Proteomic and Metabolomic Analysis of the Quercus ilex-Phytophthora cinnamomi Pathosystem Reveals a Population-Specific Response, Independent of Co-Occurrence of Drought.

Holm oak (Quercus ilex) is considered to be one of the major structural elements of Mediterranean forests and the agrosilvopastoral Spanish "dehesa", making it an outstanding example of ecological and socioeconomic sustainability in forest ecosystems. The exotic Phytophthora cinnamomi is one of the most aggressive pathogens of woody species and, together with drought, is considered to be one of the main drivers of holm oak decline. The effect of and response to P. cinnamomi inoculation were studied in the offspring of mother trees from two Andalusian populations, Cordoba and Huelva. At the two locations, acorns collected from both symptomatic (damaged) and asymptomatic (apparently healthy) trees were sampled. Damage symptoms, mortality, and chlorophyll fluorescence were evaluated in seedlings inoculated under humid and drought conditions. The effect and response depended on the population and were more apparent in Huelva than in Cordoba. An integrated proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, including amino acid metabolism pathways in Huelva, and terpenoid and flavonoid biosynthesis in Cordoba. However, no differential response was observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus was activated in response to defective photosynthetic activity in inoculated plants, which seemed to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may have conferred higher resistance in the Cordoba population. Some enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates.

A first draft genome of holm oak (Quercus ilex subsp. ballota), the most representative species of the Mediterranean forest and the Spanish agrosylvopastoral ecosystem "dehesa".

The holm oak (Quercus ilex subsp. ballota) is the most representative species of the Mediterranean Basin and the agrosylvopastoral Spanish "dehesa" ecosystem. Being part of our life, culture, and subsistence since ancient times, it has significant environmental and economic importance. More recently, there has been a renewed interest in using the Q. ilex acorn as a functional food due to its nutritional and nutraceutical properties. However, the holm oak and its related ecosystems are threatened by different factors, with oak decline syndrome and climate change being the most worrying in the short and medium term. Breeding programs informed by the selection of elite genotypes seem to be the most plausible biotechnological solution to rescue populations under threat. To achieve this and other downstream analyses, we need a high-quality and well-annotated Q. ilex reference genome. Here, we introduce the first draft genome assembly of Q. ilex using long-read sequencing (PacBio). The assembled nuclear haploid genome had 530 contigs totaling 842.2 Mbp (N50 = 3.3 Mbp), of which 448.7 Mb (53%) were repetitive sequences. We annotated 39,443 protein-coding genes of which 94.80% were complete and single-copy genes. Phylogenetic analyses showed no evidence of a recent whole-genome duplication, and high synteny of the 12 chromosomes between Q. ilex and Quercus lobata and between Q. ilex and Quercus robur. The chloroplast genome size was 142.3 Kbp with 149 protein-coding genes successfully annotated. This first draft should allow for the validation of omics data as well as the identification and functional annotation of genes related to phenotypes of interest such as those associated with resilience against oak decline syndrome and climate change and higher acorn productivity and nutraceutical value.

Effects of the size and cost reduction on a discounted payback period and levelized cost of energy of a zero-export photovoltaic system with green hydrogen storage.

Zero-export photovoltaic systems are an option to transition to Smart Grids. They decarbonize the sector without affecting third parties. This paper proposes the analysis of a zero-export PVS with a green hydrogen generation and storage system. This configuration is feasible to apply by any self-generation entity; it allows the user to increase their resilience and independence from the electrical network. The technical issue is simplified because the grid supplies no power. The main challenge is finding an economic balance between the savings in electricity billing, proportional to the local electricity rate, and the complete system's investment, operation, and maintenance expenses. This manuscript presents the effects of the power sizing on the efficacy of economic savings in billing (ηSaving) and the effects of the cost reduction on the levelized cost of energy (LCOE) and a discounted payback period (DPP) based on net present value. In addition, this study established an analytical relationship between LCOE and DPP. The designed methodology proposes to size and selects systems to use and store green hydrogen from the zero-export photovoltaic system. The input data in the case study are obtained experimentally from the Autonomous University of the State of Quintana Roo, located on Mexico's southern border. The maximum power of the load is LPmax = 500 kW, and the average power is LPmean = 250 kW; the tariff of the electricity network operator has hourly conditions for a medium voltage demand. A suggested semi-empirical equation allows for determining the efficiency of the fuel cell and electrolyzer as a function of the local operating conditions and the nominal power of the components. The analytical strategy, the energy balance equations, and the identity functions that delimit the operating conditions are detailed to be generalized to other case studies. The results are obtained by a computer code programmed in C++ language. According to our boundary conditions, results show no significant savings generated by the installation of the hydrogen system when the zero-export photovoltaic system Power ≤ LPmax and DPP ≤ 20 years is possible only with LCOE ≤ 0.1 $/kWh. Specifically for the Mexico University case study, zero-export photovoltaic system cost must be less than 310 $/kW, fuel cell cost less than 395 $/kW, and electrolyzer cost less than 460 $/kW.

Selective decline of bacteria colonizing the calf hindgut during colostrum to milk transition, with persistence of taxa correlating with host passive immunity.

In neonate calves, the association between gut microbial colonization and passive immunity acquisition remains largely unknown. We evaluated the effect of transition from colostrum to milk on the hindgut microbiota, and the correlations between acquired passive immunity and this microbiome. In 14 Holstein calves, colostrum quality and host passive immunity were measured, feces were sampled when feeding colostrum and after transition to milk. Then, in eight calves displaying a wide range of passive immunity, the hindgut microbiota was evaluated with DNA sequencing; differential abundance was analyzed with Maaslin2. With transition from colostrum to milk, many initial bacterial colonizers did not survive; genus Ralstonia decreased, but Lactobacillus and Bacteroides increased. When feeding colostrum, the amount of immunoglobulins consumed positively correlated with abundance of Lactobacillaceae and Lachnospiraceae, but Escherichia-Shigella and Clostridium sensu stricto 1 correlated negatively with host passive immunity. After transition to milk, acquired passive immunity negatively correlated with Clostridium sensu stricto 1, Ralstonia, and Veillonella. Overall, many initial hindgut colonizers did not thrive during transition from colostrum to milk, homogenizing the bacterial profile with prevalence of milk digesters. Several bacterial taxa showed strong correlation with host passive immunity, suggesting an interplay between calf passive immunity acquisition and the colonizing microbiota.

Effect of Supranutritional Dosage Selenium in Neonatal Goat Kids on Productive Performance, Physicochemical Profiles in Meat, Selenium Levels in Tissues, and Histopathological Findings.

Selenium (Se) is an essential element and antioxidant that catalyzes the destruction of hydrogen peroxide formed during cellular oxidative metabolism. Doses of Se as selenomethionine (SeMe) by oral route are 0.1-0.3 mgSe/kg DM, while the dose by parenteral route with sodium selenite (Na2SeO3) is 0.1 mgSe/BW. The effects of supranutritional Se supplementation on normal kids have rarely been studied. The objective of the study was to evaluate both Se sources on growth performance, Se in tissues, histopathological findings, and meat characteristics. Forty-five kids of the Pastoreña breed with 25-day age were distributed (4.7 ± 1.13 kg) in three treatments: a) control group, C: consumption with goat milk (GM: containing 0.135 mgSe/g); b) NaSe: GM plus Na2SeO3 injectable, 0.25 mgSe/kg BW; c) SeMe: GM plus oral dosage, 0.3 mgSe as SeMe daily. Fifteen animals per treatment were slaughtered at 7, 14, and 21 days. Feed conversion improved (P < 0.05) with Se supplement (P < 0.05) at 7 and 14 days. SeMe had higher protein and fat meat content (P < 0.05). SeMe increased Se liver at 14 and 21 days. NaSe and SeMe had higher (P < 0.05) levels of Se kidney. SeMe-21d showed 42% mononuclear and periportal cell infiltration lesions. In conclusion, Se administered through milk in goat kids was insufficient to prevent nutritional muscular dystrophy. The supranutritional dose of 0.25 mg/kg as NaSe was sufficient to maintain the Se level in tissues. SeMe increased Se liver and kidney efficiently. Both Se sources improved the bioavailability of the mineral in kids.

Multiomic Data Integration in the Analysis of Drought-Responsive Mechanisms in Quercus ilex Seedlings.

The integrated analysis of different omic layers can provide new knowledge not provided by their individual analysis. This approach is also necessary to validate data and reveal post-transcriptional and post-translational mechanisms of gene expression regulation. In this work, we validated the possibility of applying this approach to non-model species such as Quercus ilex. Transcriptomics, proteomics, and metabolomics from Q. ilex seedlings subjected to drought-like conditions under the typical summer conditions in southern Spain were integrated using a non-targeted approach. Two integrative approaches, PCA and DIABLO, were used and compared. Both approaches seek to reduce dimensionality, preserving the maximum information. DIABLO also allows one to infer interconnections between the different omic layers. For easy visualization and analysis, these interconnections were analyzed using functional and statistical networks. We were able to validate results obtained by analyzing the omic layers separately. We identified the importance of protein homeostasis with numerous protease and chaperones in the networks. We also discovered new key processes, such as transcriptional control, and identified the key function of transcription factors, such as DREB2A, WRKY65, and CONSTANS, in the early response to drought.

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How.

The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors' group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.

Identification of Proteases and Protease Inhibitors in Seeds of the Recalcitrant Forest Tree Species Quercus ilex.

Proteases and protease inhibitors have been identified in the recalcitrant species Quercus ilex using in silico and wet methods, with focus on those present in seeds during germination. In silico analyses showed that the Q. ilex transcriptome database contained 2,240 and 97 transcripts annotated as proteases and protease inhibitors, respectively. They belonged to the different families according to MEROPS, being the serine and metallo ones the most represented. The data were compared with those previously reported for other Quercus species, including Q. suber, Q. lobata, and Q. robur. Changes in proteases and protease inhibitors alongside seed germination in cotyledon and embryo axis tissues were assessed using proteomics and in vitro and in gel activity assays. Shotgun (LC-MSMS) analysis of embryo axes and cotyledons in nonviable (NV), mature (T1) and germinated (T3) seeds allowed the identification of 177 proteases and 12 protease inhibitors, mostly represented by serine and metallo types. Total protease activity, as determined by in vitro assays using azocasein as substrate, was higher in cotyledons than in embryo axes. There were not differences in activity among cotyledon samples, while embryo axis peaked at germinated T4 stage. Gel assays revealed the presence of protease activities in at least 10 resolved bands, in the Mr range of 60-260 kDa, being some of them common to cotyledons and embryo axes in either nonviable, mature, and germinated seeds. Bands showing quantitative or qualitative changes upon germination were observed in embryo axes but not in cotyledons at Mr values of 60-140 kDa. Proteomics shotgun analysis of the 10 bands with protease activity supported the results obtained in the overall proteome analysis, with 227 proteases and 3 protease inhibitors identified mostly represented by the serine, cysteine, and metallo families. The combined use of shotgun proteomics and protease activity measurements allowed the identification of tissue-specific (e.g., cysteine protease inhibitors in embryo axes of mature acorns) and stage-specific proteins (e.g., those associated with mobilization of storage proteins accumulated in T3 stage). Those proteins showing differences between nonviable and viable seeds could be related to viability, and those variables between mature and germinated could be associated with the germination process. These differences are observed mostly in embryo axes but not in cotyledons. Among them, those implicated in mobilization of reserve proteins, such as the cathepsin H cysteine protease and Clp proteases, and also the large number of subunits of the CNS and 26S proteasome complex differentially identified in embryos of the several stages suggests that protein degradation via CNS/26S plays a major role early in germination. Conversely, aspartic proteases such as nepenthesins were exclusively identified in NV seeds, so their presence could be used as indicator of nonviability.

Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for Quercus ilex.

Drought is one of the main causes of mortality in holm oak (Quercus ilex) seedlings used in reforestation programs. Although this species shows high adaptability to the extreme climate conditions prevailing in Southern Spain, its intrinsic genetic variability may play a role in the differential response of some populations and individuals. The aim of this work was to identify proteins and derived proteotypic peptides potentially useful as putative markers for drought tolerance in holm oak by using a targeted post-acquisition proteomics approach. For this purpose, we used a set of proteins identified by shotgun (LC-MSMS) analysis in a drought experiment on Q. ilex seedlings from four different provenances (viz. the Andalusian provinces Granada, Huelva, Cadiz and Seville). A double strategy involving the quantification of proteins and target peptides by shotgun analysis and post-acquisition data analysis based on proteotypic peptides was used. To this end, an initial list of proteotypic peptides from proteins highly represented under drought conditions was compiled that was used in combination with the raw files from the shotgun experiment to quantify the relative abundance of the fragment's ion peaks with the software Skyline. The most abundant peptides under drought conditions in at least two populations were selected as putative markers of drought tolerance. A total of 30 proteins and 46 derived peptides belonging to the redox, stress-related, synthesis,-folding and degradation, and primary and secondary metabolism functional groups were thus identified. Two proteins (viz., subtilisin and chaperone GrpE protein) were found at increased levels in three populations, which make them especially interesting for validation drought tolerance markers in subsequent experiments.

Quercus ilex pollen allergen, Que i 1, responsible for pollen food allergy syndrome caused by fruits in Spanish allergic patients.

BACKGROUND: Pollen food allergy syndrome (PFAS) related to PR10 from vegetables is common in northern Europe, whereas in Mediterranean countries PFAS has been preferentially associated with profilins. However, there are pollen-allergic patients reactive to Bet v 1 in birch-free regions. Since it cannot be the primary sensitizer, there has to be another culprit. Quercus ilex is a good candidate as it belongs to the order Fagales. This order includes trees with highly sensitizing pollen such as alder, hazel, hornbeam, oak and chestnut because of the presence of PR10 allergens. PR10 allergens have indeed been described in other Quercus species. OBJECTIVE: Our goals were to determine the rate of sensitization to Q. ilex in central Spain and the associated frequency of PFAS; secondly to identify and clone the Q. ilex allergen PR10. METHODS: We included 224 allergic patients with respiratory symptoms to estimate the rate of sensitization. A skin prick test (SPT) and ImmunoCAP were performed. A total of 38 Q. ilex-sensitized patients were tested using Western blotting to determine the rate of Que i 1. Peptides from Que i 1 were analysed by MALDI-TOF/TOF and Orbitrap LC-MSMS. The Que i 1 sequence was first obtained from the Holm oak transcriptome then cloned and expressed in bacteria. RESULTS: 59.8% of pollen-allergic children were sensitized to Q. ilex. We described and cloned the Q. ilex PR10, Que i 1, which has a sensitization rate of 60.5% and was recognized by 65.4% patients reporting PFAS. CONCLUSION AND CLINICAL RELEVANCE: Sensitization to Q. ilex pollen has increased significantly since 1995. This sensitization could be important, as the presence of PFAS in this population is higher than in patients not sensitized to Q. ilex. The first Q. ilex allergen has been described and is related to PFAS in Spanish patients sensitized to PR10 but not exposed to birch pollen.

Protein Interaction Networks: Functional and Statistical Approaches.

The evolution of next-generation sequencing and high-throughput technologies has created new opportunities and challenges in data science. Currently, a classic proteomics analysis can be complemented by going a step beyond the individual analysis of the proteome by using integrative approaches. These integrations can be focused either on inferring relationships among proteins themselves, with other molecular levels, phenotype, or even environmental data, giving the researcher new tools to extract and determine the most relevant information in biological terms. Furthermore, it is also important the employ of visualization methods that allow a correct and deep interpretation of data.To carry out these analyses, several bioinformatics and biostatistical tools are required. In this chapter, different workflows that enable the creation of interaction networks are proposed. Resulting networks reduce the complexity of original datasets, depicting complex statistical relationships (through PLS analysis and variants), functional networks (STRING, shinyGO), and a combination of both approaches. Recently developed methods for integrating different omics levels, such as coinertial analyses or DIABLO, are also described. Finally, the use of Cytoscape or Gephi was described for the representation and mining of the different networks.This approach constitutes a new way of acquiring a deeper knowledge of the function of proteins, such as the search for specific connections of each group to identify differentially connected modules, which may reflect involved protein complexes and key pathways.

Specific Protein Database Creation from Transcriptomics Data in Nonmodel Species: Holm Oak (Quercus ilex L.).

Proteomics encompasses efforts to identify all the proteins of a proteome, with most of studies about plant proteomics based on a bottom-up mass spectrometry (MS) strategy, in which the proteins are subjected to digestion by trypsin and the tryptic fragments are subjected to MS analysis. The identification of proteins from MS/MS spectra has been performed using different algorithms (Mascot, Sequest) against plant protein sequence databases such as UniProtKB or NCBI_Viridiplantae. But these databases are not the best choice for nonmodel species where they are underrepresented, resulting in poor identification rates. A high identification rate requires a sequenced and well-annotated genome of the species under investigation. For nonmodel organisms, the identification of proteins is challenging since, in the best of the cases, only hits or orthologs instead of gene products are identified. However, in the absence of a sequenced genome, this situation can be improved using transcriptome data to generate a specific species database to compare proteins. In this chapter, we report the protein database construction from RNA-Seq data in a nonmodel species, in this particular case Holm oak (Q. ilex).

Non-clinical performance and acceptability of a small portable respiratory stimulator device for basic neonatal resuscitation, tested by health personnel / Desempeño no clínico y aceptabilidad de un estimulador respiratorio portátil para reanimación neonatal básica, evaluado en personal de salud

Introducción: La reanimación neonatal demanda dispositivos para apoyo respiratorio que no siempre se encuentran en áreas rurales. Se requieren dispositivos innovadores y el prototipado rápido permite generarlos usando diseños e impresoras tridimensionales (3D). Objetivo: Evaluar el desempeño no clínico y la aceptabilidad por el personal de salud de un dispositivo respiratorio neonatal producido mediante prototipado rápido. Métodos: Estudio observacional, descriptivo, de prueba de concepto desarrollado en dos etapas. Etapa 1: Fabricación del dispositivo con prototipado rápido en impresoras y escáneres tridimensionales (3D). Etapa 2: Demostración del dispositivo durante programas de capacitación en reanimación neonatal para personal de salud en tres regiones del Perú (Tarapoto, Huánuco y Ayacucho). En ambas etapas se evaluó el desempeño del dispositivo conectado a un analizador de flujo de gases. Se administró una encuesta a los trabajadores de salud de Tarapoto y Ayacucho para conocer su aceptabilidad. Resultados: El prototipo desarrollado tiene forma de T con dos fuelles laterales que al presionarse con una sola mano, proyectan aire por el centro hacia un adaptador facial. El uso del prototipo en laboratorio generó un flujo de aire promedio de 4,8 Lt/min (DE ± 1,7) y una presión promedio de 5,9 cm H2O (DE ± 1,4). Este dispositivo fue considerado como "de uso muy simple" en una encuesta de aceptabilidad donde participaron 39 enfermeras y 11 médicos en zonas alejadas de la capital del Perú. Conclusiones: El prototipo evaluado fue aceptado por el personal y tuvo un desempeño capaz de generar un estímulo de la respiración espontánea al nacer.

Introduction: Neonatal resuscitation demands equipment for respiratory support not always available in rural areas. Innovative devices are required, and rapid prototyping allows to generate them using three-dimensional (3D) designs and printers. Objective: To evaluate the non-clinical performance and the acceptability by health personnel of a neonatal respiratory device produced by rapid prototyping. Methods: Observational study, descriptive, of proof of concept developed in two steps. Step 1: Manufacture of the device with rapid prototyping in three-dimensional (3D) scanners and printers. Step 2: Demonstration of the invention during training programs in neonatal resuscitation for health personnel in three regions of Peru (Tarapoto, Huánuco and Ayacucho). In both steps, we evaluated the performance of the device connected to a gas flow analyser. A survey was administered to the health workers of Tarapoto and Ayacucho to know their acceptability. Results: The developed prototype is T-shaped with two side bellows that, when pressed with one hand, project air through the centre towards a facial adapter. The use of the prototype in the laboratory generated an average air flow of 4.8 Lt /min (SD ± 1.7) and an average pressure of 5.9 cm H2O (SD ± 1.4). This device was considered to be "very simple to use" in an acceptability survey involving 39 nurses and 11 doctors in remote areas of the capital of Peru. Conclusions: The evaluated prototype is acceptable by the staff and has a performance capable of generating spontaneous breathing at birth.

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.

Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome.

Transcriptome analysis is widely used in plant biology research to explore gene expression across a large variety of biological contexts such as those related to environmental stress and plant-pathogen interaction. Currently, next generation sequencing platforms are used to obtain a high amount of raw data to build the transcriptome of any plant. Here, we compare Illumina and Ion Torrent sequencing platforms for the construction and analysis of the holm oak (Quercus ilex) transcriptome. Genomic analysis of this forest tree species is a major challenge considering its recalcitrant character and the absence of previous molecular studies. In this study, Quercus ilex raw sequencing reads were obtained from Illumina and Ion Torrent and assembled by three different algorithms, MIRA, RAY and TRINITY. A hybrid transcriptome combining both sequencing technologies was also obtained in this study. The RAY-hybrid assembly generated the most complete transcriptome (1,116 complete sequences of which 1,085 were single copy) with a E90N50 of 1,122 bp. The MIRA-Illumina and TRINITY-Ion Torrent assemblies annotated the highest number of total transcripts (62,628 and 74,058 respectively). MIRA-Ion Torrent showed the highest number of shared sequences (84.8%) with the oak transcriptome. All the assembled transcripts from the hybrid transcriptome were annotated with gene ontology grouping them in terms of biological processes, molecular functions and cellular components. In addition, an in silico proteomic analysis was carried out using the translated assemblies as databases. Those from Ion Torrent showed more proteins compared to the Illumina and hybrid assemblies. This new generated transcriptome represents a valuable tool to conduct differential gene expression studies in response to biotic and abiotic stresses and to assist and validate the ongoing Q. ilex whole genome sequencing.

A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species Quercus ilex.

Holm oak (Quercus ilex) is the most important and representative species of the Mediterranean forest and of the Spanish agrosilvo-pastoral "dehesa" ecosystem. Despite its environmental and economic interest, Holm oak is an orphan species whose biology is very little known, especially at the molecular level. In order to increase the knowledge on the chemical composition and metabolism of this tree species, the employment of a holistic and multi-omics approach, in the Systems Biology direction would be necessary. However, for orphan and recalcitrant plant species, specific analytical and bioinformatics tools have to be developed in order to obtain adequate quality and data-density before to coping with the study of its biology. By using a plant sample consisting of a pool generated by mixing equal amounts of homogenized tissue from acorn embryo, leaves, and roots, protocols for transcriptome (NGS-Illumina), proteome (shotgun LC-MS/MS), and metabolome (GC-MS) studies have been optimized. These analyses resulted in the identification of around 62629 transcripts, 2380 protein species, and 62 metabolites. Data are compared with those reported for model plant species, whose genome has been sequenced and is well annotated, including Arabidopsis, japonica rice, poplar, and eucalyptus. RNA and protein sequencing favored each other, increasing the number and confidence of the proteins identified and correcting erroneous RNA sequences. The integration of the large amount of data reported using bioinformatics tools allows the Holm oak metabolic network to be partially reconstructed: from the 127 metabolic pathways reported in KEGG pathway database, 123 metabolic pathways can be visualized when using the described methodology. They included: carbohydrate and energy metabolism, amino acid metabolism, lipid metabolism, nucleotide metabolism, and biosynthesis of secondary metabolites. The TCA cycle was the pathway most represented with 5 out of 10 metabolites, 6 out of 8 protein enzymes, and 8 out of 8 enzyme transcripts. On the other hand, gaps, missed pathways, included metabolism of terpenoids and polyketides and lipid metabolism. The multi-omics resource generated in this work will set the basis for ongoing and future studies, bringing the Holm oak closer to model species, to obtain a better understanding of the molecular mechanisms underlying phenotypes of interest (productive, tolerant to environmental cues, nutraceutical value) and to select elite genotypes to be used in restoration and reforestation programs, especially in a future climate change scenario.

[Functional outcomes in patients subjected to acetabular revision with reinforcement rings]. / Resultados funcionales de los pacientes sometidos a revisión acetabular con anillos de reforzamiento.

BACKGROUND: Total hip arthroplasty is the most successful orthopedic procedure and the frequency of use of revision components has grown exponentially. The increased number of revisions results from the longer life expectancy of the population and the greater frequency of the hip arthroplasty indication among young patients. The purpose of this study is to evaluate the functional results of patients subjected to revision of the acetabular component using reinforcement rings. MATERIAL AND METHODS: The study included patients with a diagnosis of septic or aseptic prosthetic loosening and sequelae of acetabular fractures between January 2007 and November 2009 in whom a reinforcement ring was used. The WOMAC scale was used for the functional evaluation. RESULTS: According to the WOMAC scale, the patient functionality results showed a mean preoperative score of 41.89 and a mean postoperative score of 74.26, which represented an improvement of 33.11 points in the median of patients subjected to the surgical intervention, with a statistically significant difference (p = 0.036). DISCUSSION: This study shows an improvement in the functionality of the patients subjected to surgery with a reinforcement ring, as, first and foremost, a statistically significant difference was seen between the preoperative and postoperative values and, secondly, there are papers published in the literature showing that a difference of more than 12 points between the preoperative and postoperative scores in the WOMAC scale indicates a significant clinical improvement of patients. CONCLUSION: Patients subjected to acetabular revision with a reinforcement ring together with cemented polyethylene have an improved quality of life after the surgical intervention.

Tratamiento quirúrgico de la osteoartritis en la cadera: actualidades en artroscopia de cadera / Surgical treatment of hip osteoarthritis: hpdete on hip arthroscopy

La cirugía artroscópica de cadera es un procedimiento habitual en cada vez más instituciones en el mundo. Las indicaciones de este procedimiento aumentan a medida que se adquiere más experiencia. Gracias a la artroscopia de cadera se ha identificado lesiones, como roturas de labrum y lesiones condrales y de ligamento redondo, que pueden contribuir a la génesis de la osteoartritis en la cadera. También se han transformado técnicas de cirugía abierta de cadera a técnicas artroscópicas, como en el caso del pinzamiento femoroacetabular. Se sabe que el pinzamiento femoroacetabular puede contribuir al desarrollo de osteoartritis en la cadera. La cirugía artroscópica de cadera tiene escasa utilidad en el tratamiento de la osteoartritis formalmente establecida y sólo se debe utilizarla en casos con cambios degenerativos mínimos en pacientes jóvenes (AU)

Arthroscopic surgery of the hip is a routine procedure in an increasing number of institutions around the world. Indications for this procedure increase as more experience is developed. Thanks to hip arthroscopy some intraarticular lesions like labral or ligamentum teres tears and cartilage lesions have been recognized. All of these have the potential to develop hip osteoarthritis. Open techniques for the treatment of femoroacetabular impingement have been transformed to arthroscopic techniques. Femoroacetabular impingement has the potential to cause hip osteoarthritis. The role of hip arthroscopy in the treatment of formally established hip osteoarthritis is limited and has better results in young patients with early degenerative changes (AU)