Proteins on microbial identification: past achievements, present state-of-the-art, and future challenges

The use of chemical analysis of microbial components, including proteins, became an important achievement in the 80’s of the last century to the microbial identification. This led a more objective microbial identification scheme, called chemotaxonomy, and the analytical tools used in the field are mainly 1D/2D gel electrophoresis, spectrophotometry, high-performance liquid chromatography, gas chromatography, and combined gas chromatography-mass spectrometry. The Edman degradation reaction was also applied to peptides sequence giving important insights to the microbial identification. The rapid development of these techniques, in association with knowledge generated by DNA sequencing and phylogeny based on rRNA gene and housekeeping genes sequences, boosted the microbial identification to an unparalleled scale. The recent results of mass spectrometry (MS), like Matrix-Assisted Laser Desorption/Ionisation Time-of-Flight (MALDI-TOF), for rapid and reliable microbial identification showed considerable promise. In addition, the technique is rapid, reliable and inexpensive in terms of labour and consumables when compared with other biological techniques. At present, MALDI-TOF MS adds an additional step for polyphasic identification which is essential when there is a paucity of characters or high DNA homologies for delimiting very close related species. The full impact of this approach is now being appreciated when more diverse species are studied in detail and successfully identified. However, even with the best polyphasic system, identification of some taxa remains time-consuming and determining what represents a species remains subjective. The possibilities opened with new and even more robust mass spectrometers combined with sound and reliable databases allow not only the microbial identification based on the proteome fingerprinting but also include de novo specific proteins sequencing as additional step. These approaches are pushing the boundaries in the microbial identification field.

Use of a polyphasic approach including MALDI-TOF MS for identification of Aspergillus section Flavi strains isolated from food commodities in Brazil

Brazil is one the largest producers and exporters of food commodities in the world. The evaluation of fungi capable of spoilage and the production mycotoxins in these commodities is an important issue that can be of help in bioeconomic development. The present work aimed to identify fungi of the genus Aspergillus section Flavi isolated from different food commodities in Brazil. Thirty-five fungal isolates belonging to the section Flavi were identified and characterised. Different classic phenotypic and genotypic methodologies were used, as well as a novel approach based on proteomic profiles produced by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Type or reference strains for each taxonomic group were included in this study. Three isolates that presented discordant identification patterns were further analysed using the internal transcribed spacer (ITS) region and calmodulin gene sequences. The data obtained from the phenotypic and spectral analyses divide the isolates into three groups, corresponding to taxa closely related to Aspergillus flavus, Aspergillus parasiticus, and Aspergillus tamarii. Final polyphasic fungal identification was achieved by joining data from molecular analyses, classical morphology, and biochemical and proteomic profiles generated by MALDI-TOF MS.

Polyphasic identification of a Rhizopus species and a putative novel Gongronella which both degrade the fungicide metalaxyl

Apresentação efetuada na MicroBiotec’15

Identification and energy calibration of hadronically decaying tau leptons with the ATLAS experiment in pp collisions at s√=8 TeV

This paper describes the trigger and offline reconstruction, identification and energy calibration algorithms for hadronic decays of tau leptons employed for the data collected from pp collisions in 2012 with the ATLAS detector at the LHC center-of-mass energy s√ = 8 TeV. The performance of these algorithms is measured in most cases with Z decays to tau leptons using the full 2012 dataset, corresponding to an integrated luminosity of 20.3 fb−1. An uncertainty on the offline reconstructed tau energy scale of 2% to 4%, depending on transverse energy and pseudorapidity, is achieved using two independent methods. The offline tau identification efficiency is measured with a precision of 2.5% for hadronically decaying tau leptons with one associated track, and of 4% for the case of three associated tracks, inclusive in pseudorapidity and for a visible transverse energy greater than 20 GeV. For hadronic tau lepton decays selected by offline algorithms, the tau trigger identification efficiency is measured with a precision of 2% to 8%, depending on the transverse energy. The performance of the tau algorithms, both offline and at the trigger level, is found to be stable with respect to the number of concurrent proton--proton interactions and has supported a variety of physics results using hadronically decaying tau leptons at ATLAS.

A radiofrequency identification system for the 60 GHz ISM band

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Eletrónica Médica)

Identification of duplicates of cassava accessions sampled on the North Region of Brazil using microsatellite markers

Duplicates are common in germplasm banks and their identification is needed to facilitate germplasm bank management and to reduce maintenance costs. The aim of this work was to identify duplicates of cassava from a germplasm bank in Eastern Amazon, which had been previously characterized both morphological and agronomically. In order to be genotyped with 15 microsatellite loci, 36 accessions were selected. These accessions were classified into 13 groups of similar morpho-agronomical characteristics. All loci were polymorphic, and 75 alleles were identified, with an average of five alleles per loci and H E = 0.66. There were determined 34 pairs of genotypes with identical multiloci profiles and the probability of genetic identity was 1.1x10-12 with probability of exclusion of 99.9999%. Among these duplicates, there are accessions sampled on different years and places, but with different names and accessions with the same name sampled in different places and years. The study identified genotypes that are grown in different places and that have been maintained over the years by local farmers.

Identification and characterization of deforestation hot spots in Venezuela using MODIS satellite images

Land cover changes over time as a result of human activity. Nowadays deforestation may be considered one of the main environmental problems. The objective of this study was to identify and characterize changes to forest cover in Venezuela between 2005-2010. Two maps of deforestation hot spots were generated on the basis of MODIS data, one using digital techniques and the other by means of direct visual interpretation by experts. These maps were validated against Landsat ETM+ images. The accuracy of the map obtained digitally was estimated by means of a confusion matrix. The overall accuracy of the maps obtained digitally was 92.5%. Expert opinions regarding the hot spots permitted the causes of deforestation to be identified. The main processes of deforestation were concentrated to the north of the Orinoco River, where 8.63% of the country's forests are located. In this region, some places registered an average annual forest change rate of between 0.72% and 2.95%, above the forest change rate for the country as a whole (0.61%). The main causes of deforestation for the period evaluated were agricultural and livestock activities (47.9%), particularly family subsistence farming and extensive farming which were carried out in 94% of the identified areas.

Use of anatomical root markers for species identification in Catasetum (Orchidaceae) at the Portal da Amazônia region, MT, Brazil

Orchidaceae is one of the largest botanical families, with approximately 780 genera. Among the genera of this family, Catasetum currently comprises 166 species. The aim of this study was to characterize the root anatomy of eight Catasetum species, verifying adaptations related to epiphytic habit and looking for features that could contribute to the vegetative identification of such species. The species studied were collected at the Portal da Amazônia region, Mato Grosso state, Brazil. The roots were fixed in FAA 50, cut freehand, and stained with astra blue/fuchsin. Illustrations were obtained with a digital camera mounted on a photomicroscope. The roots of examined species shared most of the anatomical characteristics observed in other species of the Catasetum genus, and many of them have adaptations to the epiphytic habit, such as presence of secondary thickening in the velamen cell walls, exodermis, cortex, and medulla. Some specific features were recognized as having taxonomic application, such as composition of the thickening of velamen cell walls, ornamentation of absorbent root-hair walls, presence of tilosomes, composition and thickening of the cortical cell walls, presence of mycorrhizae, endodermal cell wall thickening, the number of protoxylem poles, and composition and thickening of the central area of the vascular cylinder. These traits are important anatomical markers to separate the species within the genus and to generate a dichotomous identification key for Catasetum. Thus, providing a useful tool for taxonomists of this group

Updated List and identification key of 219 tree species of white sand forests of the Allpahuayo Mishana National Reserve, Loreto, Peru

White sand forests, although low in nutrients, are characterized not only by several endemic species of plants but also by several monodominant species. In general, plants in this forest have noticeably thin stems. The aim of this work was to elaborate a parallel dichotomous key for the identification of Angiosperm tree species occurring on white sand forests at the Allpahuayo Mishana National Reserve, Loreto, Peru. We compiled a list of species from several publications in order to have the most comprehensive list of species that occur on white sand forest. We found 219 species of Angiosperm, the more abundant species were Pachira brevipes (26.27%), Caraipa utilis (17.90%), Dicymbe uaiparuensis (13.27%), Dendropanax umbellatus (3.28%), Sloanea spathulata (2.52%), Ternstroemia klugiana (2.30%), Haploclathra cordata (2.28%), Parkia igneiflora (1.20%), Emmotum floribundum (1.06%), Ravenia biramosa (1.04%) among others. Most species of white sand forests can be distinguished using characteristics of stems, branches and leaves. This key is very useful for the development of floristic inventories and related projects on white sand forests from Allpahuayo Mishana National Reserve.

Influence of casting condition on the anisotropy of the fracture properties of Steel Fibre Reinforced Self-Compacting Concrete (SFRSCC)

Identification of the tensile constitutive behaviour of Fibre Reinforced Concrete (FRC) represents an important aspect of the design of structural elements using this material. Although an important step has been made with the introduction of guidance for the design with regular FRC in the recently published fib Model Code 2010, a better understanding of the behaviour of this material is still necessary, mainly for that with self-compacting properties. This work presents an experimental investigation employing Steel Fibre Self-Compacting Concrete (SFRSCC) to cast thin structural elements. A new test method is proposed for assessing the post-cracking behaviour and the results obtained with the proposed test method are compared with the ones resulted from the standard three-point bending tests (3PBT). Specimens extracted from a sandwich panel consisting of SFRSCC layers are also tested. The mechanical properties of SFRSCC are correlated to the fibre distribution by analysing the results obtained with the different tests. Finally, the stress-crack width constitutive law proposed by the fib Model Code 2010 is analysed in light of the experimental results.

Estratégias desenvolvidas por usuários de crack para lidar com os riscos decorrentes do consumo da droga

OBJETIVOS: O objetivo deste estudo foi identificar, sob a ótica de usuários de crack, quais são as estratégias que eles utilizam para minimizar ou evitar os riscos decorrentes do consumo de crack. MÉTODO: Utilizou-se método qualitativo de pesquisa, desenvolvido mediante entrevistas semiestruturadas em profundidade. Foi entrevistada uma amostra intencional por critérios, composta por 30 usuários de crack, selecionados por meio de informantes-chave e distribuídos em oito diferentes cadeias. As entrevistas foram transcritas literalmente, inseridas e analisadas no software NVivo 8, com exploração dos dados mediante a técnica de análise de conteúdo. RESULTADOS: Os entrevistados acreditam que os maiores riscos decorrentes da dependência do crack sejam os relacionados aos efeitos psíquicos da droga, como fissura, sintomas paranoides transitórios e sintomas depressivos, assim como os decorrentes da ilegalidade dela, como a polícia e as questões referentes ao tráfico. Entretanto, os riscos de complicações físicas do consumo quase não foram apontados. As estratégias se concentraram no controle dos efeitos psíquicos, principalmente pelo consumo de álcool e maconha. Para lidar com as consequências da ilegalidade da droga, mostraram se preocupar com a postura que adotam perante o traficante e a polícia. CONCLUSÕES: As estratégias desenvolvidas pelos usuários focam na tentativa de se autoprotegerem principalmente dos episódios de violência e no alívio de sintomas desagradáveis causados pela droga - principalmente fissura e sintomas paranoides transitórios. Essas estratégias podem parecer efetivas a curto prazo, porém apresentaram riscos de longo prazo, tais como dependência de álcool e maconha.

Relação entre o craving por tabaco e o craving por crack em pacientes internados para desintoxicação

OBJETIVO: Verificar se há relação entre aumento do craving por crack e aumento do craving por tabaco em pacientes internados para desintoxicação. MÉTODO: Ensaio clínico tipo quase-experimental de análise quantitativa. Amostra composta por 32 homens dependentes de cocaína (crack) e tabaco, em duas a três semanas de abstinência. Realizou-se intervenção em grupo, no qual, inicialmente, foram aplicados: CCQB (Cocaine Craving Questionnaire-Brief ), QSUB (Questionnaire of Smoking Urges-Brief ) e BAI (Inventário Beck de Ansiedade). Em seguida, foram aplicadas imagens relacionadas ao crack e reaplicados CCQB, QSUB e BAI. Após, foi realizada entrevista individual em que se aplicaram FSD (Ficha com Dados Sociodemográficos) e FTND (Fagerström Test for Nicotine Dependence). RESULTADOS: A partir da exposição de imagens relativas ao crack, houve aumento significativo do craving por crack, do craving por tabaco e dos sintomas de ansiedade, estando essas medidas correlacionadas positivamente entre si. CONCLUSÃO: Os resultados indicam uma associação significativa entre craving por crack e craving por tabaco, sugerindo que a abstinência de tabaco pode ajudar na eficácia do tratamento para dependência de crack.

Associação entre fissura e perfil antropométrico em dependentes de crack

OBJETIVO: Verificar a variação da fissura de dependentes de crack no decorrer da internação e a associação com perfil antropométrico. MÉTODOS: Trata-se de uma pesquisa quantitativa com delineamento transversal (n = 30). Avaliaram-se o perfil de consumo de substâncias psicoativas; dados sociodemográficos; variáveis antropométricas (peso, estatura, índice de massa corporal, relação cintura-quadril, perímetros, dobras cutâneas e diâmetro ósseo); e fissura avaliada por meio do Cocaine Craving Questionnaire Brief. As coletas de dados ocorreram nas 24 horas iniciais e finais do tratamento. RESULTADOS: Observou-se aumento significativo do percentual de gordura e diminuição significativa da fissura. Não se evidenciou associação entre variáveis antropométricas e fissura, tanto no início como ao final da internação. CONCLUSÃO: Houve significativa diminuição na fissura e modificação na composição corporal, entretanto não houve correlação entre essas variáveis.