A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference fullsib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance

Caracterización epidemiológica y clínica de pacientes operados con diagnóstico de quiste branquial

Introduction: Branchial Cysts are uncommon anomalies in regular clinical practice. However, among congenital cervical cysts, they represent about 30% from total. Objective: Characterize patients diagnosed with operated branquial cyst in our clinical center, and correlate clinic, imaging and final diagnose. Material and methods: Retrospective descriptive study of discharged patients diagnosed as cervical cysts, between January 2005 and July 2011, at Hospital Clinico Universidad de Chile. Selection of Clinical records with final diagnose of branchial cyst were selected. Age, sex, clinical story, imaging exams, pre-operative and post-operative diagnoses, and biopsy report were registered. Results: from a total of 149 cervical cysts, 31 (20,8%) were branchial cysts. Man 45% and women 55%. By age, 9 (29%) were 15 years (average: 33,7 years). Lateral cervical mass was the most common clinical manifestation. Regarding Imaging study, 15 cervical ultrasounds (sensibility 0,86 and specificity 0,98) and 13 cervical CTA scans (sensibility 0,92 and specificity 0,94) were conducted. In 9 patients, imaging studies weren’t conducted for the clinical diagnose (sensibility 0,77 and specificity 0,98). Correlation of pre-operative and post-operative diagnose was 87%. Discussion: According to literature, presentation age is generally during childhood; however, in our statistics it presented during adult age, which could be explained due to the main focus our medical center has for adult population. Most common clinical presentation was lateral neck mass, which had a good clinical correlation, however improves with imaging studies

Paratirotoxicosis y tumor cervical palpable: caso clínico de cáncer de paratiroides

ResumenIntroducciónEl cáncer de paratiroides es poco frecuente. Suele presentarse como hiperparatiroidismo primario, en ocasiones como crisis hipercalcémica, con malestar general, náuseas, vómitos, alteraciones del ánimo y pérdida de peso. En algunos casos se presenta como osteítis fibrosa quística, osteopenia difusa, osteoporosis y fracturas patológicas. El diagnóstico suele estar dado por biopsia quirúrgica que muestra invasión a estructuras adyacentes, o metástasis locales y distantes. El tratamiento es la resección quirúrgica del tumor, sin uso de terapias adyuvantes. Su tasa de recurrencia es alta, de 25 a 100%. Algunos factores de mal pronóstico son metástasis a linfonodos en la presentación inicial, metástasis distantes y carcinomas no funcionantes.Caso clínicoPaciente masculino de 64 años que consultó por compromiso del estado general, bradipsiquia, poliuria, cefalea y masa cervical. Además presentaba hipercalcemia y gran elevación de PTH. Se realizó resección quirúrgica de la masa cervical, con biopsia rápida con atipias y mitosis 1/10, y de un nódulo hiperplásico tiroideo. Tras esto, sus niveles de PTH disminuyeron, así como también descendieron sus niveles de calcio.DiscusiónLos pacientes que presentan cáncer de paratiroides suelen tener valores más elevados de calcemia y PTH. Para su diagnóstico, no se recomienda usar biopsia por punción, por riesgo de diseminación y por el bajo rendimiento de esta técnica.ConclusiónPese a ser poco frecuente, se debe pensar en cáncer de paratiroides en el contexto de un paciente con hipercalcemia, especialmente si presenta PTH muy elevada. La sospecha clínica de este diagnóstico tiene directa relación con la posibilidad de tratamiento y pronóstico de la enfermedad.AbstractIntroductionParathyroid cancer is rare. Usually presented as primary hyperparathyroidism, sometimes as hypercalcemic crisis, with general malaise, nausea, vomiting, mood disturbances and low weight. In some cases it occurs as osteitis fibrosa cystica, diffuse osteopenia, osteoporosis and pathological fractures. The diagnosis is usually made by surgical biopsy shows invasion of adjacent structures, or local and distant metastases. The treatment is surgical resection of the tumor, without the use of adjuvant therapies. Their recurrence rate is high, 25 to 100%. Poor prognostic factors are lymph node metastases at initial presentation, distant metastases and nonfunctional carcinomas.Case reportMale patient consulted for 64 years in general conditions, bradypsychia, polyuria, headache and neck mass. He also had hypercalcemia and high elevation of PTH. Surgical resection of the cervical mass was performed, with rapid biopsy atypia and mitosis 1/10, and hyperplastic thyroid nodule. After this, PTH decreased levels as well as levels of calcium.DiscussionPatients with parathyroid cancer tend to have higher serum calcium and PTH of values. For diagnosis, it is not recommended to use needle biopsy, risk of spread and the poor performance of this technique.ConclusionDespite being rare, you should think parathyroid cancer in the context of a patient with hypercalcemia, especially if you have very high PTH. The clinical suspicion of this diagnosis is directly related to the possibility of treatment and prognosis of the disease

Optimization of human hepatocyte cultures for citotoxicity studies

Los cultivos de hepatocitos entregan un valioso acercamiento al estudio de las funciones metabólicas específicas del hígado, evaluación de citotoxicidad. No existen líneas humanas inmortales con función normal. La inmortalización de hepatocitos humanos con el método UCHT1(medio de cultivo condicionado por células tumorales de tiroides) permitirá prolongar la sobrevida y función de estos, siendo útil para evaluar funcionalidad y citotoxicidad. Objetivo: Optimizar el cultivo de hepatocitos humanos. Metodología: En cultivos primarios de hepatocitos humanos, se agregó medio UCHT1 cultivando en superficies de colágeno, polilisina, gelatina y matrigel. Como control positivo, se utilizó línea Gherschenson (GER) para evaluar curva de crecimiento y producción de Glucógeno (PAS). Se evaluó citotoxicidad (LIVE/DEAD) en hepatocitos GER expuestos a Metotrexato (10, 100 y 1000 mM) a 24, 48 y 72 hrs. Resultados: Se realizó 3 cultivos primarios. Fue efectiva la utilización de Polilisina y Colágeno. Duración 8 meses. No se ha realizado la curva de crecimiento, ni evaluación de funcionalidad en hepatocitos humanos. La línea GER tiene un crecimiento exponencial (tiempo duplicación: 36 hrs). Se observó producción de glucógeno en condiciones de diferenciación hasta 120 hrs. La citotoxicidad por Metotrexato tiene una curva dosis dependiente, significativa en todas las concentraciones (p<0,001) (CL50 a 1000 mM a 24 hrs). Conclusiones: Se logró establecer una línea primaria de hepatocitos humanos. La polilisina y el colágeno han optimizado el establecimiento de cultivos primarios. El método PAS permitió evaluar producción de glucógeno (diferenciación). Los valores de citotoxicidad demostraron un efecto dosis dependiente en las condiciones experimentales. Logrando estandarizar el método para evaluación futura de líneas celulares humanas

Association of the TNFAIP3 rs5029939 variant with systemic sclerosis in the European Caucasian population

International audienceBackground TNFAIP3 encodes the ubiquitin-modifying enzyme, a key regulator of inflammatory signalling pathways. Convincing associations between TNFAIP3 variants and autoimmune diseases have been reported. Objective To investigate the association of TNFAIP3 polymorphisms with systemic sclerosis (SSc). Methods Three single nucleotide polymorphisms (SNPs) in a set of 1018 patients with SSc and 1012 controls of French Caucasian origin were genotyped. Two intergenic SNPs, rs10499194 and rs6920220, and one located in TNFAIP3 intron 2, rs5029939, were selected. The TNFAIP3 rs5029939 found to be associated with SSc in this first set was then genotyped in a second set of 465 patients with SSc and 182 controls from Germany and 184 patients with SSc and 124 controls from Italy. Pooled odd ratios were calculated by Mantel-Haenszel meta-analysis. Results The rs5029939 G allele was found to be significantly associated with SSc susceptibility (pooled OR=2.08 (95% CI 1.59 to 2.72); p=1.16x10(-7)), whereas the rs10499194 and rs6920220 variants displayed no association. Only one of the predicted haplotypes investigated in the French sample was significantly associated with SSc (p=8.91x10(-8)), and this haplotype was discriminating only in the presence of the rs5029939 risk allele, suggesting that this SNP tags the association signal. The strongest associations of rs5029939 with subphenotypes, having large magnitudes for complex genetic disorders, were observed for diffuse cutaneous SSc (pooled OR=2.71 (1.94 to 3.79), p=5.2x10(-9)), fibrosing alveolitis (pooled OR=2.26 (1.61 to 3.17), p=2.5x10(-6)) and pulmonary arterial hypertension (pooled OR=3.11 (1.86 to 5.17), p=1.3x10(-5)). Conclusion These results suggest that TNFAIP3 is a genetic susceptibility factor for SSc

Association of the CD226 Ser(307) Variant With Systemic Sclerosis Evidence of a Contribution of Costimulation Pathways in Systemic Sclerosis Pathogenesis

International audienceObjective. The nonsynonymous polymorphism rs763361 of the CD226 gene, which encodes DNAX accessory molecule 1, which is involved in T cell co-stimulation pathways, has recently been identified as a genetic risk factor for autoimmunity. The purpose of this study was to test for association of the CD226 rs763361 polymorphism with systemic sclerosis (SSc) in European Caucasian populations. Methods. CD226 rs763361 was genotyped in 3,632 individuals, consisting of a discovery sample (991 SSc patients and 1,008 controls) and a replication sample (999 SSc patients and 634 controls). All study subjects were of European Caucasian origin. Expression of CD226 was assessed on peripheral blood mononuclear cells obtained from 21 healthy donors genotyped for CD226 rs763361. Results. The CD226 rs763361 T allele was found to be associated with SSc in both the discovery and the replication samples, showing the following results in the combined populations: odds ratio (OR) 1.22 (95% confidence interval [95% CI] 1.10-1.34), P = 5.69 x 10(-5). The CD226 T allele was also associated with various SSc subsets, highlighting a potential contribution to disease severity. The most remarkable associations of the CD226 TT risk genotype were observed with the diffuse cutaneous SSc subtype, the anti-topoisomerase I antibody-positive, and SSc-related fibrosing alveolitis subsets: OR 1.86 (95% CI 1.42-2.43), P = 5.15 x 10(-6), OR 1.82 (95% CI 1.38-2.40), P = 2.16 x 10(-5), and OR 1.61 (95% CI 1.25-2.08), P = 2.73 x 10(-4), respectively. CD226 expression was not significantly influenced by CD226 rs763361 genotypes whatever the T cell subtype investigated. Conclusion. Our results establish CD226 as a new SSc genetic susceptibility factor underlying the contribution of costimulation pathways in the pathogenesis of SSc. Further work is nevertheless needed to define the causal variant at the CD226 locus as well as the functional consequences