Use of genome sequence data in the design and testing of SSR markers for Phytophthora species

<p>Abstract</p> <p>Background</p> <p>Microsatellites or single sequence repeats (SSRs) are a powerful choice of marker in the study of <it>Phytophthora </it>population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of <it>P. infestans</it>, <it>P. sojae </it>and <it>P. ramorum </it>were mined for candidate SSR markers that could be applied to a wide range of <it>Phytophthora </it>species.</p> <p>Results</p> <p>A first approach, aimed at the identification of polymorphic SSR loci common to many <it>Phytophthora </it>species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAG)n, (AGG)n and (AGC)n were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to <it>P. sojae </it>(<it>P. alni, P. cambivora, P. europaea </it>and <it>P. fragariae</it>). This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times.</p> <p>Conclusion</p> <p>Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of <it>Phytophthora </it>species was challenging. That said, many novel SSR loci for species other than the three 'source species' (<it>P. infestans</it>, <it>P. sojae </it>and <it>P. ramorum</it>) are reported, offering great potential for the investigation of <it>Phytophthora </it>populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as they are highly variable and easily amplifiable from different <it>Phytophthora </it>species.</p

Plant genotype influence the structure of cereal seed fungal microbiome

Plant genotype is a crucial factor for the assembly of the plant-associated microbial communities. However, we still know little about the variation of diversity and structure of plant microbiomes across host species and genotypes. Here, we used six species of cereals (Avena sativa, Hordeum vulgare, Secale cereale, Triticum aestivum, Triticum polonicum, and Triticum turgidum) to test whether the plant fungal microbiome varies across species, and whether plant species use different mechanisms for microbiome assembly focusing on the plant ears. Using ITS2 amplicon metagenomics, we found that host species influences the diversity and structure of the seed-associated fungal communities. Then, we tested whether plant genotype influences the structure of seed fungal communities across different cultivars of T. aestivum (Aristato, Bologna, Rosia, and Vernia) and T. turgidum (Capeiti, Cappelli, Mazzancoio, Trinakria, and Timilia). We found that cultivar influences the seed fungal microbiome in both species. We found that in T. aestivum the seed fungal microbiota is more influenced by stochastic processes, while in T. turgidum selection plays a major role. Collectively, our results contribute to fill the knowledge gap on the wheat seed microbiome assembly and, together with other studies, might contribute to understand how we can manipulate this process to improve agriculture sustainability

O ABORTO E SEUS DILEMAS ÉTICOS

Introdução: O abortamento é a interrupção precoce de uma gestação antes que o feto seja capaz de sobreviver fora do corpo da mãe e pode ser classificado como aborto espontâneo, quando acontece a expulsão involuntária, casual e não intencional de um embrião ou feto antes de 20 a 22 semanas de gestação; ou, aborto induzido, aquele causado deliberadamente por razões médicas admitidas pela lei ou clandestinamente, o que constitui crime perante a lei brasileira. Objetivo: Refletir sobre o abortamento e a forma como ele é tratado conforme a lei nacional. Método: Trata-se de um estudo reflexivo. A discussão iniciou-se a partir do tema "Dilemas Éticos", no componente de Ética e Bioética em Enfermagem, ministrado na 6ª fase do Curso de Enfermagem da UNOESC. Resultados: O aborto é disciplinado pelo sistema jurídico pelos artigos 124 a 128 do código penal, tendo como tutela jurídica o direito a vida do feto. Conforme o Art. 128 do código penal não se pune o aborto praticado por médico quando não há outro meio de salvar a vida da gestante; a gravidez resulta de estupro e o aborto é precedido de consentimento da gestante ou, quando incapaz, de seu representante legal; e, no caso da gravidez resultar em feto com anencefalia. Conclusão: O aborto sempre foi um tema bastante polêmico, havendo posicionamentos a favor e contra a sua prática, por se tratar de um tema que abrange um enorme contexto envolvendo religião, fatores jurídicos e políticos, socioeconômicos, além de conceitos éticos e morais. Por conta disso, recai a necessidade de impulsionar reflexões e discussões sobre esta temática

Evaluation of a Pomegranate Peel Extract as an Alternative Means to Control Olive Anthracnose

Olive anthracnose is caused by different species of Colletotrichum spp. and may be regarded as the most damaging disease of olive fruit worldwide, greatly affecting quality and quantity of the productions. A pomegranate peel extract (PGE) proved very effective in controlling the disease. The extract had a strong in vitro fungicidal activity against Colletotrichum acutatum sensu stricto, was very effective in both preventive and curative trials with artificially inoculated fruit, and induced resistance in treated olive tissues. In field trials, PGE was significantly more effective than copper, which is traditionally used to control the disease. The highest level of protection was achieved by applying the extract in the early ascending phase of the disease outbreaks because natural rots were completely inhibited with PGE at 12 g/liter and were reduced by 98.6 and by 93.0% on plants treated with PGE at 6 and 3 g/liter, respectively. Two treatments carried out 30 and 15 days before the expected epidemic outbreak reduced the incidence of the disease by 77.6, 57.0, and 51.8%, depending on the PGE concentration. The analysis of epiphytic populations showed a strong antimicrobial activity of PGE, which sharply reduced both fungal and bacterial populations. Because PGE was obtained from a natural matrix using safe chemicals and did not have any apparent phytotoxic effect on treated olive fruit, it may be regarded as a safe and effective natural antifungal preparation to control olive anthracnose and improve olive productions

Phytophthora × pelgrandis Causes Root and Collar Rot of Lavandula stoechas in Italy.

In 2007, Phytophthora isolates with atypical morphological and biological characteristics were found associated with root and collar rot of potted plants of Stoechas lavender (Lavandula stoechas) in an ornamental nursery in Italy. A polyphasic approach, including morphological and cultural observations, sequencing the ITS-rDNA region, the Pheca and the mitochondrial coxI genes, multiplex PCRs with primers specific for P. nicotianae or P. cactorum, as well as random amplified polymorphic DNA–polymerase chain reaction, was used to characterize these isolates. On the basis of morpho-cultural and molecular analyses, the isolates from Stoechas lavender were identified as Phytophthora × pelgrandis, a natural hybrid of P. nicotianae × P. cactorum previously reported in other European countries, the Americas, and Taiwan, as a pathogen of ornamentals and loquat plants. In pathogenicity tests using potted plants of Stoechas lavender, the P. × pelgrandis isolates, similarly to the parental species P. nicotianae, induced the symptoms observed on plants with natural infections and were reisolated only from artificially inoculated plants. Dispersal of P. × pelgrandis on this host could exacerbate the damage caused by Phytophthora root and collar rot, of which the main causal agent presently is P. nicotianae on lavender in Europe. Application of hygienic measures is important to reduce the proliferation and spread of the Phytophthora hybrids

Simcluster: clustering enumeration gene expression data on the simplex space

Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST &#x22;digital northern&#x22;, are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space.&#xd;&#xa;&#xd;&#xa;Here we present a software tool, Simcluster, designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. Both versions are available at: http://xerad.systemsbiology.net/simcluster.&#xd;&#xa;&#xd;&#xa;Simcluster is designed in accordance with a well-established mathematical framework for compositional data analysis, which provides principled procedures for dealing with the simplex space, and is thus applicable in a number of contexts, including enumeration-based gene expression data

Olive leachates affect germination of Colletotrichum godetiae conidia and the development of appressoria

The effects of nutrients and microorganisms from olive carpospheres on germination of conidia and the development of appressoria of Colletotrichum godetiae were investigated. The final germination ratio was the result of a dynamic equilibrium between the positive action of nutrients and the negative competition of indigenous microorganisms. In contrast, formation of appressoria was greatly increased by microorganisms and reduced by nutrients. Removal of the microbial fraction from olive leachates rich in natural nutrients amplified the vegetative phase after conidium germination, resulting in increased germtube length, and delayed and reduced production of appressoria. Three exogenous nutrients (sucrose, asparagine and glycine) increased germination of conidia and reduced the formation of appressoria. These results provide evidence that nutrients and microorganisms of the olive carposphere play important roles in the infection processes of C. godetiae. Since appressoria are necessary for successful host infection, microorganisms may favour the penetration of C. godetiae by stimulating the production of appressoria, reducing saprophyitic pre-infectional mycelial growth and reducing duration of the critical moist period required for host penetration

Colletotrichum clavatum sp. nov. identified as the causal agent of olive anthracnose in Italy

Molecular analyses of a large population of isolates, previously identified as group B or genetic group A4 of the Colletotrichum acutatum species complex, mainly of Italian origin from olive, but also from other hosts collected since 1992, confirmed a well-resolved phylogenetic lineage with distinctive phenotypic characters which can be recognized as a separate species. Based on RAPD genomic fingerprinting, ITS and &beta;-tubulin DNA sequences, this species was clearly distinct from C. acutatum sensu stricto, C. fioriniae and C. simmondsii as well as from the genetic groups A1, A6, A7 and A8, all previously referred to as C. acutatum sensu lato. Group A4 is widespread in Europe, being responsible for olive anthracnose epidemics in some Mediterranean countries, including Greece, Italy, Montenegro, Portugal and Spain; moreover, it causes anthracnose diseases on a wide range of other hosts including about 20 different genera of woody and herbaceous plants, ornamentals and fruit trees. This new anamorphic taxon is described as Colletotrichum clavatum sp. nov

Exploring muscle activation during nordic walking: a comparison between conventional and uphill walking

Nordic Walking (NW) owes much of its popularity to the benefits of greater energy expenditure and upper body engagement than found in conventional walking (W). Muscle activation during NW is still understudied, however. The aim of the present study was to assess differences in muscle activation and physiological responses between NW and W in level and uphill walking conditions. Nine expert Nordic Walkers (mean age 36.8\ub111.9 years; BMI 24.2\ub11.8 kg/m2) performed 5-minute treadmill trials of W and NW at 4 km/h on inclines of 0% and 15%. The electromyographic activity of seven upper body and five leg muscles and oxygen consumption (VO2) were recorded and pole force during NW was measured. VO2 during NW was 22.3% higher at 0% and only 6.9% higher at 15% than during W, while upper body muscle activation was 2- to 15-fold higher under both conditions. Lower body muscle activation was similarly increased during NW and W in the uphill condition, whereas the increase in erector spinae muscle activity was lower during NW than W. The lack of a significant increase in pole force during uphill walking may explain the lower extra energy expenditure of NW, indicating less upper body muscle activation to lift the body against gravity. NW seemed to reduce lower back muscle contraction in the uphill condition, suggesting that walking with poles may reduce effort to control trunk oscillations and could contribute to work production during NW. Although the difference in extra energy expenditure between NW and W was smaller in the uphill walking condition, the increased upper body muscle involvement during exercising with NW may confer additional benefit compared to conventional walking also on uphill terrains. Furthermore, people with low back pain may gain benefit from pole use when walking uphill