Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes

The exocarp, or skin, of fleshy fruit is a specialized tissue that protects the fruit, attracts seed dispersing fruit eaters, and has large economical relevance for fruit quality. Development of the exocarp involves regulated activities of many genes. This research analyzed global gene expression in the exocarp of developing sweet cherry (Prunus avium L., 'Regina'), a fruit crop species with little public genomic resources. A catalog of transcript models (contigs) representing expressed genes was constructed from de novo assembled short complementary DNA (cDNA) sequences generated from developing fruit between flowering and maturity at 14 time points. Expression levels in each sample were estimated for 34 695 contigs from numbers of reads mapping to each contig. Contigs were annotated functionally based on BLAST, gene ontology and InterProScan analyses. Coregulated genes were detected using partitional clustering of expression patterns. The results are discussed with emphasis on genes putatively involved in cuticle deposition, cell wall metabolism and sugar transport. The high temporal resolution of the expression patterns presented here reveals finely tuned developmental specialization of individual members of gene families. Moreover, the de novo assembled sweet cherry fruit transcriptome with 7760 full-length protein coding sequences and over 20 000 other, annotated cDNA sequences together with their developmental expression patterns is expected to accelerate molecular research on this important tree fruit crop.

Associations between liking for fat, sweet or salt and obesity risk in French adults

International audience

Genes found in partial sequencing od Phytophthora cinnamomi

Members of the oomycete cause extensive losses in agriculture and widespread degradation in natural plant communities, being responsible for the death of thousands of trees every year. Two of the representative species are Phytophthora infestans, which causes late blight of potato, and Phytophthora cinnamomi, which causes chestnut ink disease, responsible for losses on sweet chestnut production in Europe. Genome sequencing efforts have been focused on the study of three species: P. infestans, P. sojae and P. ramorum. Phytophthora infestans has been developed as the model specie for the genus, possessing excellent genetic and genomics resources including genetic maps, BAC libraries, and EST sequences. Our research team is trying to sequence the genome of P. cinnamomi in order to gain a better understanding of this oomycete, to study changes in plant-pathogen relationships including those resulting from climate change and trying to decrease the pathogen’s impact on crops and plants in natural ecosystems worldwide. We present here a preliminary report of partially sequenced genomic DNA from P. cinnamomi encoding putative protein-coding sequences and tRNAs. Database analysis reveals the presence of genes conserved in oomycetes.

Home sweet home: evidence for nest-fidelity in the rocky intertidal fish, the shanny Lipophrys pholis

The ability to be faithful to a particular area or site was analysed in the shanny Lipophrys pholis. Using passive integrated transponders, adults from a population of L. pholis at Cabo Raso, Portugal, were followed over a period of 3 years. The findings showed that site fidelity is a consistent behaviour during the breeding season with specific breeding males being found only in particular sectors within the area, and in specific nests throughout the years. The fact that, in general, L. pholis individuals were absent from the study area during the non-breeding season and breeding males were recorded returning to the same nests and sectors for consecutive breeding seasons suggests that they have developed excellent homing abilities. Translocation data corroborate this idea showing that breeding males successfully returned to their nests after a displacement of >100 m. Altogether, these findings highlight the relevance of life-history traits (e.g. nesting) in the conditioning of site fidelity and homing for this species of rocky intertidal fish, and more importantly, provide evidence for the need of a well-developed navigational system.

Sweet syndrome presenting late after non Hodgkin’s lymphoma and dermatomyositis

Abstract Sweet syndrome is a rare neutrophilic dermatosis consisting in the onset of high fever, neutrophilia, and typical painful skin lesions including erythematous papules, nodules, and plaques on the face, trunk, and extremities, with a bilateral and asymmetrical pattern. Sweet syndrome is classiied as idiopathic, predominating in women; malignancy-associated, mainly with hematological cancer, and drug-induced. The diagnosis is based on clinical history and skin manifestations, being conirmed by a complete blood count showing neutrophilic leukocytosis, and speciic indings in the skin biopsy. We report the case of a 68 year-old man with a 10-year evolution of dermatomyositis complicated by lung ibrosis, followed 8 years later by non-Hodgkin lymphoma (NHL) accompanied by worsening of his ibrosis. Two years after the successful treatment of NHL the patient developed an acute episode of severe dyspnea, multiple skin lesions, and 95% neutrophilia. At that time the patient had a severe lung function impairment complicated by nosocomial pneumonia that led to his death, a few days after the diagnosis of Sweet syndrome was established by histopathology examination. Sweet syndrome is a rare dermatologic entity that can appear several years after diseases characterized by immune dysfunction such as dermatomyositis and NHL.

Molecular characterization of 'sweet' cassavas (Manihot esculenta) from a germplasm bank in Brazilian Eastern Amazonia.

2016

Selectivity and efficiency of herbicides in weed control on sweet sorghum.

A carência de herbicidas registrados para o controle de plantas daninhas, em sorgo sacarino, torna-se fator limitante à produção. Objetivou-se avaliar a seletividade de herbicidas em sorgo sacarino e a eficiência no controle de plantas daninhas. O delineamento experimental foi de blocos ao acaso, com quarto repetições. Os tratamentos incluíram cultivares de sorgo sacarino (BRS 506, BRS 509 e BRS 511) e herbicidas aplicados isoladamente em pré-emergência (atrazine - 1.500 g ha-1; atrazine + s-metolachlor - 1.665 g ha-1 + 1.035 g ha-1; flumioxazin - 50 g ha-1; s-metolachlor - 1.440 g ha-1) e pós-emergência (tembotrione - 100,8 g ha-1) e de forma sequencial em pré e pós-emergência (atrazine + s-metolachlor + tembotrione - 1.665 g ha-1 + 1.035 g ha-1 + 100,8 g ha-1; atrazine + tembotrione - 1.500 g ha-1 + 100,8 g ha-1; flumioxazin + tembotrione - 50 g ha-1 + 100,8 g ha-1), mais duas testemunhas, uma capinada e outra sem capina. A fitotoxicidade ao sorgo foi de 98,0 %, 98,0 % e 100 % de tembotrione; 100 %, 98,7 % e 100 % de flumioxazin + tembotrione; 100 %, 100 % e 100 % de atrazine + s-metolachlor + tembotrione; e 98,7 %, 98,7 % e 99,7 % de atrazine + tembotrione, respectivamente para as cultivares BRS 509, BRS 506 e BRS 511. Tembotrione, flumioxazin + tembotrione, atrazine + s-metolachlor + tembotrione e atrazine + tembotrione apresentaram bom controle de Ipomoea indivisa, Digitaria ciliaris e Urochloa plantaginea, porém, não demonstraram seletividade às cultivares de sorgo. O atrazine, de modo geral, apresentou maior seletividade aos componentes de rendimento das cultivares BRS 509 e BRS 506.

Citrus HLB x Potato "Zebra Chip" in Brazil: Attempting to transmit citrus Candidatus liberibacter spp (asiaticus and americanus) to potato plants.

2009

Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses

The situation in Europe concerning honeybees has in recent years become increasingly aggravated with steady decline in populations and/or catastrophic winter losses. This has largely been attributed to the occurrence of a variety of known and "unknown", emerging novel diseases. Previous studies have demonstrated that colonies often can harbour more than one pathogen, making identification of etiological agents with classical methods difficult. By employing an unbiased metagenomic approach, which allows the detection of both unexpected and previously unknown infectious agents, the detection of three viruses, Aphid Lethal Paralysis Virus (ALPV), Israel Acute Paralysis Virus (IAPV), and Lake Sinai Virus (LSV), in honeybees from Spain is reported in this article. The existence of a subgroup of ALPV with the ability to infect bees was only recently reported and this is the first identification of such a strain in Europe. Similarly, LSV appear to be a still unclassified group of viruses with unclear impact on colony health and these viruses have not previously been identified outside of the United States. Furthermore, our study also reveals that these bees carried a plant virus, Turnip Ringspot Virus (TuRSV), potentially serving as important vector organisms. Taken together, these results demonstrate the new possibilities opened up by high-throughput sequencing and metagenomic analysis to study emerging new diseases in domestic and wild animal populations, including honeybees.

Utility of a panviral microarray for detection of swine respiratory viruses in clinical samples

Several factors have recently converged, elevating the need for highly parallel diagnostic platforms that have the ability to detect many known, novel, and emerging pathogenic agents simultaneously. Panviral DNA microarrays represent the most robust approach for massively parallel viral surveillance and detection. The Virochip is a panviral DNA microarray that is capable of detecting all known viruses, as well as novel viruses related to known viral families, in a single assay and has been used to successfully identify known and novel viral agents in clinical human specimens. However, the usefulness and the sensitivity of the Virochip platform have not been tested on a set of clinical veterinary specimens with the high degree of genetic variance that is frequently observed with swine virus field isolates. In this report, we investigate the utility and sensitivity of the Virochip to positively detect swine viruses in both cell culture-derived samples and clinical swine samples. The Virochip successfully detected porcine reproductive and respiratory syndrome virus (PRRSV) in serum containing 6.10 × 10(2) viral copies per microliter and influenza A virus in lung lavage fluid containing 2.08 × 10(6) viral copies per microliter. The Virochip also successfully detected porcine circovirus type 2 (PCV2) in serum containing 2.50 × 10(8) viral copies per microliter and porcine respiratory coronavirus (PRCV) in turbinate tissue homogenate. Collectively, the data in this report demonstrate that the Virochip can successfully detect pathogenic viruses frequently found in swine in a variety of solid and liquid specimens, such as turbinate tissue homogenate and lung lavage fluid, as well as antemortem samples, such as serum.

The exploration of potato-associated bacteria in the Central Andean Highlands and their application in integrated crop management systems

Potato is the most important food crop after wheat and rice. A changing climate, coupled with a heightened consumer awareness of how food is produced and legislative changes governing the usage of agrochemicals, means that alternative more integrated and sustainable approaches are needed for crop management practices. Bioprospecting in the Central Andean Highlands resulted in the isolation and in vitro screening of 600 bacterial isolates. The best performing isolates, under in vitro conditions, were field trialled in their home countries. Six of the isolates, Pseudomonas sp. R41805 (Bolivia), Pseudomonas palleroniana R43631 (Peru), Bacillus sp. R47065, R47131, Paenibacillus sp. B3a R49541, and Bacillus simplex M3-4 R49538 (Ecuador), showed significant increase in the yield of potato. Using – omic technologies (i.e. volatilomic, transcriptomic, proteomic and metabolomic), the influence of microbial isolates on plant defence responses was determined. Volatile organic compounds of bacterial isolates were identified using GC/MS. RT-qPCR analysis revealed the significant expression of Ethylene Response Factor 3 (ERF3) and the results of this study suggest that the dual inoculation of potato with Pseudomonas sp. R41805 and Rhizophagus irregularis MUCL 41833 may play a part in the activation of plant defence system via ERF3. The proteomic analysis by 2-DE study has shown that priming by Pseudomonas sp. R41805 can induce the expression of proteins related to photosynthesis and protein folding in in vitro potato plantlets. The metabolomics study has shown that the total glycoalkaloid (TGA) content of greenhouse-grown potato tubers following inoculation with Pseudomonas sp. R41805 did not exceed the acceptable safety limit (200 mg kg-1 FW). As a result of this study, a number of bacteria have been identified with commercial potential that may offer sustainable alternatives in both Andean and European agricultural settings.

Maturation curves of sweet sorghum genotypes.

O sorgo sacarino [Sorghum bicolor (L.) Moench] se destaca como cultura complementar à cana-de-açúcar Saccharum spp. na produção de etanol, uma vez que este possui colmos suculentos com presença de açúcares diretamente fermentescíveis. Em decorrência deste fato, existe a necessidade de se analisar as propriedades do sorgo, a fim de atender às demandas da agroindústria. No presente trabalho, buscou-se desenvolver e estudar as curvas de maturação de sete cultivares de sorgo sacarino em dez épocas de colheita. Os resultados mostram que houve diferença significativa para cultivares e épocas de colheita para todos os parâmetros (p≤0,01). Quanto aos teores de açúcares, as cultivares BRS508, XBWS80147 e CMSXS629 apresentaram as maiores médias para as variáveis açúcares redutores totais (ART) e açúcares totais recuperáveis (ATR). Em relação à produção de etanol por tonelada de biomassa, as cultivares BRS 508 e a CMSXS629 apresentaram os melhores resultados.

No evidence of transmission of grapevine leafroll-associated viruses by phylloxera (Daktulosphaira vitifoliae).

Abstract Grapevine leafroll disease is associated with several species of phloem-limited grapevine leafrollassociated viruses (GLRaV), some of which are transmitted by mealybugs and scale insects. The grape phylloxera, Daktulosphaira vitifoliae (Fitch) Biotype A (Hemiptera: Phylloxeridae), is a common vineyard pest that feeds on the phloem of vine roots. There is concern that these insects may transmit one or more GLRaV species, particularly GLRaV-2, a species in the genus Closterovirus. A field survey was performed in vineyards with a high incidence of grapevine leafroll disease and D. vitifoliae was assessed for acquisition of GLRaV. In greenhouse experiments, the ability of D. vitifoliae to transmit GLRaV from infected root sections or vines to co-planted virus-free recipient vines was tested. There were no GLRaV-positive D. vitifoliae in the field survey, nor did D. vitifoliae transmit GLRaV- 1, ?2, ?3, or -4LV in greenhouse transmission experiments. Some insects tested positive for GLRaV after feeding on infected source vines in the greenhouse, however there was no evidence of virus transmission to healthy plants. These findings, in combination with the sedentary behaviour of the soil biotype of D. vitifoliae, make it unlikely that D. vitifoliae is a vector of any GLRaV.

Efeito do processamento mínimo sobre a qualidade de uvas cultivar sweet celebration.

O principal objetivo do processamento mínimo é fornecer produtos frescos, mantendo suas qualidades nutricionais e apresentando vida útil que possibilite sua comercialização e distribuição, além de agregar valor aos produtos (Srebernich, 2007 ). O cloro é um componente químico bastante utilizado no processamento mínimo, podendo ser adotado na segunda lavagem dos produtos vegetais, visando à redução da carga microbiana da casca, ou, na etapa de enxágue, tendo como função a redução da carga microbiana adquirida durante a manipulação das frutas (Bastos, 2006). Além do cloro, o uso do metabissulfito de sódio, que possui características antioxidantes e antimicrobianas, tem o objetivo de cessar a atividade de enzimas de escurecimento e inibir a proliferação de microrganismos (Silva et al., 2012). Desta forma, o presente trabalho objetivou avaliar a qualidade de uvas da cultivar Sweet Celebration submetidas ao processamento mínimo, assim como a efetividade de três soluções de enxágue e da intensidade de corte do pedicelo das bagas na conservação desses frutos, durante 21 dias de armazenamento refrigerado a 8ºC.

Avaliação da qualidade de uvas Sweet Globe submetidas ao processamento mínimo.

Apesar das vantagens geradas pelo processamento mínimo, já se sabe que esses produtos apresentam maior perecibilidade, devido aos danos sofridos, sendo necessária a adoção de técnicas que prolonguem a vida útil dos mesmos (MATTIUZ et al., 2009). Deste modo, a refrigeração é um método de extrema importância para a manutenção desses produtos, podendo também ser associada ao enxágue com soluções contendo produtos químicos como o metabissulfito de sódio e o cloro. Trabalhos relacionados ao processamento mínimo de uvas são escassos, sendo assim, objetivou-se avaliar a qualidade de uvas Sweet Globe minimamente processadas, assim como a efetividade de três soluções de enxágue (água, metabissulfito de sódio e cloro) e da intensidade de corte do pedicelo (com e sem pedicelo), na conservação destes frutos.