Long-term risk of delayed postoperative Crohn's disease recurrence in patients with no or mild endoscopic recurrence at first assessment.

BACKGROUND: Early endoscopic evaluation is recommended for assessment of postoperative recurrence (POR) of Crohn's disease (CD) but no further monitoring recommendations are available. AIM: To evaluate the long-term outcome of patients without endoscopic POR at first endoscopic assessment. METHODS: Retrospective four-centre study including consecutive CD patients with ileocolonic resection (ICR) without endoscopic POR (Rutgeerts score i0-i1) at first endoscopic assessment performed within 18 months from ICR. All patients had a clinical follow-up ≥24 months and at least one further endoscopic assessment. Main outcomes were endoscopic, clinical and surgical POR, need for rescue therapy and "delayed POR" (any need for rescue therapy or clinical or surgical POR) during follow-up. RESULTS: Overall, 183 patients were included (79% with risk factors for POR, 44% without postoperative prophylaxis). Endoscopic POR was observed in 42% of patients. Clinical POR-free survival was 89.4% and 81.5% at 3 and 5 years, and delayed POR-free survival was 76.9% and 63.4% at 5 and 10 years, respectively. In multivariate analysis, postoperative prophylaxis (HR .55; 95% CI .325-.942) and active smoking (HR 1.72; 95%CI 1.003-2.962) were independent risk factors for clinical POR, whereas presence of mild endoscopic lesions at index ileocolonoscopy (i1) was the only risk factor for delayed POR (HR 1.824; 95% CI 1.108-3.002). CONCLUSIONS: Long-term risk of POR among patients with no or mild endoscopic lesions at first ileocolonoscopy after surgery is steadily low, being higher among smokers, in the absence of postoperative prophylaxis and when mild endoscopic lesions are observed in the first endoscopic assessment.

Effectiveness and safety of a third-line rescue treatment for acute severe ulcerative colitis refractory to infliximab or ciclosporin (REASUC study).

BACKGROUND: The advent of new therapeutic agents and the improvement of supporting care might change the management of acute severe ulcerative colitis (ASUC) and avoid colectomy. AIMS: To evaluate the colectomy-free survival and safety of a third-line treatment in patients with ASUC refractory to intravenous steroids and who failed either infliximab or ciclosporin. METHODS: Multicentre retrospective cohort study of patients with ASUC refractory to intravenous steroids who had failed infliximab or ciclosporin and received a third-line treatment during the same hospitalisation. Patients who stopped second-line treatment due to disease activity or adverse events (AEs) were eligible. We assessed short-term colectomy-free survival by logistic regression analysis. Kaplan-Meier curves and Cox regression models were used for long-term assessment. RESULTS: Among 78 patients, 32 received infliximab and 46 ciclosporin as second-line rescue treatment. Third-line treatment was infliximab in 45 (58%), ciclosporin in 17 (22%), tofacitinib in 13 (17%) and ustekinumab in 3 (3.8%). Colectomy was performed in 29 patients (37%) during follow-up (median 21 weeks). Of the 78 patients, 32 and 18 were in clinical remission at, respectively, 12 and 52 weeks. At the last visit, 25 patients were still on third-line rescue treatment, while 12 had stopped it due to clinical remission. AEs were reported in 26 (33%) patients. Two patients died (2.6%), including one following colectomy. CONCLUSION: Third-line rescue treatment avoided colectomy in over half of the patients with ASUC and may be considered a therapeutic strategy.

Incidence of herpes zoster in patients with inflammatory bowel disease. / Incidencia de herpes zóster en pacientes con enfermedad inflamatoria intestinal: estudio observacional y retrospectivo en dos hospitales españoles de tercer nivel.

BACKGROUND: Herpes zoster (HZ) is a prevalent disease caused by the reactivation of the varicella-zoster virus (VZV) and associated with chronic morbidity, particularly with post-herpetic neuralgia (PHN). Inflammatory bowel disease (IBD) has been associated with an increased risk of HZ, mainly when immunosuppressive treatment (IMT) is used. However, studies assessing the risk of HZ in IBD are scarce. AIMS: To evaluate the incidence rate and risk factors of HZ in IBD. METHODS: Retrospective study in IBD patients with a positive VVZ serology from two referral hospitals from the area of Barcelona. Diagnosis of HZ and its clinical features were recorded. RESULTS: A total of 398 IBD patients with a positive IgG-VVZ serology were identified. Fifty-eight percent of the patients received IMT (46.5% immunosuppressants monotherapy, 20.6% biologics monotherapy and, 32.7% combination therapy). After a median follow-up of 71 months (IQR 41.5-138.0), 17 (4.3%) patients developed HZ (cumulative incidence of 5.2 per 1000 person-year), 12 of them (70.6%) while receiving IMT. Median age at HZ episode was 38 years (IQR 27.5-52.5). Two (11%) developed PHN. Biological therapy was the only risk factor for developing HZ (OR 3.8 IC 95% 1.3-11.5; p=0.018). CONCLUSIONS: HZ is quite prevalent in IBD, occurring at early ages and particularly among patients using IMT. NPH appears to occur in a notable proportion of cases.

Initial management of intraabdominal abscesses and preventive strategies for abscess recurrence in penetrating Crohn's disease: a national multicenter study based on ENEIDA registry.

INTRODUCTION: Intra-abdominal abscesses complicating Crohn's disease (CD) are a challenging situation. Their management, during the hospitalization and after resolution, is still unclear. METHODS: Adult patients with CD complicated with intraabdominal abscess who required hospitalization were included from the prospectively maintained ENEIDA registry from GETECCU. Initial strategy effectiveness and safety to resolve abscess was assessed. Survival analysis was performed to evaluate recurrence risk. Predictive factors associated with resolution were evaluated by multivariate regression and predictive factors associated with recurrence were assessed by Cox regression. RESULTS: 520 patients from 37 Spanish hospitals were included; 322 (63%) were initially treated with antibiotics alone, 128 (26%) with percutaneous drainage, and 54 (17%) with surgical drainage. The size of the abscess was critical to the effectiveness of each treatment. In abscesses < 30mm, the antibiotic was as effective as percutaneous or surgical drainage. However, in larger abscesses, percutaneous or surgical drainage was superior. In abscesses > 50mm, surgery was superior to percutaneous drainage, although it was associated with a higher complication rate. After abscess resolution, luminal resection was associated with a lower 1-year abscess recurrence risk (HR 0.43, 95% CI 0.24-0.76). However, those patients who initiated anti-TNF therapy had a similar recurrence risk whether luminal resection had been performed. CONCLUSIONS: Small abscesses (<30mm) can be managed with antibiotics alone, while larger ones require drainage. Percutaneous drainage will be effective and safer than surgery in many cases. After discharge, anti-TNF therapy reduces abscess recurrence risk in a similar way to bowel resection.

Liver Transplantation for Porto-sinusoidal Vascular Liver Disorder: Long-term Outcome.

BACKGROUND: Porto-sinusoidal vascular liver disorder (PSVD) is a rare disease that occasionally requires liver transplantation (LT), despite usually presenting preserved liver function. There remains a paucity of data pertaining to LT in PSVD. The aim was to identify features associated with post-LT outcomes in PSVD. METHODS: Retrospective multicentre study of 79 patients who received LT for PSVD. RESULTS: Median post-LT follow-up was 37 (range 1-261) mo. Refractory ascites 24 (30%), hepatic encephalopathy 16 (20%), and hepatopulmonary syndrome 13 (16.3%) were the most frequent indications for LT. Hepatocellular carcinoma was the indication in only 2 patients. Twenty-four patients died, 7 due to liver and 17 to non-liver related causes. Post-LT survival was 82.2%, 80.7%, and 68.6% at 1, 2, and 5 y, respectively. Post-LT survival was significantly better in patients without (n = 58) than in those with a persistent severe PSVD-associated condition (n = 21). Pre-LT hyperbilirubinemia levels and creatinine >100 µmol/L were also independently associated with poor survival. Six patients (7.6%) required a second LT. Recurrence of PSVD was confirmed by liver biopsy in only 1 patient and in 3 further patients it was likely. CONCLUSIONS: LT in PSVD is associated with an acceptable outcome in the absence of associated severe conditions. However, persistence of a severe associated condition, pre-LT high bilirubin levels, or creatinine >100 µmol/L impact outcome, and these are features that should be considered when evaluating PSVD patients for LT. PSVD recurrence is possible after LT and needs to be explored, at least, in cases of posttransplant portal hypertension.

Maternal and perinatal outcomes in women ≥40 years undergoing induction of labor compared with women <35 years: Results from 4027 mothers.

AIM: Cesarean section is known to be increased with advanced maternal age in women undergoing induction of labor (IOL), but there is less information regarding other possible adverse maternal and fetal outcomes. METHODS: Retrospective cohort study of singleton, nulliparous, at-term women undergoing IOL between January 2007 and September 2020. Outcomes studied were: cesarean section, failed induction rate, fetal distress, post-partum hemorrhage, post-partum hysterectomy, and need of transfusion. Neonatal variables analyzed were: Apgar score, umbilical cord pH, need of admission to neonatal intensive care unit, and mortality. RESULTS: A total of 4027 women met the inclusion criteria; 1968 (48.9%) of mothers were <35 years, 1283 (31.9%) were 35-39 years, 658 (16.3%) were 40-44 years, and 118 (2.9%) were ≥45 years. Results showed a significantly increased incidence of c-section in women ≥35 years, with an OR 1.79 (95% CI 1.50-2.14) for women 40-44 years and OR 3.95 (95% CI 2.66-5.98) for women ≥45 years. The main indication for cesarean delivery was failed IOL, and this risk was also significantly increased in women ≥40 years. These differences remained significant after adjustment for confounding factors. No other adverse maternal or fetal outcomes showed an association with age. CONCLUSION: Maternal age ≥40 years was associated with an increased risk of c-section after IOL at term compared with younger women, mainly because of failed induction, but no association with other adverse maternal or neonatal outcomes were found in our population. Risks and benefits of IOL in older women should be individually evaluated and adequately discussed with mothers.

Impact of immunosuppressants on SARS-CoV-2 infection in elderly patients with inflammatory bowel disease.

BACKGROUND: Older age has been reported as a risk factor for severe SARS-CoV-2 disease (COVID-19). The impact of immunosuppressants (IMS) on COVID-19 is still under debate. AIM: To describe the incidence and severity of COVID-19 in elderly patients with inflammatory bowel disease (IBD) in relation to the use of IMS. METHODS: IBD patients over 65 years of age were selected and grouped in terms of IMS use. Confirmed COVID-19, adherence to IST, comorbidities and concomitant non-IBD-related treatments between 1st of March 2020 to 1st of March 2021 were recorded. RESULTS: Out of 418 patients included, 89 (21.3%) were on IMS. Thirty-two patients (7.7%) had COVID-19, 7 of whom were on IMS (7.6% not on IMS vs. 7.9% on IMS; P = 0.933) and 7 (22%) patients died. CONCLUSIONS: Incidence of COVID-19 among elderly IBD patients was similar to that reported in the background population, regardless of the use of IMS.

Adherencia al tratamiento en pacientes mayores de 65 años que sufren reingresos precoces / Treatment adherence in patients more than 65 years who experience early readmissions

Objetivo: Analizar la frecuencia del incumplimiento terapéutico en pacientes que sufren reingresos hospitalarios precoces e identificar los factores asociados al mismo. Método: Estudio observacional descriptivo de tres meses de duración (marzo-mayo de 2014). Se incluyeron todos los pacientes mayores de 65 años que reingresaron en los 3-30 días siguientes al alta hospitalaria. Fueron excluidos los reingresos programados y los reingresos en la Unidad de Cuidados Intensivos. Las variables recogidas fueron: edad, sexo, servicio médico, categoría diagnóstica mayor, polimedicación, número de días desde el alta, presencia de hipertensión y/o diabetes. Se evaluó el cumplimiento terapéutico y la dificultad en la administración de medicación mediante el test de Morisky-Green y el test de Haynes-Sackett, respectivamente. Se realizó un análisis descriptivo de las variables y se relacionaron estas con la adherencia terapéutica. Las variables con significación estadística se incluyeron en un modelo de regresión logística multivariante. Resultados: El 57% de los pacientes presentaron falta de adherencia al tratamiento farmacológico. El 23% presentaba dificultad en la administración de la medicación. Un 86% presentaba comorbilidades (hipertensión y/o diabetes) y el 79% tenía cuidador. El 86% de los pacientes estaban polimedicados (≥ 5 fármacos). Existe relación entre la falta de adherencia y la dificultad en la administración de los medicamentos (p = 0,021), la polimedicación (p = 0,002) y la presencia de diabetes mellitus (p=0,018). Conclusiones: La polimedicación, la presencia de diabetes mellitus y la existencia de dificultad en la administración de la medicación se evidencian como factores pronósticos de la falta de adherencia al tratamiento en pacientes mayores de 65 años

Objective: To analyse the rate of therapeutic nonadherence in patients who experience early readmissions, and identify the factors associated with nonadherence. Methods: An observational descriptive 3-month study (March-May 2014), which included all patients more than 65 years who were readmitted between 3 to 30 days following the last hospital discharge. Exclusion criteria: programmed re-admissions and readmissions to the Intensive Care Unit. Variables included in the study: age, sex, medical service, major diagnostic category, polypharmacy, number of days since the last hospital discharge, and hypertension and diabetes. Therapeutic adherence and difficulty in taking medication were assessed using the Morisky-Green test and the Haynes-Sackett test, respectively. A descriptive analysis of the variables was conducted, showing they were associated with therapeutic adherence. Statistically significant variables were included in a multivariate logistic regression model. Results: In total, 57% of the patients were nonadherent to pharmacological treatment; 23% had difficulty taking their medication; 86% had comorbidities (hypertension and diabetes); 79% had a caregiver; and 86% were polymedicated (≥ 5 medications). There was an association between lack of adherence and difficulty in taking medications (P = 0.021), polypharmacy (P = 0.002), and diabetes mellitus (P = 0.018). Conclusions: Polymedication, diabetes mellitus, and difficulty in taking medication were shown to be prognostic factors of lack of adherence to treatment in patients more than 65 years

Treatment adherence in patients older than 65 years who suffer early readmissions.

OBJECTIVE: Analyze the frequency of therapeutic noncompliance in patients who  suffer early readmissions, and identify the factors associated with it. METHOD: Observational, descriptive study of three months duration (March -  May 2014). All patients older than 65 years who readmitted in the 3-30 days  following the last hospital discharge were included. We excluded programmed  re-admissions and readmissions in the Intensive Care Unit. The variables  collected were: age, sex, medical service, major diagnostic category,  polypharmacy, number of days since the last hospital discharge, presence of  hypertension and/or diabetes. The therapeutic compliance and the difficulty in  the administration of medication were evaluated by means of the Morisky-Green  test and the Haynes-Sackett test respectively. A descriptive analysis of the  variables was carried out and they were related to the therapeutic adherence.  The variables with statistical significance were included in a multivariate logistic  regression model. RESULTS: Fifty seven percent of the patients presented lack of adherence to  pharmacological treatment. Twenty three percent had difficulty administering the medication. Eighty six percent had comorbidities  (hypertension and/or diabetes) and 79% had a caregiver. Eighty six percent of patients were polymedicated (≥ 5 drugs). There is a relationship between lack of adherence and difficulty in the administration of medications (p=0.021),  polypharmacy (p=0.002), and the presence of diabetes mellitus (p=0.018). CONCLUSIONS: Polymedication, the presence of diabetes mellitus and the existence of difficulty in the administration of medication are evidenced as prognostic factors of the lack of adherence to treatment in patients older than 65 years.

Objetivo: Analizar la frecuencia del incumplimiento terapéutico en pacientes que sufren reingresos hospitalarios precoces e identificar los factores asociados  al mismo.Método: Estudio observacional descriptivo de tres meses de duración (marzo­ mayo de 2014). Se incluyeron todos los pacientes mayores de 65 años que  reingresaron en los 3-30 días siguientes al alta hospitalaria. Fueron excluidos los reingresos programados y los reingresos en la Unidad de Cuidados Intensivos.  Las variables recogidas fueron: edad, sexo, servicio médico, categoría  diagnóstica mayor, polimedicación, número de días desde el alta, presencia de  hipertensión y/o diabetes. Se evaluó el cumplimiento terapéutico y la dificultad  en la administración de medicación mediante el test de Morisky-Green y el test  de Haynes-Sackett, respectivamente. Se realizó un análisis descriptivo de las  variables y se relacionaron estas con la adherencia terapéutica. Las variables  con significación estadística se incluyeron en un modelo de regresión logística multivariante.Resultados: El 57% de los pacientes presentaron falta de adherencia al tratamiento farmacológico. El 23% presentaba dificultad en la administración de la medicación. Un 86% presentaba comorbilidades  hipertensión y/o diabetes) y el 79% tenía cuidador. El 86% de los pacientes  estaban polimedicados (≥ 5 fármacos). Existe relación entre la falta de  adherencia y la dificultad en la administración de los medicamentos (p = 0,021), la polimedicación (p = 0,002) y la presencia de diabetes mellitus (p = 0,018).Conclusiones: La polimedicación, la presencia de diabetes mellitus y la  existencia de dificultad en la administración de la medicación se evidencian como factores pronósticos de la falta de adherencia al tratamiento en pacientes  mayores de 65 años.

Estudio observacional sobre interacciones farmacológicas en pacientes oncológicos ingresados / Observational study of drug-drug interactions in oncological inpatients

Objetivo: Determinar la prevalencia de potenciales interacciones clínicamente relevantes en pacientes oncológicos adultos ingresados, mediante una base de datos de uso habitual, así como describir las interacciones más frecuentes. Método: Estudio observacional, transversal, descriptivo, que incluye pacientes ingresados a cargo del Servicio de Oncología de un hospital de referencia. Se recopilaron todas las prescripciones dos veces por semana durante un periodo de un mes. Se analizaron mediante la base de datos Lexicomp ® , registrando todas las interacciones clasificadas con un nivel de riesgo C, D o X. Resultados: Se detectaron un total de 1.850 interacciones farmacológicas en 218 tratamientos. La prevalencia de tratamientos con al menos una interacción clínicamente relevante fue de un 95%, siendo del 94,5% para las de nivel C y del 26,1% para los niveles D y X. Los analgésicos opioides, antipsicóticos (butirofenonas), benzodiacepinas, pirazolonas, glucocorticoides y heparinas fueron los fármacos más comúnmente involucrados en las interacciones detectadas, mientras que las interacciones con antineoplásicos fueron mínimas, destacando las relacionadas con paclitaxel y entre metamizol y diversos antineoplásicos. Conclusiones: La prevalencia de tratamientos con interacciones farmacológicas clínicamente relevantes fue muy elevada, destacando el elevado porcentaje de riesgo X. Por la frecuencia de aparición y potencial gravedad destacan el uso concomitante de fármacos depresores del sistema nervioso central con riesgo de depresión respiratoria, el riesgo de aparición de síntomas anticolinérgicos cuando se combinan morfina o haloperidol con butilescopolamina, bromuro de ipratropio o dexclorfe-niramina, así como las múltiples interacciones que implican al metamizol (AU)

Objective: To determine the prevalence of potential clinically relevant drug-drug interactions in adult oncological inpatients, as well as to describe the most frequent interactions. A standard database was used. Method: An observational, transversal, and descriptive study including patients admitted to the Oncology Service of a reference hospital. All prescriptions were collected twice a week during a month. They were analysed using Lexicomp ®database, recording all interactions classified with a level of risk: C, D or X. Results: A total of 1 850 drug-drug interactions were detected in 218 treatments. The prevalence of treatments with at least one clinically relevant interaction was 95%, being 94.5% for those at level C and 26.1% for levels D and X. The drugs most commonly involved in the interactions detected were opioid analgesics, antipsychotics (butyrophenones), benzodiazepines, pyrazolones, glucocorticoids and heparins, whereas interactions with antineoplastics were minimal, highlighting those related to paclitaxel and between metamizole and various antineoplastics. Conclusions: The prevalence of clinically relevant drug-drug interactions rate was very high, highlighting the high risk percentage of them related to level of risk X. Due to the frequency of onset and potential severity, highlighted the concomitant use of central nervous system depressants drugs with risk of respiratory depression, the risk of onset of anticholinergic symptoms when combining morphine or haloperidol with butyl scopolamine, ipratropium bromide or dexchlorpheniramine and the multiple interactions involving metamizole (AU)

Observational study of drug-drug interactions in oncological inpatients.

OBJECTIVE: To determine the prevalence of potential clinically relevant drug- drug interactions in adult oncological inpatients, as well as to describe the most  frequent interactions. A standard database was used. METHOD: An observational, transversal, and descriptive study including patients  admitted to the Oncology Service of a reference hospital. All prescriptions were  collected twice a week during a month. They were analysed using Lexicomp®  database, recording all interactions classified with a level of risk: C, D or X. RESULTS: A total of 1 850 drug-drug interactions were detected in 218  treatments. The prevalence of treatments with at least one clinically relevant  interaction was 95%, being 94.5% for those at level C and 26.1% for levels D  and X. The drugs most commonly involved in the interactions detected were  opioid analgesics, antipsychotics (butyrophenones), benzodiazepines,  pyrazolones, glucocorticoids and heparins, whereas interactions with  antineoplastics were minimal, highlighting those related to paclitaxel and  between metamizole and various antineoplastics. CONCLUSIONS: The prevalence of clinically relevant drug-drug interactions rate  was very high, highlighting the high risk percentage of them related to level of  risk X. Due to the frequency of onset and potential severity, highlighted the  concomitant use of central nervous system depressants drugs with risk of  respiratory depression, the risk of onset of anticholinergic symptoms when  combining morphine or haloperidol with butylscopolamine, ipratropium bromide  or dexchlorpheniramine and the multiple interactions involving metamizole.

Objetivo: Determinar la prevalencia de potenciales interacciones clínicamente relevantes en pacientes oncológicos adultos ingresados, mediante una base de datos de uso habitual, así como describir las interacciones más frecuentes.Método: Estudio observacional, transversal, descriptivo, que incluye pacientes ingresados a cargo del Servicio de Oncología de un hospital de referencia. Se recopilaron todas las prescripciones dos veces por semana durante un periodo de un mes. Se analizaron mediante la base de datos Lexicomp®, registrando todas las interacciones clasificadas con un nivel de riesgo C, D o X.Resultados: Se detectaron un total de 1.850 interacciones farmacológicas en  218 tratamientos. La prevalencia de tratamientos con al menos una interacción  clínicamente relevante fue de un 95%, siendo del 94,5% para las de nivel C y  del 26,1% para los niveles D y X. Los analgésicos opioides, antipsicóticos  (butirofenonas), benzodiacepinas, pirazolonas, glucocorticoides y heparinas  fueron los fármacos más comúnmente involucrados en las interacciones  detectadas, mientras que las interacciones con antineoplásicos fueron mínimas,  destacando las relacionadas con paclitaxel y entre metamizol y diversos  antineoplásicos.Conclusiones: La prevalencia de tratamientos con interacciones farmacológicas clínicamente relevantes fue muy elevada, destacando el elevado  porcentaje de riesgo X. Por la frecuencia de aparición y potencial gravedad  destacan el uso concomitante de fármacos depresores del sistema nervioso  central con riesgo de depresión respiratoria, el riesgo de aparición de síntomas  anticolinérgicos cuando se combinan morfina o haloperidol con  butilescopolamina, bromuro de ipratropio o dexclorfeniramina, así como las  múltiples interacciones que implican al metamizol.

Informe del Taller Ibérico de Histocompatibilidad 2013. Componente de análisis de situación de procedimiento de pruebas cruzadas en guardias de trasplante de órganos / Report of the 2013 Iberian Histocompatibility Workshop of 2013. Component analysis of the proceedings of cross-matching procedures in emergency organ transplantation

No disponible

SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium.

Novel sequencing technologies were recently used to generate sequences from multiple melon (Cucumis melo L.) genotypes, enabling the in silico identification of large single nucleotide polymorphism (SNP) collections. In order to optimize the use of these markers, SNP validation and large-scale genotyping are necessary. In this paper, we present the first validated design for a genotyping array with 768 SNPs that are evenly distributed throughout the melon genome. This customized Illumina GoldenGate assay was used to genotype a collection of 74 accessions, representing most of the botanical groups of the species. Of the assayed loci, 91 % were successfully genotyped. The array provided a large number of polymorphic SNPs within and across accessions. This set of SNPs detected high levels of variation in accessions from this crop's center of origin as well as from several other areas of melon diversification. Allele distribution throughout the genome revealed regions that distinguished between the two main groups of cultivated accessions (inodorus and cantalupensis). Population structure analysis showed a subdivision into five subpopulations, reflecting the history of the crop. A considerably low level of LD was detected, which decayed rapidly within a few kilobases. Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in melon. Since many of the genotyped accessions are currently being used as the parents of breeding populations in various programs, this set of mapped markers could be used for future mapping and breeding efforts.

Root transcriptional responses of two melon genotypes with contrasting resistance to Monosporascus cannonballus (Pollack et Uecker) infection.

BACKGROUND: Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo 'Piel de sapo' ('PS') and C. melo 'Pat 81', with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. RESULTS: Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. 'PS' responded with a more rapid infection response than 'Pat 81' at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in 'PS' declined from 451 to 359, while the total number of differentially expressed transcripts in 'Pat 81' increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in 'Pat 81' compared to 'PS' suggested that JA response might be partially responsible for their observed differences in resistance. CONCLUSIONS: As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation.

Transcriptome sequencing for SNP discovery across Cucumis melo.

BACKGROUND: Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD™ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species. RESULTS: The deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes. CONCLUSIONS: This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.

BACKGROUND: Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). RESULTS: We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. CONCLUSION: Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties.

Towards a TILLING platform for functional genomics in Piel de Sapo melons.

BACKGROUND: The availability of genetic and genomic resources for melon has increased significantly, but functional genomics resources are still limited for this crop. TILLING is a powerful reverse genetics approach that can be utilized to generate novel mutations in candidate genes. A TILLING resource is available for cantalupensis melons, but not for inodorus melons, the other main commercial group. RESULTS: A new ethyl methanesulfonate-mutagenized (EMS) melon population was generated for the first time in an andromonoecious non-climacteric inodorus Piel de Sapo genetic background. Diverse mutant phenotypes in seedlings, vines and fruits were observed, some of which were of possible commercial interest. The population was first screened for mutations in three target genes involved in disease resistance and fruit quality (Cm-PDS, Cm-eIF4E and Cm-eIFI(iso)4E). The same genes were also tilled in the available monoecious and climacteric cantalupensis EMS melon population. The overall mutation density in this first Piel de Sapo TILLING platform was estimated to be 1 mutation/1.5 Mb by screening four additional genes (Cm-ACO1, Cm-NOR, Cm-DET1 and Cm-DHS). Thirty-three point mutations were found for the seven gene targets, six of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was demonstrated for a loss-of-function mutation in the Phytoene desaturase gene, which is involved in carotenoid biosynthesis. CONCLUSIONS: The TILLING approach was successful at providing new mutations in the genetic background of Piel de Sapo in most of the analyzed genes, even in genes for which natural variation is extremely low. This new resource will facilitate reverse genetics studies in non-climacteric melons, contributing materially to future genomic and breeding studies.

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae).

BACKGROUND: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding. RESULTS: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions. CONCLUSION: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties.

An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.).

BACKGROUND: Melon (Cucumis melo) is a horticultural specie of significant nutritional value, which belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. Its small genome of approx. 450 Mb coupled to the high genetic diversity has prompted the development of genetic tools in the last decade. However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression. RESULTS: We report the construction of an oligo-based microarray using a total of 17,510 unigenes derived from 33,418 high-quality melon ESTs. This chip is particularly enriched with genes that are expressed in fruit and during interaction with pathogens. Hybridizations for three independent experiments allowed the characterization of global gene expression profiles during fruit ripening, as well as in response to viral and fungal infections in plant cotyledons and roots, respectively. Microarray construction, statistical analyses and validation together with functional-enrichment analysis are presented in this study. CONCLUSION: The platform validation and enrichment analyses shown in our study indicate that this oligo-based microarray is amenable for future genetic and functional genomic studies of a wide range of experimental conditions in melon.

A set of EST-SNPs for map saturation and cultivar identification in melon.

BACKGROUND: There are few genomic tools available in melon (Cucumis melo L.), a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR), restriction fragment length polymorphisms (RFLP) and amplified fragment length polymorphisms (AFLP) in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP), more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs) from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs. RESULTS: EST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC) x 'Piel de sapo' (PS) genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars. CONCLUSION: This is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 x 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR). This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty-eight melon accessions as efficiently as with SSR markers, and these markers may also be useful for cultivar identification in Occidental melon varieties.