New insights into the biomechanics of Legg-Calvé-Perthes' disease: The Role of Epiphyseal Skeletal Immaturity in Vascular Obstruction

Objectives

Legg–Calvé–Perthes’ disease (LCP) is an idiopathic osteonecrosis of the femoral head that is most common in children between four and eight years old. The factors that lead to the onset of LCP are still unclear; however, it is believed that interruption of the blood supply to the developing epiphysis is an important factor in the development of the condition.

Methods

Finite element analysis modelling of the blood supply to the juvenile epiphysis was investigated to understand under which circumstances the blood vessels supplying the femoral epiphysis could become obstructed. The identification of these conditions is likely to be important in understanding the biomechanics of LCP.

Results

The results support the hypothesis that vascular obstruction to the epiphysis may arise when there is delayed ossification and when articular cartilage has reduced stiffness under compression.

Conclusion

The findings support the theory of vascular occlusion as being important in the pathophysiology of Perthes disease.

Cite this article: M. Pinheiro, C. A. Dobson, D. Perry, M. J. Fagan. New insights into the biomechanics of Legg-Calvé-Perthes’ disease: The Role of Epiphyseal Skeletal Immaturity in Vascular Obstruction. Bone Joint Res 2018;7:148–156. DOI: 10.1302/2046-3758.72.BJR-2017-0191.R1.

Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing

Background

Pseudomonas aeruginosa healthcare outbreaks can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical for decision-making.

Aim

To explore the usefulness of whole-genome sequencing (WGS) in the investigation of a P. aeruginosa outbreak, describing how it compares with pulsed-field gel electrophoresis (PFGE) and variable number tandem repeat (VNTR) analysis.

Methods

Six patient isolates and six environmental samples from an intensive care unit (ICU) positive for P. aeruginosa over two years underwent VNTR, PFGE and WGS.

Findings

VNTR and PFGE were required to fully determine the potential source of infection and rule out others. WGS results unambiguously distinguished linked isolates, giving greater assurance of the transmission route between wash-hand basin water and two patients, supporting the control measures employed.

Conclusion

WGS provided detailed information without the need for further typing. When allied to epidemiological information, WGS can be used to understand outbreak situations rapidly and with certainty. Implementation of WGS in real-time would be a major advance in day-to-day practice. It could become a standard of care as it becomes more widespread due to its reproducibility and lower costs.

A Prospective Intervention in Patients with Complicated Grief

Introduction

Most reactions to grief are adaptive. However, there is the possibility that some individuals present a complicated grief disorder, where there is a pathological intensification of symptoms lasting more than 6 months, deserving special treatment.

Objectives/aims

Evaluate the effectiveness of two types of intervention in complicated grief: group intervention (GI) and cognitive-narrative (CN) therapy.

Methods

Patients in a complicated grief process were selected (n = 70), and distributed in three groups: cognitive–narrative therapy group (CNTG), group intervention group (GIG) and a control group (CG). Inclusion criteria: adults, with a reference to mourning situation, with personal meaning, for over six months and results in ICG ≥30points (cutoff). The Inventory of Complicated Grief (ICG), the Center for epidemiologic studies depression scale (CES-D) and the trauma questionnaire (ICD-11) were used. Follow-up was performed 3 months after the end of each intervention. Data analysis was performed using the statistical package from social sciences (SPSS 20).

Results

With respect to complicated grief symptoms (CGx) and depression symptoms (Dx) there were statistically significant differences between the CNTG and the CG, but not with the GIG. There was no statistically significant effect in post-traumatic symptoms (PTx), even though both interventions had a slight decrease. When the CNTG and the GIG were directly compared, there was only a statistically significant difference between PTx.

Conclusions

In our single center cohort, CNTG was a more effective intervention in complicated grief patients for CGx and Dx reduction. For PTx, no intervention was superior. Larger multi-center studies are needed to validate these results.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Pollination of Campomanesia phaea (Myrtaceae) by night-active bees: a new nocturnal pollination system mediated by floral scent

Bees are the most important diurnal pollinators of angiosperms. In several groups of bees a nocturnal/crepuscular habit developed, yet little is known about their role in pollination and whether some plants are adapted specifically to these bees. We used a multidisciplinary approach to investigate the reproductive biology and to understand the role of nocturnal/crepuscular bees in pollination of Campomanesia phaea (Myrtaceae), popularly named cambuci. We studied the floral biology and breeding system of C. phaea. We collected the floral visitors and tested the pollinators' effectiveness. We also determined the floral scents released at night and during daytime, and studied behavioural responses of crepuscular/nocturnal bees towards these scents. The flowers of cambuci were self-incompatible and had pollen as the only resource for flower visitors. Anthesis lasted around 14 h, beginning at 04:30 h at night. The flowers released 14 volatile compounds, mainly aliphatic and aromatic compounds. We collected 52 species of floral visitors, mainly bees. Nocturnal and crepuscular bees (four species) were among the most frequent species and the only effective pollinators. In field bioassays performed at night, nocturnal/crepuscular bees were attracted by a synthetic scent blend consisting of the six most abundant compounds. This study describes the first scent-mediated pollination system between a plant and its nocturnal bee pollinators. Further, C. phaea has several floral traits that do not allow classification into other nocturnal pollination syndromes (e.g. pollinator attraction already before sunrise, with pollen as the only reward), instead it is a plant specifically adapted to nocturnal bees.

Frailty Syndrome: Visceral Adipose Tissue and Frailty in Patients with Symptomatic Severe Aortic Stenosis

BACKGROUND/OBJECTIVES

In patients with severe aortic stenosis (AS), frailty is a clinically relevant measure of increased vulnerability that should be included in the preoperative risk assessment. Bioelectrical impedance analysis (BIA) derived phase angle (PA) reflects cell membrane integrity and function. Few studies are available on the relative contribution of adiposity distribution on frailty, and about the influences of frailty and visceral obesity in PA value. Therefore, we aimed to evaluate associations among frailty, visceral fat depots and PA in patients with symptomatic severe AS.

METHODS

In a cohort of patients with symptomatic severe AS and preserved ejection fraction, we examined the associations between frailty, visceral fat depots and bioelectrical impedance analysis (BIA) derived phase angle (PA); and between visceral fat and PA. Frailty was defined according the Fried et al. scale criteria and the body fat distribution was determined by multidetector computed tomography and by BIA.

RESULTS

Of the fifty-five included patients, 26 were frail (47%). Adjusting for age and gender, frailty was associated with indexed epicardial adipose tissue volume (EATVi) (the odds of frailty increased 4.1-fold per additional 100 cm3/m2 of EAT [95% confidence interval (CI) of 1.03 to 16.40, p=0.04] and with PA (OR of 0.50, 95% CI, 0.26 to 0.97, p=0.04), but not with body mass index (BMI), waist circumference (WC), indexed total, visceral and subcutaneous abdominal fat areas (TAFAi, VAFAi and SAFAi) nor with indexed mediastinal adipose tissue volume (MATVi). In an age and gender adjusted linear model, PA was inversely correlated with EATVi (β=-0.008, 95% CI, -0.016 to -0.001, p=0.03), but not with BMI, WC, nor with MATVi, VAFAi, SAFAi and TAFAi.

CONCLUSIONS

In patients with symptomatic severe AS, EATVi is associated with frailty, independently of age and gender, but not with MAFVi or VAFAi. Moreover, frailty and EATVi are associated with impaired cell membrane integrity and function assessed by PA.

Diagnostic Accuracy of 2-Dimensional Computed Tomography for Articular Involvement and Fracture Pattern of Posterior Malleolar Fractures

BACKGROUND

Up to 44% of ankle fractures have involvement of the posterior tibial margin. Fracture size and morphology are important factors to guide treatment of these fragments, but reliability of plain radiography in estimating size is low. The aim of the current study was to evaluate the accuracy of 2-dimensional computed tomography (2DCT) in the assessment of posterior malleolar fractures. Additionally, the diagnostic accuracy of 2DCT and its value in preoperative planning was evaluated.

METHODS

Thirty-one patients with 31 ankle fractures including a posterior malleolar fragment were selected. Preoperative CT scans were analyzed by 50 observers from 23 countries. Quantitative 3-dimensional CT (Q3DCT) reconstructions were used as a reference standard.

RESULTS

Articular involvement of the posterior fragment was overestimated on 2DCT by factors 1.6, 1.4, and 2.2 for Haraguchi types I, II, and III, respectively. Interobserver agreement on operative management ("to fix, or not to fix?") was substantial (κ = 0.69) for Haraguchi type I fractures, fair (κ = 0.23) for type II fractures, and poor (κ = 0.09) for type III fractures. 2DCT images led to a change in treatment of the posterior malleolus in 23% of all fractures. Surgeons would operatively treat type I fractures in 63%, type II fractures in 67%, and type III fractures in 22%.

CONCLUSION

Surgeons overestimated true articular involvement of posterior malleolar fractures on 2DCT scans. 2DCT showed some additional value in estimating the involved articular surface when compared to plain radiographs; however, this seemed not yet sufficient to accurately read the fractures. Analysis of the CT images showed a significant influence on choice of treatment in 23% with a shift toward operative treatment in 12% of cases compared to evaluating plain lateral radiographs alone.

LEVEL OF EVIDENCE

Level III, comparative study.

The lanthipeptides of Bacillus methylotrophicus and their association with genomic islands

Bacillus methylotrophicus strains are known for their potential as plant-growth promoters and as microbial pesticides that effectively control plant diseases caused by bacteria and fungi. Over the past few years, a wide diversity of their secondary metabolites has been extensively characterized. Among these are the RiPPs lanthipeptides, which are an important and growing group of notable compounds. The increasing interest in B. methylotrophicus species, accompanied by the development of high throughput sequencing techniques, has resulted in a substantial number of full genomes being available. Here, an in silico analysis was performed on these genomes in order to survey the presence of lanthipeptide biosynthetic clusters. It was found that the pan genome of B. methylotrophicus only encoded the biosynthesis of mersacidin and amylolysin, which are lanthipeptides with antibacterial activity. However, the amylolysin gene cluster identified was comprised of more genetic elements than those previously described, and it had certain features of two-peptide lantibiotics. Additionally, it was also established that the association of lanthipeptides with genomic islands (GIs) was not confined to mersacidin. This was also found for the amylolysin cluster as well as other class I and class II lanthipeptides, supporting the idea that their production is probably related to functional adaptation.

Guesstimation of posterior malleolar fractures on lateral plain radiographs

BACKGROUND

Accurate assessment of articular involvement of the posterior malleolar fracture fragments in ankle fractures is essential, as this is the leading argument for internal fixation. The purpose of this study is to assess diagnostic accuracy of measurements on plain lateral radiographs.

METHODS

Quantification of three-dimensional computed tomography (Q-3D-CT) was used as a reference standard for true articular involvement (mm(2)) of posterior malleolar fractures. One-hundred Orthopaedic Trauma surgeons were willing to review 31 trimalleolar ankle fractures to estimate size of posterior malleolus and answer: (1) what is the involved articular surface of the posterior malleolar fracture as a percentage of the tibial plafond? and (2) would you fix the posterior malleolus?

RESULTS

The average posterior malleolar fragment involved 13.5% (SD 10.8) of the tibial plafond articular surface, as quantified using Q-3D-CT. The average involvement of articular surface of the posterior malleolar fragment, as estimated by 100 observers on plain radiographs was 24.4% (SD 10.0). The factor 1.8 overestimation of articular involvement was statistically significant (p<0.001). Diagnostic accuracy of measurements on plain lateral radiographs was 22%. Interobserver agreement (ICC) was 0.61. Agreement on operative fixation, showed an ICC of 0.54 (Haraguchi type I=0.76, Haraguchi type II=0.40, Haraguchi type III=0.25).

CONCLUSIONS

Diagnostic accuracy of measurements on plain lateral radiographs to assess articular involvement of posterior malleolar fractures is poor. There is a tendency to misjudge posteromedial involvement (Haraguchi type II).

Wine fermentation microbiome: a landscape from different Portuguese wine appellations

Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation - Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines.

Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT): Unravelling the effects from the molecular level to the organism

Aeromonas molluscorum Av27 cells were exposed to 0, 5 and 50 μM of TBT and the respective transcriptomes were obtained by pyrosequencing. Gene Ontology revealed that exposure to 5 μM TBT results in a higher number of repressed genes in contrast with 50 μM of TBT, where the number of over-expressed genes is greater. At both TBT concentrations, higher variations in gene expression were found in the functional categories associated with enzymatic activities, transport/binding and oxidation-reduction. A number of proteins are affected by TBT, such as the acriflavin resistance protein, several transcription-related proteins, several Hsps, ABC transporters, CorA and ZntB and other outer membrane efflux proteins, all of these involved in cellular metabolic processes, important to maintain overall cell viability. Using the STRING tool, several proteins with unknown function were related with others involved in degradation processes, such as the pyoverdine chromophore biosynthetic protein, that has been described as playing a role in the Sn-C cleavage of organotins. This approach has allowed a better understanding of the molecular effects of exposure of bacterial cells to TBT. Furthermore it contributes to the knowledge of the functional genomic aspects of bacteria exposed to this pollutant. Furthermore, the transcriptomic data gathered, and now publically available, constitute a valuable resource for comparative genome analysis.

The generalist Inga subnuda subsp. luschnathiana (Fabaceae): negative effect of floral visitors on reproductive success?

Inga species are characterised by generalist or mixed pollination system. However, this feature does not enhance reproductive rates in species with very low fruit set under natural conditions. Some ecological and genetic factors are associated with this feature, and to test the effect of massive visits on pollination success in Inga subnuda subsp. luschnathiana, we studied the efficacy of polyads deposited on stigmas of flowers isolated from visitors and polyads exposed to visitors. The proportion of polyads fixed in stigmas decreased after exposure to visitors (24 h) in comparison to stigmas isolated from visitors (hummingbirds, bees, wasps, hawkmoths and bats), and fruit set was very low. Furthermore, nectar production, sugar composition and other floral biology traits were evaluated. Increased nectar production, sugar availability and sucrose dominance during the night indicates adaptation to nocturnal visitors and supports their role as main pollinators; although the brush-flower morphology, time of anthesis, nectar dynamics and chemical composition also allow daytime visitors. Thus the species is an important resource for a diverse group of floral visitors. We conclude that excess visits (diurnal and nocturnal) are responsible for the decrease in fixed polyads in stigmas of I. subnuda subsp. luschnathiana flowers, thus contributing, with others factors, to its low fruit set. Therefore, the generalist pollination system does not result in reproductive advantages because the low fruit set in natural conditions could be the result of a negative effect of visitors/pollinators.

Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities

In the context of the sixth wave of extinction, reliable surveys of biodiversity are increasingly needed to infer the cause and consequences of species and community declines, identify early warning indicators of tipping points, and provide reliable impact assessments before engaging in activities with potential environmental hazards. DNA metabarcoding has emerged as having potential to provide speedy assessment of community structure from environmental samples. Here we tested the reliability of metabarcoding by comparing morphological and molecular inventories of invertebrate communities associated with seagrasses through estimates of alpha and beta diversity, as well as the identification of the most abundant taxa. Sediment samples were collected from six Zostera marina seagrass meadows across Brittany, France. Metabarcoding surveys were performed using both mitochondrial (Cytochrome Oxidase I) and nuclear (small subunit 18S ribosomal RNA) markers, and compared to morphological inventories compiled by a long-term benthic monitoring network. A sampling strategy was defined to enhance performance and accuracy of results by preventing the dominance of larger animals, boosting statistical support through replicates, and using two genes to compensate for taxonomic biases. Molecular barcodes proved powerful by revealing a remarkable level of diversity that vastly exceeded the morphological survey, while both surveys identified congruent differentiation of the meadows. However, despite the addition of individual barcodes of common species into taxonomic reference databases, the retrieval of only 36% of these species suggest that the remaining were either not present in the molecular samples or not detected by the molecular screening. This finding exemplifies the necessity of comprehensive and well-curated taxonomic reference libraries and multi-gene surveys. Overall, results offer methodological guidelines and support for metabarcoding as a powerful and repeatable method of characterizing communities, while also presenting suggestions for improvement, including implementation of pilot studies prior to performing full "blind" metabarcoding assessments to optimize sampling and amplification protocols.

Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen

The results of high-resolution whole-genome sequencing data provide compelling evidence that Mycoplasma amphoriforme produces chronic relapsing infection and, importantly, is transmitted in a hospital environment.

Background. Mycoplasma amphoriforme has been associated with infection in patients with primary antibody deficiency (PAD). Little is known about the natural history of infection with this organism and its ability to be transmitted in the community.

Methods. The bacterial load was estimated in sequential sputum samples from 9 patients by quantitative polymerase chain reaction. The genomes of all available isolates, originating from patients in the United Kingdom, France, and Tunisia, were sequenced along with the type strain. Genomic data were assembled and annotated, and a high-resolution phylogenetic tree was constructed.

Results. By using high-resolution whole-genome sequencing (WGS) data, we show that patients can be chronically infected with M. amphoriforme manifesting as a relapsing-remitting bacterial load, interspersed by periods when the organism is undetectable. Importantly, we demonstrate transmission of strains within a clinical environment. Antibiotic resistance mutations accumulate in isolates taken from patients who received multiple courses of antibiotics.

Conclusions. Mycoplasma amphoriforme isolates form a closely related species responsible for a chronic relapsing and remitting infection in PAD patients in the United Kingdom and from immunocompetent patients in other countries. We provide strong evidence of transmission between patients attending the same clinic, suggesting that screening and isolation may be necessary for susceptible patients. This work demonstrates the critical role that WGS can play in rapidly unraveling the biology of a novel pathogen.

Site-related differences in gene expression and bacterial densities in the mussel Bathymodiolus azoricus from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites

The deep-sea hydrothermal vent mussel Bathymodiolus azoricus is a symbiont bearing bivalve that is found in great abundance at the Menez Gwen and Lucky Strike hydrothermal vent sites and in close vicinity of the Azores region near the Mid-Atlantic Ridge (MAR). The physiological relationships that vent mussels have developed with their physical and chemical environments are likely to influence global gene expression profiles providing thus the means to investigate distinct biological markers predicting the origin of Bathymodiolus sp. irrespectively of their geographical localization. Differences found at gene expression levels, and between fluorescence in situ hybridization (FISH) and 16S rRNA amplicon sequencing results provided experimental evidence for the distinction of both Menez Gwen and Lucky Strike vent mussel individuals based on bacterial and vent mussel gene expression signatures and on the constitutive distribution and relative abundance of endosymbiotic bacteria within gill tissues. Our results confirmed the presence of methanotroph endosymbionts in Menez Gwen vent mussels whereas Lucky Strike specimens seem to harbor a different bacterial morphotype when a methane monooxygenase gene specific probe was used. No qualitative differences could be visualized between Menez Gwen and Lucky Strike individuals when tested with a sulfur-oxidizing-related probe. Quantitative PCR (qPCR) studies revealed different gene expression profiles in both Menez Gwen and Lucky Strike mussel gill tissues for the immune genes selected. Genes encoding transcription factors presented noticeably low levels of fold expression whether in Menez Gwen or Lucky Strike animals whereas the genes encoding effector molecules appeared to have higher levels expression in gill tissues from Menez Gwen animals. The peptidoglycan recognition molecule encoding gene, PGRP, presented the highest level of transcriptional activity among the genes analyzed in Menez Gwen mussel gill tissues, seconded by carcinolectin and thus denoting the relevance of immune recognition molecules in early stage of the immune responses onset. Genes regarded as encoding molecules involved in signaling pathways were consistently expressed in both Menez Gwen and Lucky Strike mussel gill tissues. Remarkably, the immunity-related GTPase encoding gene demonstrated, in Lucky Strike samples, the highest level of expression among the signaling molecule encoding genes tested when expressions levels were compared between Menez Gwen and Lucky Strike animals. A differential expression analysis of bacterial genes between Menez Gwen and Lucky Strike mussels indicated a clear expression signature in the latter animal gill tissues. The bacterial community structure ensued from the 16S rRNA sequencing analyses pointed at an unpredicted conservation of endosymbiont bacterial loads between Menez Gwen and Lucky Strike samples. Taken together, our results support the hypothesis that B. azoricus exhibits different transcriptional statuses while living in distinct hydrothermal vent sites may result in distinct gene expressions because of physico-chemical and/or symbiont densities differences.

The role of targeted BRCA1/BRCA2 mutation analysis in hereditary breast/ovarian cancer families of Portuguese ancestry

We report the analysis of altogether 1050 suspected hereditary breast/ovarian cancer (HBOC) families, 524 fully screened for BRCA1/BRCA2 mutations and 526 tested only for the most common mutations. Of the 119 families with pathogenic mutations, 40 (33.6%) had the BRCA2 c.156_157insAlu rearrangement and 15 (12.6%) the BRCA1 c.3331_3334del mutation, the former being specific of Portuguese ancestry and the latter showing a founder effect in Portugal. Interestingly, the two most common mutations were found in a significant proportion of the HBOC families with an a priori BRCAPRO mutation probability <10%. We recommend that all suspected HBOC families from Portugal or with Portuguese ancestry, even those fulfilling moderately stringent clinical-criteria for genetic testing, should be specifically analyzed for the two most common BRCA1/BRCA2 founder mutations, and we here present a simple method for this first tier test. Screening of the entire coding regions of BRCA1 and BRCA2 should subsequently be offered to those families with a mutation probability ≥10% if none of those founder mutations are found.

Large foot schwannoma with bone invasion - a case report

A rare case of a large foot schwannoma with an intraosseous component is presented. Due to suspicion of malignancy, an amputation had previously been proposed. When the patient presented to us, the prolonged clinical course as well as some elements of the imaging exams suggested benignancy and we decided for complete tumor excision. Intraoperative findings supported the benign character of the neoplasm and pathology would later confirm the diagnosis of a benign schwannoma. The outcome, at 18 months of follow-up was a fully functional limb. Recurrence must still be considered but malignant transformation is very rare in a solitary schwannoma and can be discounted. Solitary benign schwannomas have a negligible malignization potential independently of their size or osseous component. When benignancy is considered, primary total tumor excision, as part of a staged procedure, is a safe approach. It allows for a thorough pathologic examination and eventually for a definitive treatment.

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background

Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management.

Results

We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org.

Conclusions

This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

Gomes A. Unravelling the diversity of grapevine microbiome

Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.

MOSAL: software tools for multiobjective sequence alignment

: Multiobjective sequence alignment brings the advantage of providing a set of alignments that represent the trade-off between performing insertion/deletions and matching symbols from both sequences. Each of these alignments provide a potential explanation of the relationship between the sequences. We introduce MOSAL, a software tool that provides an open-source implementation and an on-line application for multiobjective pairwise sequence alignment.