Comprehensive prediction of plant cytoplasmic and apoplastic effectors underlying Erwinia psidii pathogenicity

Erwinia psidii (Eps) is the causal agent of emerging diseases of eucalypt and guava; however, the mechanisms underlying its pathogenicity are not fully understood. Here, we predicted factors involved in the ability of Eps to cause disease on its host plants. For that, the genomes of four Eps strains exhibiting different virulence on eucalypt were sequenced, and hrp/hrc genes coding for the type III secretion system (T3SS), effectors injected into the plant cell cytoplasm through the T3SS (T3SEs) and their plant subcellular localizations, as well as proteins deployed to the host apoplast, were predicted. It was found that Eps possesses a complete hrp/hrc gene cluster based on comparison with Erwinia amylovora. A total of 18 T3SEs were predicted, 11 of which were shared among all strains, none were exclusive to any strain and seven were absent in at least one strain. No sequence variation among strains was found for five T3SE candidates whereas extensive variation was found for six, suggesting the latter may be determinants of virulence differences. The T3SE candidates are predicted to target the plant cell nucleus, cytoplasm, mitochondrion, chloroplast and peroxisome. The predicted apoplastic effector repertoire common to all four strains was over-represented in proteins of unknown functions or predicted to possess enzymatic activities, among which the most abundant were oxidoreductases and peptidases. Proteins with lytic transglycosylase activity were predicted in strain-specific apoplastic effector repertoires. These results provide an important framework for future research aimed at uncovering the factors underlying Eps pathogenicity.     

Intake,performance, and efficiency of nutrient utilization in Saanen goat kids fed diets containing calcium salts of fatty acids

Tropical Animal Health and Production - The objective of this study was to evaluate the effect of feeding Saanen goat kids with calcium salts of fatty acids (CSFA) in diet, on intake, performance,...     

Validation and use of a qPCR protocol to quantify the spread of Ralstonia solanacearum in susceptible and resistant eucalypt plants

Bacterial wilt caused by Ralstonia solanacearum is a serious disease of eucalypt in humid and high temperature areas worldwide. Spreading of the bacterium in the field or to other nurseries occurs mainly by symptomless infected plant material. The use of pathogen-free propagating material as well as planting of resistant genotypes are currently the only strategies used for disease control. Therefore, a reliable and sensitive method for detection of low titres of R. solanacearum in infected plant tissue is essential for the success of management programmes. In this work, we adapted an efficient intercalating dye-based real-time PCR protocol to detect the bacterium in symptomless eucalypt plants as well as to investigate its movement in eucalypt clones CLR172 and CLR371, which exhibit resistant and susceptible phenotypes, respectively. We found that the bacterium translocates acropetally and basipetally in inoculated but symptomless cuttings of the resistant clone, as in cuttings of the susceptible clone displaying symptoms. Nevertheless, a smaller concentration of bacterial DNA was detected in tissues of the resistant clone. Mature biofilms occluding the xylem vessels were present in the susceptible clone whereas only single cells or small aggregates were observed in the resistant clone. This work contributes to improve our knowledge of the colonization process of R. solanacearum in eucalypt clones with different levels of susceptibility and to understand how the defence mechanisms against bacterial wilt in Eucalyptus work. Our findings could aid in the selection of the most resistant eucalypt clones to be used in wilt disease management programmes.     

Temperature and dietary starch level affected protein but not starch digestibility in gilthead sea bream juveniles

A study was carried out with gilthead sea bream juveniles to assess the effect of water temperature (18 and 25°C) and dietary pregelatinized starch level (10, 20 and 30%) on digestibility of protein and starch and on the activity of proteolytic and amylolytic enzymes. ADC of pregelatinized starch was very high (>99%) irrespectively of dietary inclusion level, and it was not affected by water temperature. ADC of protein was also high (>90%) but improved at the higher water temperature. Dietary starch interacted with protein digestibility, which decreased as dietary starch level increased. Temperature affected both acid and basic protease activities, with acid protease activity being higher at 25°C and basic protease activity being higher at 18°C. However, total proteolytic activity and amylase activities were not affected by water temperature. Dietary carbohydrate exerted no effect on proteolytic or amylolitic activities. It is concluded that gilthead sea bream juveniles digest pregelatinized starch very efficiently irrespective of water temperature, due to adjustments of amylase activity to cope with temperature differences. Pregelatinized starch interacts negatively with protein digestibility, with the ADC of protein decreasing as dietary starch levels increase.     

Boron and zinc inhibit embryonic development,hatching and reproduction of Meloidogyne incognita

Nematodes have difficult control and complex handling, but considering the physiological and biochemical changes that micronutrients promoting in plants, there is possibility that the supply with these chemicals increases the resistance of plants against nematodes. Thus, the present study aimed to assess the effect of the application of boron and zinc on the reproduction of Meloidogyne incognita, embryonic development and juvenile nematode hatching. Nematode reproduction was evaluated in tomato plant inoculated with 2000 eggs and treated in the aerial part with boron or zinc at the following doses: 0, 1/2, 1×, 2× and 4× the manufacturer's recommendation (100 and 30?g/L, respectively), with the plants assessed 60 days after inoculation. For assessment of embryonic development and juvenile hatching, 1?mL nematode suspension was placed in Petri dishes containing 9?mL of the same doses of boron and zinc, and assessment occurred four and eight days after incubation. Results obtained showed that boron controlled nematode population at the dose of 400?g/L and promoted juvenile hatching when used at maximum dosage on the eighth day. Zinc reduced the number of galls and the number of eggs at the dose of 60?g/L, but did not exhibit direct effect on nematode.     

GOAnnotator: linking protein GO annotations to evidence text

Background

Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators.

Results

In this paper we describe an approach that links uncurated annotations to text extracted from literature. The selection of the text is based on the similarity of the text to the term from the uncurated annotation. Besides substantiating the uncurated annotations, the extracted texts also lead to novel annotations. In addition, the approach uses the GO hierarchy to achieve high precision. Our approach is integrated into GOAnnotator, a tool that assists the curation process for GO annotation of UniProt proteins.

Conclusion

The GO curators assessed GOAnnotator with a set of 66 distinct UniProt/SwissProt proteins with uncurated annotations. GOAnnotator provided correct evidence text at 93% precision. This high precision results from using the GO hierarchy to only select GO terms similar to GO terms from uncurated annotations in GOA. Our approach is the first one to achieve high precision, which is crucial for the efficient support of GO curators. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

     

Gut microbiota and gut morphology of gilthead sea bream (Sparus aurata) juveniles are not affected by chromic oxide as digestibility marker

The present work aimed to evaluate whether the use of chromic oxide (Cr₂O₃) as dietary inert marker in fish digestibility studies interferes with gut microbial community modulation and gut morphology. To assess the effects of Cr₂O₃ under potential diverse microbiota populations, dietary Cr₂O₃ was tested using challenging plant feedstuffs (PF)‐based diets supplemented or not with prebiotics, as prebiotics are expected to modify gut microbiota populations. For that purpose, three diets were formulated to include circa 20:80 fish meal and PF as protein sources, without (CTR) or with prebiotic supplementation (10 g/kg XOS or GOS). These diets did not include Cr₂O₃ (?Cr₂O₃ diets). Three similar additional diets were formulated to include 5 g/kg Cr₂O₃ (+Cr₂O₃ diets). Cr₂O₃ effects on gut microbiota were assessed for the first time in the allochthonous (digesta) and autochthonous (mucosa) community by a culture‐independent molecular approach, using denaturing gradient gel electrophoresis (DGGE). No differences in gut bacterial profiles (number of operational taxonomic units, microbiota richness, diversity and similarity indices) were observed between dietary treatments. No significant alterations in submucosa layer structure, enterocytes and eosinophilic granular cells structure, goblet cells and leucocytes quantity were detected in the distal intestine among diets. In conclusion, data indicate that dietary inclusion of 5 g/kg Cr₂O₃ does not interfere with gilthead sea bream (Sparus aurata) gut microbiota and gut morphology, suggesting that a dietary incorporation level of 5 g/kg Cr₂O₃ can safely be used as inert marker in digestibility studies.     

Populations of Ceratocystis fimbriata on Colocasia esculenta and other hosts in the Mata Atlântica region in Brazil

Ceratocystis fimbriata is native to Brazil, where it is able to cause serious diseases on numerous hosts, especially on non‐native plants. Because C. fimbriata is soilborne and not wind dispersed, highly differentiated populations are found in different regions of Brazil. The present study compared populations of C. fimbriata on taro, mango, eucalyptus and kiwifruit from the coastal Mata Atlântica region with native populations of the fungus from the Cerrado‐transition region in Brazil by using 14 SSR markers and DNA sequences of ITS and mating type genes. Microsatellite and phylogenetic analyses were performed to test the hypothesis that populations on different hosts from the Mata Atlântica region are related to each other and are native to the region. The ITS sequences varied greatly among the taro isolates, with six sequences identified, from which two had not been previously reported. For mating type genes, four sequences were identified among the isolates on taro, mango, eucalyptus and kiwifruit. Phylogenetic analyses showed that Mata Atlântica populations formed a monophyletic group distinct from Cerrado‐transition region populations, although earlier studies had shown that isolates from the two regions are interfertile and are considered as a single biological species. Microsatellite analysis revealed low gene diversity for each of the three Mata Atlântica populations on taro, mango and kiwifruit, suggesting that these populations had gone through genetic bottlenecks, probably by dispersal of select genotypes in vegetative propagation material. Also, microsatellite markers showed that two microsatellite genotypes from taro are widely spread in Brazil, probably by infected corms.