Detailed analysis of inversions predicted between two human genomes: errors, real polymorphisms, and their origin and population distribution.

The growing catalogue of structural variants in humans often overlooks inversions as one of the most difficult types of variation to study, even though they affect phenotypic traits in diverse organisms. Here, we have analysed in detail 90 inversions predicted from the comparison of two independently assembled human genomes: the reference genome (NCBI36/HG18) and HuRef. Surprisingly, we found that two thirds of these predictions (62) represent errors either in assembly comparison or in one of the assemblies, including 27 misassembled regions in HG18. Next, we validated 22 of the remaining 28 potential polymorphic inversions using different PCR techniques and characterized their breakpoints and ancestral state. In addition, we determined experimentally the derived allele frequency in Europeans for 17 inversions (DAF = 0.01-0.80), as well as the distribution in 14 worldwide populations for 12 of them based on the 1000 Genomes Project data. Among the validated inversions, nine have inverted repeats (IRs) at their breakpoints, and two show nucleotide variation patterns consistent with a recurrent origin. Conversely, inversions without IRs have a unique origin and almost all of them show deletions or insertions at the breakpoints in the derived allele mediated by microhomology sequences, which highlights the importance of mechanisms like FoSTeS/MMBIR in the generation of complex rearrangements in the human genome. Finally, we found several inversions located within genes and at least one candidate to be positively selected in Africa. Thus, our study emphasizes the importance of careful analysis and validation of large-scale genomic predictions to extract reliable biological conclusions.

Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions.

PURPOSE: Diagnostic exome sequencing was immediately successful in diagnosing patients in whom traditional technologies were uninformative. Herein, we provide the results from the first 500 probands referred to a clinical laboratory for diagnostic exome sequencing. METHODS: Family-based exome sequencing included whole-exome sequencing followed by family inheritance-based model filtering, comprehensive medical review, familial cosegregation analysis, and analysis of novel genes. RESULTS: A positive or likely positive result in a characterized gene was identified in 30% of patients (152/500). A novel gene finding was identified in 7.5% of patients (31/416). The highest diagnostic rates were observed among patients with ataxia, multiple congenital anomalies, and epilepsy (44, 36, and 35%, respectively). Twenty-three percent of positive findings were within genes characterized within the past 2 years. The diagnostic rate was significantly higher among families undergoing a trio (37%) as compared with a singleton (21%) whole-exome testing strategy. CONCLUSION: Overall, we present results from the largest clinical cohort of diagnostic exome sequencing cases to date. These data demonstrate the utility of family-based exome sequencing and analysis to obtain the highest reported detection rate in an unselected clinical cohort, illustrating the utility of diagnostic exome sequencing as a transformative technology for the molecular diagnosis of genetic disease.

Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm.

BACKGROUND: Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is also true for structural variation detected from sequence data. However, the genotypes at known variable sites can only be inferred with uncertainty from low coverage data. Thus, statistical approaches that infer genotype likelihoods, test hypotheses, and estimate population parameters without requiring accurate genotypes are becoming popular. Unfortunately, the current implementations of these methods are intended to analyse only single nucleotide and short indel variation, and they usually assume that the two alleles in a heterozygous individual are sampled with equal probability. This is generally false for structural variants detected with paired ends or split reads. Therefore, the population genetics of structural variants cannot be studied, unless a painstaking and potentially biased genotyping is performed first. RESULTS: We present svgem, an expectation-maximization implementation to estimate allele and genotype frequencies, calculate genotype posterior probabilities, and test for Hardy-Weinberg equilibrium and for population differences, from the numbers of times the alleles are observed in each individual. Although applicable to single nucleotide variation, it aims at bi-allelic structural variation of any type, observed by either split reads or paired ends, with arbitrarily high allele sampling bias. We test svgem with simulated and real data from the 1000 Genomes Project. CONCLUSIONS: svgem makes it possible to use low-coverage sequencing data to study the population distribution of structural variants without having to know their genotypes. Furthermore, this advance allows the combined analysis of structural and nucleotide variation within the same genotype-free statistical framework, thus preventing biases introduced by genotype imputation.

Assessment of a Coated Mitomycin-Releasing Biodegradable Ureteral Stent as an Adjuvant Therapy in Upper Urothelial Carcinoma: A Comparative In Vitro Study.

A major limitation of the treatment of low-grade upper tract urothelial carcinoma is the difficulty of intracavitary instillation of adjuvant therapy. Therefore, the aim of this in vitro study was to develop and to assess a new design of biodegradable ureteral stent coated with a silk fibroin matrix for the controlled release of mitomycin C as a chemotherapeutic drug. For this purpose, we assessed the coating of a biodegradable ureteral stent, BraidStent®, with silk fibroin and subsequently loaded the polymeric matrix with two formulations of mitomycin to evaluate its degradation rate, the concentration of mitomycin released, and changes in the pH and the weight of the stent. Our results confirm that the silk fibroin matrix is able to coat the biodegradable stent and release mitomycin for between 6 and 12 h in the urinary environment. There was a significant delay in the degradation rate of silk fibroin and mitomycin-coated stents compared to bare biodegradable stents, from 6-7 weeks to 13-14 weeks. The present study has shown the feasibility of using mitomycin C-loaded silk fibroin for the coating of biodegradable urinary stents. The addition of mitomycin C to the coating of silk fibroin biodegradable stents could be an attractive approach for intracavitary instillation in the upper urinary tract.

Expression of MicroRNAs in Periodontal Disease: A Systematic Review.

INTRODUCTION: Periodontal disease (PD) is a chronic inflammation of the soft tissues that support the structure of the tooth, and miRNAs are highly dynamic molecules that participate in the regulation of gene expression interfering with multiple genetic targets. The dysregulation of the expression of miRNAs has been associated with different types of pathologies; therefore, they are excellent molecules to be studied as biomarkers. Material and Methods. A search was made in the electronic databases of PubMed, Scopus, and Science Direct. The following key words were used: "microRNAs," "miRNAs," "periodontal disease," "periodontitis," and "biomarker"; employee independent search strategies with the Boolean operators "OR" and "AND"; a further search of the references of the selected studies was performed to detect potential studies that met the selection criteria. The data recollected from each article were author, country, year of publication, sample size, type of sample used to identify miRNAs, methodology used to identify miRNAs, type of periodontal disease, and miRNAs identified. RESULTS: Of the 13 selected studies, 6 used gingival tissue as a sample for the identification of miRNAs, 3 used gingival fluid, 2 used saliva, 1 used serum, and another used periodontal tissue. Chronic periodontitis was the most studied periodontal disease in 9 of the 13 selected articles; 7 used microarrays as the main technique for the identification of miRNAs. qRT-PCR was the assay choice to validate the identified miRNAs. CONCLUSION: The main type of periodontal disease on which most studies are focused is chronic periodontitis, with the main miRNAs being hsa-miR-146a, hsa-miR-146b, hsa-miR-155, and hsa-miR-200. This systematic review is one of the first to carry out an analysis of the current role of miRNAs in PD as biomarkers.

Synthesis, Characterization, and In Vitro and In Vivo Evaluations of Cellulose Hydrogels Enriched with Larrea tridentata for Regenerative Applications.

INTRODUCTION: Tissue engineering is an elementary necessity for several applications in the biomedical field through the use of several biopolymers derived from plants. Larrea tridentata (LT) is a very used plant for various medicinal applications with interesting properties; however, its use into cellulose hydrogels for possible regenerative therapeutics is still limited. Cellulose films could be applied in medical field as wound healing, scaffold for connective tissue for periodontal applications, and so on. The aim of this study was to evaluate the mechanical properties and in vivo and in vitro biocompatibility of cellulose hydrogels that have been enriched with LT in a rat model. METHODS: By in vivo and in vitro assays, the concentration of LT was varied from 1 to 5 wt%, respectively. Hydrogel films were implanted intramuscularly into female Wistar rats, 250 g in weight and aged 2 months, to analyze their cytocompatibility and biocompatibility. RESULTS: No case showed any evidence of inflammation or toxicity. Regarding cell morphology and adhesion, the prepared LT cellulose films had better cytocompatibility values than when polystyrene (PS) dishes were used as the control. In all cases, the results suggest that the addition of LT to the hydrogel films did not affect their cytocompatibility or biocompatibility properties and increases their clinical application due to the reported uses of LT. CONCLUSIONS: Cellulose hydrogel films enriched with LT have the potential to be used in the biomedical field acting as regenerative scaffolds.

Evaluación antifúngica del ozono contra Candida albicans: estudio in vitro / Antifungal evaluation of ozone against Candida albicans: in vitro study

Introducción: la Candida albicans (C. albicans) es un patógeno fúngico que puede causar infecciones superficiales o potencialmente mortales. Los biofilms de C. albicans muestran rasgos fenotípicos únicos, el más destacado es su notable resistencia a una amplia variedad de agentes antimicóticos. Una de las alternativas para inhibir el crecimiento de este microorganismo es el ozono debido a sus propiedades bactericidas, fungicidas y virucidas; sin embargo, escasa información ha sido reportada en C. albicans. Objetivo: el objetivo de este estudio fue evaluar el efecto fungicida del ozono en C. albicans. Material y métodos: la metodología consistió en agregar ozono a tubos de ensayo con medios de caldo nutritivo en diversas concentraciones y tiempos de ozonización. El efecto fungicida fue determinado con la determinación del número de colonias de C. albicans en agar nutritivo a través de procedimiento microbiológicos estandarizados por triplicado. Resultados: todas las muestras con ozono mostraron adecuados niveles de inhibición de crecimiento del microorganismo. Además, el efecto fungicida del ozono se encontró para ser significativamente dependiente del tiempo de ozonización y de la concentración. Conclusión: el uso de terapia con ozono podría tener potencial en el control de infecciones micóticas causadas por la presencia de C. albicans (AU)

Introduction: Candida albicans (C. albicans) is a fungal pathogen that can cause superficial or life-threatening infections. Biofilms of C. albicans display unique phenotypic traits, the most prominent being their remarkable resistance to a wide variety of antifungal agents. One of the alternatives to inhibit the growth of this microorganism is ozone due to its bactericidal, fungicidal and virucidal properties; however, little information has been reported on C. albicans. Objective: the objective of this study was to evaluate the fungicidal effect of ozone on C. albicans. Material and methods: the methodology consisted in adding ozone to test tubes with nutrient broth media in various concentrations and ozonation times. The fungicidal effect was determined by determining the number of colonies of C. albicans in nutrient agar through standardized microbiological procedures in triplicate. Results: all the ozone samples showed adequate levels of growth inhibition of the microorganism. Furthermore, the fungicidal effect of ozone was found to be significantly dependent on ozonation time and concentration. Conclusion: the use of ozone therapy could have potential in the control of fungal infections caused by the presence of C. albicans (AU)

Evaluación de lesiones orales en pacientes intubados y su asociación con el motivo de hospitalización / Evaluation of oral lesions in intubated patients and its association with the reason of hospitalization

asistencia ventilatoria cuando la vía aérea y la consciencia están comprometidas. Los elementos utilizados en este procedimiento se encuentran en contacto directo con estructuras dentofaciales, causando diversos tipos de lesiones, principalmente bucales. Aunque existen cuidados clínicos durante procesos de intubación, hay poca información, particularmente de la zona norte del país donde se hayan evaluado las posibles asociaciones entre los motivos de consulta más frecuentes y las diversas características, tanto clínicas como no clínicas de pacientes que han sido intubados. Objetivo: Identificar las alteraciones bucodentales más frecuentes en pacientes intubados, así como explorar las posibles asociaciones de acuerdo con los motivos de intubación más frecuentes. Material y métodos: Se realizó un estudio observacional, transversal y comparativo en el cual se evaluaron alteraciones bucodentales y sistémicas de pacientes intubados. Los grupos de estudio se desarrollaron de acuerdo con el motivo de intubación y la determinación de las asociaciones fue con cada una de las alteraciones bucodentales y sistémicas. Resultados: El motivo de intubación más frecuente fue el evento cerebral vascular (EVC) y las alteraciones dentofaciales más prevalentes fueron caries, lengua saburral y cálculo dental, entre otras. Además, se encontraron diferencias significativas entre pacientes con EVC, mostrando una mayor frecuencia en tabaquismo, hipertensión arterial y diabetes mellitus, así como en la presencia de gingivitis y úlceras. Pacientes con traumatismo craneoencefálico (TCE) tuvieron mayor frecuencia en la presencia de periodontitis. Conclusión: El motivo de hospitalización y las condiciones sistémicas preexistentes pueden ser un factor de riesgo para desarrollar lesiones bucales específicas antes y durante el periodo de intubación (AU)

Introduction: Intubation is a procedure that allows ventilatory assistance when the airway and consciousness are compromised. The elements used in this procedure are in direct contact with dentofacial structures causing various types of injuries, mainly oral. Although there is clinical care during intubation processes, there is little information, particularly from the northern part of the country where the possible associations between the most frequent reasons for consultation and the various clinical and non-clinical characteristics of patients who have been intubated have been evaluated. Objective: The objectives of the present study were to identify the most frequent oral alterations in intubated patients, as well as to explore possible associations according to the most frequent reasons for intubation. Material and methods: An observational, cross-sectional and comparative study was carried out in which oral and systemic alterations of intubated patients were evaluated. The study groups were formed according to the reason for intubation and the association was determined with each of the oral and systemic disorders. Results: The most frequent reason for intubation was the vascular cerebral event (CVA) and the most prevalent dentofacial alterations were caries, coated tongue, and dental calculus, among others. In addition, significant differences were found between patients with CVA, showing a higher frequency in smoking, hypertension, and diabetes mellitus, as well as in the presence of gingivitis and ulcers. Patients with traumatic brain injury (TBI) had a higher frequency in the presence of periodontitis. Conclusion: The reason for hospitalization and pre-existing systemic conditions can be a risk factor for developing specific oral lesions before and during the intubation period (AU)

Processed Pseudogene Confounding Deletion/Duplication Assays for SMAD4.

Mutations in SMAD4 have been associated with juvenile polyposis syndrome and combined juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome. SMAD4 is part of the SMAD gene family. To date, there has been no report in the literature of a SMAD4 pseudogene. An unusual SMAD4 duplication pattern was seen in multiple patient samples using two different duplication/deletion platforms: multiplex ligation-dependent probe amplification and chromosomal microarray. Follow-up confirmatory testing included real-time quantitative PCR and sequencing of an exon/exon junction, all results leading to the conclusion of the existence of a processed pseudogene. Examination of clinical results from two laboratories found a frequency of 0.26% (12 in 4672 cases) for this processed pseudogene. This is the first report of the presence of a processed pseudogene for SMAD4. We believe that knowledge of its existence is important for accurate interpretation of clinical diagnostic test results and for new assay designs. This study also indicates how a processed pseudogene may confound quantitative results, dependent on placement of probes and/or primers in a particular assay design, potentially leading to both false-positive and false-negative results. We also found that the SMAD4 processed pseudogene affects next-generation sequencing results by confounding the alignment of the sequences, resulting in erroneous variant calls. We recommend Sanger sequencing confirmation for SMAD4 variants.