriavidus metallidurans. Promoter activity was monitored by expression of the reporter gene coding for the enhanced green fluorescent protein (EGFP), and cellular intensity fluorescence was quantified by flow cytometry. Expression levels in C. metallidurans driven by the heterologous promoter, here called pan, ranged from 20- to 53-fold the expression level driven by the Escherichia coli lac promoter (which is constitutively expressed in C. metallidurans), whether in the absence or presence of metal ions, respectively. The pan promoter did also function in E. coli in a constitutive pattern, regardless of the presence of Mn(II) or Fe(II). In conclusion, the pan promoter proved to be a powerful tool to express heterologous proteins in Gram-negative bacteria, especially in C. metallidurans grown upon high levels of toxic metals, with potential applications in bioremediation. Biotechnol. Bioeng. 2010; 107: 469-477. (C) 2010 Wiley Periodicals, Inc.

The hidden martingale restriction in Gram-Charlier option prices

A hidden martingale restriction is developed for option pricing models based on Gram-Charlier expansions of the normal density function. The restriction is hidden behind a reduction in parameter space for the Gram-Charlier expansion coefficients. The resulting restriction is invisible in the option price.

New crevice corrosion testing method and its use in the investigation of oil stain

A new electrochemical method was developed to investigate crevice corrosion and its inhibitors. A wire beam electrode was used to allow electrochemical parameters to be measured directly from the crevice area. As an example, oil stain was investigated using this method.

Gram-scale and template-free synthesis of ultralong tin disulfide nanobelts and their lithium ion storage performances

Ultralong SnS2 nanobelts with a high production yield up to _98% were synthesized via a gram-scale and template-free solvothermal route. The synthetic mechanism of these intriguing ultralong nanobelts was proposed to be from the synergetic effect of the layered CdI2-type structure of SnS2 and surfacemodification of the capping reagent dodecanethiol. The resulting SnS2 nanobelts showed a high specific capacity of 640 mA h g_1 and stable cycling ability (560 mA h g_1 after 50 cycles), which is much better than a graphite anode.

Sentencing: from vagueness to arbitrariness - the need to abolish the stain that is the instinctive synthesis

Criminal sanctions involve the deliberate infliction of hardship on offenders. In sentencing, the state acts in its most coercive and decisive manner: ‘the state may use its most awesome power: the power to use force against its citizens and others’. Despite the importance of the interests at stake in the sentencing realm,sentencing is arguably the least coherent, predictable and principled area of law. The High Court of Australia has not facilitated attempts to inject clarity and precision into sentencing determinations. It has repeatedly endorsed the ‘instinctive synthesis’ approach to sentencing, emphasising the need for ‘individual justice’ over the need for transparency and a step-wise systematic approach to sentencing.

May 2000: Copyright: Stain the Waters Clear

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O escarro induzido no diagnóstico das doenças pulmonares em pacientes positivos ao vírus da imunodeficiência humana

A indução de escarro é uma técnica utilizada amplamente para monitorar a inflamação de vias aéreas, porém sua importância como ferramenta diagnóstica de doenças pulmonares em pacientes imunocomprometidos ainda necessita de melhor definição. Com o objetivo de determinar o seu rendimento no diagnóstico das doenças pulmonares em pacientes positivos ao HIV, no período de janeiro de 2001 a setembro de 2002, foram avaliados todos os pacientes com idade superior a 14 anos, infectados com o vírus da imunodeficiência humana, admitidos no Hospital Nereu Ramos (Florianópolis – Santa Catarina – Brasil). Foram incluídos no estudo aqueles indivíduos que apresentavam manifestações clínicas do aparelho respiratório há pelo menos 7 dias, associadas, ou não, a sinais radiológicos de doença pulmonar. Também foram incluídos indivíduos assintomáticos do ponto de vista respiratório, mas que apresentavam alterações no radiograma de tórax. Todos os pacientes foram submetidos à avaliação clínica, radiológica e laboratorial e realizaram a indução de escarro, seguida pela broncofibroscopia, lavado broncoalveolar e biópsia pulmonar transbrônquica. As amostras obtidas foram processadas para bacterioscopia pelo método de Gram e Ziehl-Neelsen, cultura quantitativa para bactérias, exame micológico direto, cultura para micobactérias e fungos, pesquisa de citomegalovírus e Pneumocystis jiroveci, bem como celularidade total e diferencial. De um total de 547 pacientes, 54 com idade média de 35,7 anos foram incluídos no estudo. Destes, 79,6% pertencentes ao sexo masculino e 85,2% caucasianos. A contagem média de linfócitos TCD4+ foi de 124,8/mm3. O padrão radiológico mais comum foi o intersticial (44,4%). A pesquisa de agente etiológico resultou negativa em 7 pacientes, sendo que nos 47 casos restantes foram isolados 60 agentes. Dentre os agentes isolados, 46,7% foram P. jiroveci; 33,5% bactérias piogênicas e 16,7% M. tuberculosis. O escarro induzido apresentou sensibilidade de 57,5%, especificidade de 42,9%, valor preditivo positivo de 87,1%, valor preditivo negativo de 13,0% e acurácia de 55,6%. Estes resultados sugerem que, nesta população, a análise do escarro induzido é um procedimento simples, seguro e com bom rendimento diagnóstico.