K-mer applied in Mycobacterium tuberculosis genome cluster analysis.

According to studies carried out, approximately 10 million people developed tuberculosis in 2018. Of this total, 1.5 million people died from the disease. To study the behavior of the genome sequences of Mycobacterium tuberculosis (MTB), the bacterium responsible for the development of tuberculosis (TB), an analysis was performed using k-mers (DNA word frequency). The k values ranged from 1 to 10, because the analysis was performed on the full length of the sequences, where each sequence is composed of approximately 4 million base pairs, k values above 10, the analysis is interrupted, as consequence of the program's capacity. The aim of this work was to verify the formation of the phylogenetic tree in each k-mer analyzed. The results showed the formation of distinct groups in some k-mers analyzed, taking into account the threshold line. However, in all groups, the multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains remained together and separated from the other strains.

Suicide cases in developed and emerging countries: an analysis using wavelets / Casos de suicídio em países desenvolvidos e emergentes: uma análise usando ondaletas

OBJECTIVE: The aim of this study was to use a wavelet technique to determine whether the number of suicides is similar between developed and emerging countries. METHODS: Annual data were obtained from World Health Organization (WHO) reports from 1986 to 2015. Discrete nondecimated wavelet transform was used for the analysis, and the Daubechies wavelet function was applied with five-level decomposition. Regarding clustering, energy (variance) was used to analyze the clusters and visualize the clustering process. We constructed a dendrogram using the Mahalanobis distance. The number of groups was set using a specific function in the R program. RESULTS: The cluster analysis verified the formation of four groups as follows: Japan, the United States and Brazil were distinct and isolated groups, and other countries (Austria, Belgium, Chile, Israel, Mexico, Italy and the Netherlands) constituted a single group. CONCLUSION: The methods utilized in this paper enabled a detailed verification of countries with similar behaviors despite very distinct socioeconomic, geographic and climate characteristics.

OBJETIVO: Verificar se existe relação de similaridade entre o número de suicídio em países desenvolvidos e emergentes usando a técnica de ondaletas. MÉTODOS: Os dados anuais foram obtidos a partir do relatório da Organização Mundial da Saúde (OMS), no período de 1986 a 2015. Para análise, foi empregada a transformada discreta não decimada de ondaleta (NDWT), a função ondaleta aplicada foi a Daubechies com cinco níveis de decomposição. Com relação ao agrupamento, utilizou-se a energia (variância) para analisar os clusters e, para a visualização do processo de clusterização, trabalhamos com o dendograma, no qual se empregou a distância de Mahalanobis. A quantidade de grupos foi definida por meio da função NbCluster. RESULTADOS: A partir da análise de cluster, verificou-se a formação de quatros grupos. No qual, Japão e Estados Unidos e Brasil localizam-se em grupos distintos e isolados. E os demais países (Áustria, Bélgica, Chile, Israel, México, Itália e Holanda) em um único grupo. CONCLUSÃO: Utilizando esse método, foi possível verificar com mais detalhes quais países apresentaram comportamentos semelhantes, mesmo apresentando características bem distintas entre si, tanto socioeconômica, geográfica e climática.

Use of molecular markers SSR and SCAR for identification of olive accessions / Uso de marcadores moleculares SSR e SCAR para identificação de acessos de oliveira

Morphological and agronomical describers are traditionally used in plant characterization. However, the usage of these describers have some limitations such as susceptibility to abiotic and biotic stress and environmental factors. Furthermore, the describers are not stable over time and many can only be evaluated during the adult phase of the plants, which requires time and physical space. Molecular markers offer numerous advantages compared to the conventional alternatives based on phenotype: they are stable and detectable in all vegetable tissues, and are independent of the environment and development phase. One of the main advantages of the use of molecular markers is the time reduction in the identification of genetic diversity among the studied subjects, as the genotypes may even be described for the seed or seedling phase. Many countries have already adopted molecular markers to identify olive cultivars more accurately. The aim of this study was to evaluate the genetic identity of eight olive accessions supposedly belonging to cultivar Arbequina by using microsatellite (SSR) and Sequence Characterized Amplified Region (SCAR) markers. One accession corresponding to the cultivar was also incorporated into the analysis as a reference genotype. The molecular marker data were analyzed on the software GENALEX6.The markers generated an accumulated PI and PE of 1.26 x 10-6 and 0.949, respectively.The results supported the hypothesis that all accessions belong to the cultivar Arbequina, and the markers can therefore be applied to other varieties of olive species.

Descritores morfológicos e agronômicos são tradicionalmente utilizados na caracterização de plantas. Apesar de recomendado, o emprego destes descritores apresenta algumas limitações como a influência a estresses abióticos e bióticos e aos efeitos do ambiente. Além disso, não são estáveis ao longo do tempo e muitos só podem ser avaliados durante a fase adulta das plantas, o que requer tempo e espaço físico para as avaliações. Os marcadores moleculares oferecem numerosas vantagens relativamente às alternativas convencionais baseadas no fenótipo, pois são estáveis e detectáveis em todos os tecidos vegetais, independente do ambiente e fase de desenvolvimento e uma das principais vantagens da utilização destes é proporcionar a redução do tempo na identificação da diversidade genética entre os indivíduos trabalhados, podendo ser avaliadas genótipos ainda na fase de semente ou de plântula. O objetivo deste estudo foi avaliar a identidade genética de oito acessos de oliveira supostamente pertencentes a cultivar Arbequina usando microssatélites (SSR) e Sequence Characterized Amplified Region (SCAR) marcadores. Um acesso correspondente a cultivar também foi incorporado na análise como o genótipo de referência. Os dados de marcadores moleculares foram analisados com o software GENALEX 6. Como resultado, os marcadores SSR geraram um PI acumulada e PE de 1,26 x 10- 6 e 0,949, respectivamente. Os resultados suportam a hipótese de que todos os acessos pertencem a cultivar Arbequina, e, por conseguinte, esses marcadores podem ser aplicados em situações semelhantes em outras variedades de espécies de oliveira.

Evaluation of genome similarities using a wavelet-domain approach.

INTRODUCTION: Tuberculosis is listed among the top 10 causes of deaths worldwide. The resistant strains causing this disease have been considered to be responsible for public health emergencies and health security threats. As stated by the World Health Organization (WHO), around 558,000 different cases coupled with resistance to rifampicin (the most operative first-line drug) have been estimated to date. Therefore, in order to detect the resistant strains using the genomes of Mycobacterium tuberculosis (MTB), we propose a new methodology for the analysis of genomic similarities that associate the different levels of decomposition of the genome (discrete non-decimated wavelet transform) and the Hurst exponent. METHODS: The signals corresponding to the ten analyzed sequences were obtained by assessing GC content, and then these signals were decomposed using the discrete non-decimated wavelet transform along with the Daubechies wavelet with four null moments at five levels of decomposition. The Hurst exponent was calculated at each decomposition level using five different methods. The cluster analysis was performed using the results obtained for the Hurst exponent. RESULTS: The aggregated variance, differenced aggregated variance, and aggregated absolute value methods presented the formation of three groups, whereas the Peng and R/S methods presented the formation of two groups. The aggregated variance method exhibited the best results with respect to the group formation between similar strains. CONCLUSION: The evaluation of Hurst exponent associated with discrete non-decimated wavelet transform can be used as a measure of similarity between genome sequences, thus leading to a refinement in the analysis.

Evaluation of genome similarities using a wavelet-domain approach

Abstract INTRODUCTION: Tuberculosis is listed among the top 10 causes of deaths worldwide. The resistant strains causing this disease have been considered to be responsible for public health emergencies and health security threats. As stated by the World Health Organization (WHO), around 558,000 different cases coupled with resistance to rifampicin (the most operative first-line drug) have been estimated to date. Therefore, in order to detect the resistant strains using the genomes of Mycobacterium tuberculosis (MTB), we propose a new methodology for the analysis of genomic similarities that associate the different levels of decomposition of the genome (discrete non-decimated wavelet transform) and the Hurst exponent. METHODS: The signals corresponding to the ten analyzed sequences were obtained by assessing GC content, and then these signals were decomposed using the discrete non-decimated wavelet transform along with the Daubechies wavelet with four null moments at five levels of decomposition. The Hurst exponent was calculated at each decomposition level using five different methods. The cluster analysis was performed using the results obtained for the Hurst exponent. RESULTS: The aggregated variance, differenced aggregated variance, and aggregated absolute value methods presented the formation of three groups, whereas the Peng and R/S methods presented the formation of two groups. The aggregated variance method exhibited the best results with respect to the group formation between similar strains. CONCLUSION: The evaluation of Hurst exponent associated with discrete non-decimated wavelet transform can be used as a measure of similarity between genome sequences, thus leading to a refinement in the analysis.

Wavelet-domain elastic net for clustering on genomes strains.

We propose to evaluate genome similarity by combining discrete non-decimated wavelet transform (NDWT) and elastic net. The wavelets represent a signal with levels of detail, that is, hidden components are detected by means of the decomposition of this signal, where each level provides a different characteristic. The main feature of the elastic net is the grouping of correlated variables where the number of predictors is greater than the number of observations. The combination of these two methodologies applied in the clustering analysis of the Mycobacterium tuberculosis genome strains proved very effective, being able to identify clusters at each level of decomposition.

Karyotype characterization and comparison of three hexaploid species of Bromus Linnaeus, 1753 (Poaceae).

Chromosome morphometry and nuclear DNA content are useful data for cytotaxonomy and to understand the evolutionary history of different taxa. For the genus Bromus Linnaeus, 1753, distinct ploidy levels have been reported, occurring from diploid to duodecaploid species. The geographic distribution of Bromus species has been correlated with chromosome number and ploidy level. In this study, the aims were to determine the nuclear genome size and characterize the karyotype of the South American Bromus species: Bromus auleticus Trinius ex Nees, 1829, Bromus brachyanthera Döll, 1878 and Bromus catharticus Vahl, 1791. The mean nuclear 2C value ranged from 2C = 12.64 pg for B. catharticus to 2C = 17.92 pg for B. auleticus, meaning a maximum variation of 2C = 5.28 pg, equivalent to 41.70%. Despite this significant difference in 2C value, the three species exhibit the same chromosome number, 2n = 6x = 42, which confirms their hexaploid origin. Corroborating the genome size, the chromosome morphometry (total, short- and long-arm length) and, consequently, the class differed among the karyotypes of the species. Based on the first karyograms for these Bromus species, some morphologically similar and several distinct chromosome pairs were found. Therefore, the karyotype characterization confirmed the hexaploid origin of the studied Bromus species, which differ in relation to the karyogram and the nuclear 2C value. Considering this, cytogenetics and flow cytometry can be used to discriminate Bromus species, contributing to taxonomy and systematic studies and providing information on the evolutionary history of this taxa.

An improved method for genomic DNA extraction from strawberry leaves / Otimização de um método para extração de DNA genômico a partir de folhas de morangueiro

Several extraction methods of genomic DNA for identification and characterization of genetic diversity in different plant species are routinely applied during molecular analysis. However, the presence of undesirable compounds such as polyphenols and polysaccharides is one of the biggest problems faced during the isolation and purification of high quality DNA in plants. Therefore, achievement of fast and accurate methods for DNA extraction is crucial in order to produce pure samples. Leaves of strawberry genotypes (Fragaria ananassa) have high contents of polysaccharides and polyphenols which increase the sample viscosity and decrease the DNA quality, interfering with the PCR performance. Thereby, in this study we evaluated the quality and amount of genomic DNA extracted from young leaves of strawberry after tissue lyophilization and maceration in presence of polivinilpirrolidone (PVP). The CTAB method was used as reference procedure and it was modified to improve the DNA extraction. The modifications consisted of tissue lyophilization overnight until it was completely freeze-dried and addition of PVP during the tissue maceration in liquid nitrogen. The results showed the efficiency and reliability of the modified method compared to the unmodified method, indicating that combination of lyophilization and PVP improve the quality and amount of the DNA extracted from strawberry leaves.

Vários métodos de extração de DNA genômico para a identificação e caracterização da diversidade genética em diferentes espécies de plantas são rotineiramente aplicados durante a análise molecular. Entretanto, a presença de compostos indesejáveis, tais como polifenóis e polissacarídeos, é um dos maiores problemas que ocorrem durante o isolamento e purificação de DNA de alta qualidade em plantas. Dessa forma, o sucesso no desenvolvimento de métodos de extração de DNA rápidos e acurados é crucial para produzir amostras puras. Folhas de genótipos de morangueiro (Fragaria ananassa) têm elevado conteúdo de polissacarídeos e polifenóis que aumentam a viscosidade da amostra e reduzem a qualidade do DNA, interferindo no desempenho da PCR. Neste estudo, avaliamos a qualidade e a quantidade de DNA genômico extraído de folhas jovens de morangueiro após a liofilização do tecido e a maceração na presença de polivinilpirrolidona (PVP). O método CTAB foi utilizado como procedimento de referência e foi modificado para melhorar a extração do DNA. As modificações consistiram na liofilização do tecido a baixa temperatura até que ele tivesse sido desidratado completamente, associada à adição de PVP durante a maceração do tecido no nitrogênio líquido. Os resultados demonstraram a eficiência e a confiabilidade do método modificado comparado ao método não modificado, indicando que a combinação da liofilização com PVP melhora a qualidade e quantidade do DNA extraído de folhas de morangueiro.

Avaliação de três características fisiológicas em 4 ciclos de seleção no cultivar de milho BRS-4154 sob o solo encharcado / Evaluation of three physiologic characteristics in four cycles of selection in maize cultivar BRS-4154 under tolerance to waterlogging of the soil

Conduziu-se este trabalho, com o objetivo de avaliar plantas de milho (Zea mays L.) dos diferentes ciclos de seleção recorrentes da variedade de milho BRS 4154 - 'Saracura' quanto aos ganhos genéticos obtidos ao longo dos ciclos de seleção sob encharcamento do solo. Quatro ciclos de seleção da variedade de milho BRS 4154 foram plantados sob delineamento em blocos casualizados nos quais foram avaliados os ciclos 1, 5, 9 e 15, incluindo a variedade BR 107 e o híbrido simples BRS 1010 como testemunhas, por serem sensíveis ao encharcamento. Foram avaliados: fluorescência e teor de clorofila, área foliar e porosidade de raiz. O estresse causado pelo excesso de água no solo não influenciou a característica fluorescência da clorofila, demonstrando que essa não é uma boa característica para avaliação de tolerância ao encharcamento do solo. Houve uma significativa redução de área foliar do milho nas áreas de solo encharcado. Adicionalmente, a porosidade da raiz foi uma característica que apresentou significativa discrepância entre os dois ambientes de cultivo, tendo um aumento significativo em função do encharcamento.

This work aimed to evaluate plants of different cycles of recurrent selection of the maize (Zea mays L.) variety BRS 4154 - 'Saracura' for the genetic faced to the gains obtained along the selection cycles under waterlogging of the soil. Four cycles of selection of the maize variety BRS 4154 were planted in randomized block outline for evaluation of cycles 1, 5, 9 and 15, including the variety BR 107 and the simple hybrid BRS 1010 used as control, once they are sensitive to the waterlogging. One evaluated: chlorophylls fluorescence and content, leaf surface area and root porosity. The stress caused by the excess of water in the soil didn't influence the characteristic of chlorophyll fluorescence, demonstrating this is not a good characteristic to evaluate flooding tolerance. There was significant leaf surface area decrease of the corn in the areas of soaked soil. Additionally, the porosity of the root was a characteristic that presented significant discrepancy between the two cultivation environments, having a significant increase in function of waterlogging.

Melhoramento do feijoeiro comum com grão tipo carioca, visando resistência à antracnose e à mancha angular / Breeding of common bean with carioca type grain for the resistance to anthracnose and angular leaf spot

Objetivou-se no trabalho, selecionar linhagens de feijoeiro comum que reunissem, além da alta produtividade, porte ereto e grãos do tipo Carioca, também a resistência à antracnose e à mancha angular. O material experimental constituiu-se de 143 linhagens oriundas de três famílias segregantes F1:4RC2 {[(G2333 X ESAL 696) X ESAL 696] X CI 140}. Foram conduzidos quatro experimentos em três localidades da região sul de Minas Gerais, avaliando-se a produção, o tipo de grão, o porte e a reação à mancha angular. A reação à antracnose foi determinada a partir de inoculações de plantas jovens de cada linhagem, com as raças 2047 e 1545, mantidas em câmara de nevoeiro por três dias e transferidas para casa de vegetação com irrigação por aspersão, a cada quatro horas. Selecionaram-se quatro linhagens com alta produtividade, porte mais arbustivo, grãos tipo carioca e com resistência à mancha angular (nota até 4). Uma das linhagens selecionada possui o alelo Co-4², outras duas possuem o alelo Co-7 de resistência à antracnose e a última, embora seja suscetível à antracnose, possui resistência à mancha angular (nota 3,97) e maior produtividade de grãos.

Aiming to select common bean lines with high grain yield, Carioca grain type, upright plant habit and resistant to anthracnose and angular leaf spot, 143 lines were selected from three families of the cross F1:4RC2 {[(G2333 X ESAL 696) X ESAL 696] X CI 140}. The promising lines were selected based on the agronomical traits in four field experiments, set up in three places in Southern MG State using the square lattice design. The reaction of each line to the anthracnose was evaluated by inoculating the seedlings using the races 1545 and 2047, and kept in humid chamber during three days, and then moved to greenhouse with sprinkle irrigation every four hours. Four lines with high grain yield, upright plant habit, Carioca grain type, and resistance to angular leaf spot (score up to 4) were selected. Among them one of the lines has the Co-4² allele for anthracnose resistance, two lines have the Co-7 allele, and the last one, although susceptible do anthracnose, presented the highest grain yield and angular leaf spot resistance (score 3,97).

Quantificação de açúcares solúveis totais, açúcares redutores e amido nos grãos verdes de cultivares de milho na colheita / Quantification of total soluble sugars, reducing sugars and starch in immature kernels of corn cultivars

O objetivo deste trabalho foi quantificar os teores de açúcares solúveis totais (AST), açúcares redutores (AR) e amido em nove cultivares de milho colhidos no estádio verde, uma vez que estes influenciam diretamente o sabor, o aroma e a aceitação do consumidor. O experimento foi conduzido em Ponte Nova, MG, no ano agrícola 2002/2003. Para a determinação das características, foi retirada uma amostra de três espigas de cada unidade experimental. O ponto de colheita foi identificado por método empírico, quando o estilo-estigma se desprendia da espiga com facilidade. As cultivares apresentaram umidades diferentes no momento da colheita, variando de 56 a 64 por cento. Não foi detectada diferença entre as cultivares quanto aos teores de AR, porém, P3232 e AG4051 apresentaram boa relação entre AR e AST, destacando-se para esta finalidade.

Total soluble sugars (TSS), reducing sugars (RS), moisture and starch directly influence flavor and consumption. In this work, TSS, RS and starch were determined at harvest in young kernels of nine corn cultivars. The experiment was carried out in Ponte Nova, MG, Brazil. To determine chemical characters of young kernels a sample was obtained of three cobs from each experimental plot. Corn ears were harvested using an empirical method, when the silk was loose from the ear. Moisture varied among samples of different cultivars at harvest. Moisture content ranged from 56 to 64 percent. There were no differences among cultivars regarding RS. However, cultivars P3232 and AG4051 showed good RS to TSS ratio, being adequate for fresh consumption.

Avaliação do 'stay green' em famílias segregantes de feijão (Phaseolus vulgaris L.) / Performance of common bean segregating families based on stay green

Vários programas de melhoramento genético de feijoeiro no Brasil visam obter cultivares com menor índice de acamamento, ou seja, com porte ereto. Um dos caracteres relacionados a este fenótipo é o 'stay green', que é a senescência tardia do caule e folhas em relação às vagens. Com intuito de verificar a eficiência da seleção direta sobre o fenótipo 'stay green', utilizou-se a descendência do cruzamento entre as cultivares Carioca MG (com 'stay green') e Carioca 300 Vagens (sem 'stay green'). O caráter foi avaliado em 89 famílias F2:3 na safra da seca de 2000 e F2:4 na safra de inverno 2000. Juntamente com as famílias, foram incluídos os dois genitores e nove cultivares em um experimento em látice 10 x 10, com duas repetições nas secas e três repetições no inverno. Foi utilizado um diagrama de notas para avaliação do 'stay green'. Verificou-se que a seleção direta foi pouco efetiva, especialmente quando realizada em uma época para se obter o ganho em outra, em razão da interação famílias x ambientes ser um complicador para obtenção de cultivares com esse fenótipo, como mostrou a herdabilidade realizada de 22,9 por cento. A seleção baseada no comportamento médio das famílias foi mais eficiente.

Some common bean breeding programs in Brazil aim at obtaining upright cultivars. The stay green is one of the phenotypes responsible for that type of plant habit, and it means late senescence of stem and leaves in relation to the pods. Aiming at verifying the efficiency of selection for stay green, the cultivars Carioca MG (with stay green) and Carioca 300 Vagens (without stay green) were crossed, and derived 89 F2:3 families that were evaluated in the dry season, and in the winter of year 2000. Besides the families, both parents and nine checks were included in the experiments using a 10 x 10 square lattice, with two replications in the dry season and three in the winter. The treatments were evaluated using a score diagram for stay green. Direct selection showed low efficiency due to the high families by environments interaction, since it was confirmed by the realized heritability of only 22.9 percent. Selection based on average family performance showed to be more effective.