Estudio preliminar de diversidad genética de Manta birostris que visitaron la Isla de la Plata durante los años 2010, 2011 y 2012

Manta birostris is a highly migratory species, as well as the largest member of the genus Manta. In 2009, the genus Manta was reevaluated and divided into two species: Manta alfredi and Manta birostris. Manta birostris is broadly distributed, ranging from tropical to semi-temperate oceans. Currently, unregulated fishing for gill rakers and low reproduction rates are reducing subpopulations worldwide. This species is particularly vulnerable to overfishing due to their late maturity, slow gestation periods and long life spans. A large group of M. birostris individuals visits the Isla de la Plata during the months of July to September. The present study characterize the genetic diversity of Isla de la Plata M. birostris individuals using microsatellites. A total of 57 samples collected during three years (2010, 2011 and 2012) were analyzed using eight pairs of heterologous primers. A total of 46 alleles were identified in the eight loci analyzed, with an average of 4,375 alleles per locus. Exclusive alleles were found in three loci (MA14, MA43 and MA30), and three loci (MA21, MA15, MA30) were not in Hardy-Weinberg equilibrium. The genetic diversity indicators analyzed (expected heterozygosity, Shannon index, fixation index) show a high level of genetic variability. The estimation of the population structure of M. birostris using Bayesian inference suggests that the samples studied possibly belong to one population. A greater insight about genetic diversity indexes and the population structure of M. birostris can be achieved through the analysis of more samples, over a broader period of time. . The information of genetic diversity and population structure obtained in this preliminary investigation can be used to establish specific conservation and management programs of this species.Manta birostris es una especie altamente migratoria y la más grande del género Manta. En el 2009, el género Manta fue reevaluado y se lo dividió en dos especies Manta alfredi y Manta birostris. La distribución de Manta birostris es muy amplia dispersándose en áreas tropicales a semi-templadas alrededor de todos los océanos. Actualmente, la pesca no reglamentada para conseguir branquioespinas, junto con su baja tasa de reproducción está reduciendo las subpoblaciones a nivel mundial. Esta especie es vulnerable a la sobrepesca, debido a su madurez tardía, lenta gestación y períodos de vida largos. Una agrupación grande de M. birostris visita la Isla de la Plata durante los meses de julio a septiembre. La presente investigación tuvo como objetivo caracterizar la diversidad genética de individuos de dicho grupo mediante el uso de microsatélites. Se analizó 57 muestras de M. birostris recolectadas en tres años diferentes (2010, 2011 y 2012), con ocho pares de primers heterólogos. Se identificó 46 alelos en los ocho loci y un promedio de 4,375 alelos por cada uno. Se encontró que en tres loci (MA14, MA43 Y MA30) existe un alelo exclusivo y que tres loci (MA21, MA15, MA30) no estaban en equilibrio de Hardy-Weinberg. Los indicadores de diversidad genética analizados (heterocigosidad esperada, índice de Shannon, índice de fijación) muestran una alta variabilidad genética. La estimación de la estructura poblacional de M. birostris mediante inferencia Bayesiana indica que posiblemente las muestras pertenecen a una sola población. Para tener una idea más clara de los índices de diversidad genética y de la estructura poblacional de M. birostris es necesario ampliar el número de individuos analizados y el tiempo de estudio. La información encontrada en este estudio preliminar sobre la diversidad genética y estructura poblacional de M. birostris puede ser utilizada para ayudar a la conservación y prácticas de manejo de esta especie

Cytogenetic and genomic analysis of a patient with turner syndrome and t(2;12): a case report

Background: Turner syndrome is a genetic disorder that afects women. It is caused by an absent or incomplete X chromosome, which can be presented in mosaicism or not. There are 12 cases of Turner syndrome patients who present structural alterations in autosomal chromosomes. Case presentation: The present case report describes a patient with a reciprocal, maternally inherited translocation between chromosomes 2 and 12 with a mosaicism of X monosomy 45,X,t(2;12)(p13;q24)[95]/46,XX,t(2;12)(p13;q24) [5]. Through genetic mapping arrays, altered genes in the patient were determined within the 23 chromosome pairs. These genes were associated with the patient’s clinical features using a bioinformatics tool Conclusion: To our knowledge, this is the frst case in which a translocation (2;12) is reported in a patient with Turner syndrome and confrmed by conventional cytogenetics, FISH and molecular genetics. Clinical features of our patient are closely related with the loss of one X chromosome, however mild intellectual disability can be likely explained by autosomal genes. The presence of familial translocations was a common fnding, thus emphasizing the need for familiar testing for further genetic counselling

A Quick Guide for Using Microsoft Onenote as an Electronic Laboratory Notebook

[Abstract] Scientific data recording and reporting systems are of a great interest for endorsing reproducibility and transparency practices among the scientific community. Current research generates large datasets that can no longer be documented using paper lab notebooks (PLNs). In this regard, electronic laboratory notebooks (ELNs) could be a promising solution to replace PLNs and promote scientific reproducibility and transparency. We previously analyzed five ELNs and performed two survey-based studies to implement an ELN in a biomedical research institute. Among the ELNs tested, we found that Microsoft OneNote presents numerous features related to ELN best functionalities. In addition, both surveyed groups preferred OneNote over a scientifically designed ELN (PerkinElmer Elements). However, OneNote remains a general note-taking application and has not been designed for scientific purposes. We therefore provide a quick guide to adapt OneNote to an ELN workflow that can also be adjusted to other nonscientific ELNs

USO DE MICROSOFT ONENOTE COMO CUADERNO ELECTRÓNICO DE LABORATORIO

Los sistemas de registro y de reporte de datos son de gran interés, puesto que respaldan la reproducibilidad y transparencia científica. La investigación actual genera una gran cantidad de datos que ya no se pueden documentar utilizando cuadernos de laboratorio de papel (CLP). Los cuadernos electrónicos de laboratorio (CEL) podrían ser una solu-ción prometedora para reemplazar los CLP y promover la reproducibilidad científica y su transparencia. Anteriormente analizamos cinco CEL y realizamos dos encuestas para implementar un CEL en un instituto de investigación biomédica. Entre los CEL proba-dos, encontramos que Microsoft OneNote presenta numerosas características relacio-nadas con las mejores funcionalidades del CEL. Además, ambos grupos encuestados prefirieron OneNote sobre un CEL científico (Elements de PerkinElmer). Sin embargo, OneNote es una aplicación general para tomar notas que no ha sido diseñada para fi-nes científicos. Por lo tanto, en este trabajo proporcionamos varias pautas para adaptar OneNote a un flujo de trabajo experimental

Ring chromosome 15 - cytogenetics and mapping arrays: a case report and review of the literature

© The Author(s).[Background]: Ring chromosome 15 has been associated in previous studies with different clinical characteristic such as cardiac problems, digit and musculoskeletal abnormalities, and mental and motor problems among others. Only 97 clinical cases of ring chromosome 15 syndrome have been reported since 1966 and a common phenotype for these patients has not been established.[Case presentation]: The present case report describes a 15-month-old girl from the Amazon region of Ecuador, of Mestizo ancestry, who after cytogenetic tests showed a 46,XX,r(15) karyotype in more than 70% of metaphases observed. Her parents were healthy and non-related. The pregnancy was complicated and was positive for intrauterine growth retardation. Her birth weight was 1950 g, her length was 43.5 cm, and she had a head circumference of 29.3. In addition to postnatal growth delay, she had scant frontal hair, small eyes, hypertelorism, low-set of ears, flattened nasal bridge, anteverted nostrils, down-turned mouth, three café au lait spots, and delayed dentition.[Conclusions]: Despite the frequency of some phenotypes expressed in the different clinical cases reviewed and the present case, a common phenotype for patients with ring 15 could not be determined and it is restricted to the region of the chromosome lost during the ring formation.Funding for this research was completely managed by the institutions affiliated. Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador. Facultad de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador. Unidad de Investigación en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador. Servicio de Hematología, Hospital Universitario de Salamanca, Universidad de Salamanca, Salamanca, Spain. Molecular Medicine Unit, Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain. Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-SACYL-CSIC, Salamanca, Spain

Ring chromosome 15 – cytogenetics and mapping arrays: a case report and review of the literature

Abstract Background Ring chromosome 15 has been associated in previous studies with different clinical characteristic such as cardiac problems, digit and musculoskeletal abnormalities, and mental and motor problems among others. Only 97 clinical cases of ring chromosome 15 syndrome have been reported since 1966 and a common phenotype for these patients has not been established. Case presentation The present case report describes a 15-month-old girl from the Amazon region of Ecuador, of Mestizo ancestry, who after cytogenetic tests showed a 46,XX,r(15) karyotype in more than 70% of metaphases observed. Her parents were healthy and non-related. The pregnancy was complicated and was positive for intrauterine growth retardation. Her birth weight was 1950 g, her length was 43.5 cm, and she had a head circumference of 29.3. In addition to postnatal growth delay, she had scant frontal hair, small eyes, hypertelorism, low-set of ears, flattened nasal bridge, anteverted nostrils, down-turned mouth, three café au lait spots, and delayed dentition. Conclusions Despite the frequency of some phenotypes expressed in the different clinical cases reviewed and the present case, a common phenotype for patients with ring 15 could not be determined and it is restricted to the region of the chromosome lost during the ring formation

TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes

Telomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85–90% reactivate telomerase, while 10–15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors switch from a telomerase-dependent mechanism to ALT; in fact, the co-existence between both mechanisms has been observed in some cancers. Although different elements in the ALT pathway are uncovered, some molecular mechanisms are still poorly understood. Therefore, with the aim to identify potential molecular markers for the study of ALT, we combined in silico approaches in a 411 telomere maintenance gene set. As a consequence, we conducted a genomic analysis of these genes in 31 Pan-Cancer Atlas studies from The Cancer Genome Atlas and found 325,936 genomic alterations; from which, we identified 20 genes highly mutated in the cancer studies. Finally, we made a protein-protein interaction network and enrichment analysis to observe the main pathways of these genes and discuss their role in ALT-related processes, like homologous recombination and homology directed repair. Overall, due to the lack of understanding of the molecular mechanisms of ALT cancers, we proposed a group of genes, which after ex vivo validations, could represent new potential therapeutic markers in the study of ALT

Characterization of Ancestral Origin of Cystic Fibrosis of Patients with New Reported Mutations in CFTR

The incidence of cystic fibrosis (CF) and the frequency of the variants reported for CFTR depend on the population; furthermore, CF symptomatology is characterized by obstructive lung disease and pancreatic insufficiency among other symptoms, which are reliant on the individual's genotype. The Ecuadorian population is a mixture of Native Americans, Europeans, and Africans. That population admixture could be the reason for the new mutations reported in a previous study by Ruiz et al. (2019). A panel of 46 Ancestry Informative Markers was used to estimate the ancestral proportions of each available sample (12 samples in total). As a result, the Native American ancestry proportion was the most prevalent in almost all individuals, except for three patients from Guayaquil with the mutation [c.757G>A:p.Gly253Arg; c.1352G>T:p.Gly451Val] who had the highest European composition

Multi‐institutional experience of genetic diagnosis in Ecuador: National registry of chromosome alterations and polymorphisms

Abstract Background Detection of chromosomal abnormalities is crucial in various medical areas; to diagnose birth defects, genetic disorders, and infertility, among other complex phenotypes, in individuals across a wide range of ages. Hence, the present study wants to contribute to the knowledge of type and frequency of chromosomal alterations and polymorphisms in Ecuador. Methods Cytogenetic registers from different Ecuadorian provinces have been merged and analyzed to construct an open‐access national registry of chromosome alterations and polymorphisms. Results Of 28,806 karyotypes analyzed, 6,008 (20.9%) exhibited alterations. Down syndrome was the most frequent autosome alteration (88.28%), followed by Turner syndrome (60.50%), a gonosome aneuploidy. A recurrent high percentage of Down syndrome mosaicism (7.45%) reported here, as well as by previous Ecuadorian preliminary registries, could be associated with geographic location and admixed ancestral composition. Translocations (2.46%) and polymorphisms (7.84%) were not as numerous as autosomopathies (64.33%) and gonosomopathies (25.37%). Complementary to conventional cytogenetics tests, molecular tools have allowed identification of submicroscopic alterations regions or candidate genes which can be possibly implicated in patients' symptoms and phenotypes. Conclusion The Ecuadorian National Registry of Chromosome Alterations and Polymorphisms provides a baseline to better understand chromosomal abnormalities in Ecuador and therefore their clinical management and awareness. This data will guide public policy makers to promote and financially support cytogenetic and genetic testing