Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis.

Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200) females. XCI skewing has been also linked to abnormal X-linked gene expression with the broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2 CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA), including 3 sites that could not be analysed with previously used EpiTYPER system. The method was applied for detection of skewed XCI in FM females and in different types of SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG < 40), and 148 FM and 90 SCA individuals. MS-QMA identified: (i) most SCAs if combined with a Y chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant correlation with the EpiTYPER reference method in FM males and females (P < 0.0001) and SCAs (P < 0.05). In conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with diagnostic utility

Comparación de métodos para el tratamiento de valores perdidos en la EPV-R

Background: The development of an effective instrument to assess the risk of partner violence is a topic of great social relevance. This study evaluates the scale of “Predicción del Riesgo de Violencia Grave Contra la Pareja” –Revisada– (EPV-R - Severe Intimate Partner Violence Risk Prediction Scale-Revised), a tool developed in Spain, which is facing the problem of how to treat the high rate of missing values, as is usual in this type of scale. Method: First, responses to the EPV-R in a sample of 1215 male abusers who were reported to the police were used to analyze the patterns of occurrence of missing values, as well as the factor structure. Second, we analyzed the performance of various imputation methods using simulated data that emulates the missing data mechanism found in the empirical database. Results: The imputation procedure originally proposed by the authors of the scale provides acceptable results, although the application of a method based on the Item Response Theory could provide greater accuracy and offers some additional advantages. Conclusions: Item Response Theory appears to be a useful tool for imputing missing data in this type of questionnaireAntecedentes: el desarrollo de un instrumento eficaz para evaluar el riesgo de violencia contra la pareja representa un tema de gran relevancia social. En el presente estudio se evalúa la escala de Predicción del Riesgo de Violencia Grave Contra la Pareja –Revisada– (EPV-R), una herramienta desarrollada en nuestro contexto, que se enfrenta al problema de cómo tratar la elevada tasa de valores perdidos, que es usual en este tipo de escalas. Método: en primer lugar, se estudia en una muestra empírica (N = 1215) el patrón de aparición de los valores perdidos, así como la estructura factorial del EPV-R. En segundo lugar, se analiza el funcionamiento de distintos métodos de imputación en datos simulados en los que se emula el mecanismo de pérdida de datos encontrado para la base de datos empírica. Resultados: el procedimiento de imputación originalmente propuesto por los autores de la escala ofrece resultados aceptables, si bien la aplicación de un método basado en la Teoría de la Respuesta al Ítem podría proporcionar una mayor precisión y ofrece algunas ventajas adicionales. Conclusiones: la Teoría de la Respuesta al Ítem demuestra ser una herramienta útil para la imputación de respuestas en este tipo de cuestionariosThe research has been funded by the Ministry of Economy and Competitivity of Spain, project PSI2013-44300-

One Welfare : Assessing the Effects of Drought and the COVID-19 Pandemic on Farmers' Well-Being and Their Perception of Goats' Welfare

Considering the interconnections between human well-being, animal welfare, and the environment, this study aimed to investigate the impacts of drought and the COVID-19 pandemic on small-scale goat farmers' well-being and their perception of goats' welfare following the One Welfare framework. Using a telephone survey, close-ended questions, and Likert scales, we assessed the impacts of drought and the COVID-19 pandemic on human well-being and animal welfare in the Coquimbo region of Chile. The DASS-21 questionnaire was used to evaluate farmers' mental health. Goat farmers perceived the scarcity of water and food for animals as factors that negatively affected animal productivity and welfare and caused an increase in farmers' stress levels. Farmers who had not been visited by a veterinarian showed higher levels of stress than those who received one visit during the year (M = 10 vs. 2, p = 0.025). Additionally, farmers who perceived better welfare of their animals showed lower levels of depression (r = −0.17, p = 0.048), anxiety (r = −0.21, p = 0.016), and stress (r = −0.33, p < 0.001). These findings emphasize the importance of addressing farmers' mental health and veterinary support as crucial aspects to ensure both goat welfare and farm productivity

H\"older Continuity of the Integrated Density of States for the Fibonacci Hamiltonian

We prove H\"older continuity of the integrated density of states for the Fibonacci Hamiltonian for any positive coupling, and obtain the asymptotics of the H\"older exponents for large and small couplings.Comment: 18 page

Neuropathology of childhood‐onset basal ganglia degeneration caused by mutation of VAC14

ObjectiveTo characterize the clinical features and neuropathology associated with recessive VAC14 mutations.MethodsWhole‐exome sequencing was used to identify the genetic etiology of a rapidly progressive neurological disease presenting in early childhood in two deceased siblings with distinct neuropathological features on post mortem examination.ResultsWe identified compound heterozygous variants in VAC14 in two deceased siblings with early childhood onset of severe, progressive dystonia, and neurodegeneration. Their clinical phenotype is consistent with the VAC14–related childhood‐onset, striatonigral degeneration recently described in two unrelated children. Post mortem examination demonstrated prominent vacuolation associated with degenerating neurons in the caudate nucleus, putamen, and globus pallidus, similar to previously reported ex vivo vacuoles seen in the late‐endosome/lysosome of VAC14‐deficient neurons. We identified upregulation of ubiquitinated granules within the cell cytoplasm and lysosomal‐associated membrane protein (LAMP2) around the vacuole edge to suggest a process of vacuolation of lysosomal structures associated with active autophagocytic‐associated neuronal degeneration.InterpretationOur findings reveal a distinct clinicopathological phenotype associated with recessive VAC14 mutations.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142276/1/acn3487_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142276/2/acn3487.pd

Genetic Background Can Result in a Marked or Minimal Effect of Gene Knockout (GPR55 and CB2 Receptor) in Experimental Autoimmune Encephalomyelitis Models of Multiple Sclerosis

PMCID: PMC379391

Characterizing microglial gene expression in a model of secondary progressive multiple sclerosis

Multiple sclerosis (MS) is the most common inflammatory, demyelinating and neurodegenerative disease of the central nervous system in young adults. Chronic-relapsing experimental autoimmune encephalomyelitis (crEAE) in Biozzi ABH mice is an experimental model of MS. This crEAE model is characterized by an acute phase with severe neurological disability, followed by remission of disease, relapse of neurological disease and remission that eventually results in a chronic progressive phase that mimics the secondary progressive phase (SPEAE) of MS. In both MS and SPEAE, the role of microglia is poorly defined. We used a crEAE model to characterize microglia in the different phases of crEAE phases using morphometric and RNA sequencing analyses. At the initial, acute inflammation phase, microglia acquired a pro-inflammatory phenotype. At the remission phase, expression of standard immune activation genes was decreased while expression of genes associated with lipid metabolism and tissue remodeling were increased. Chronic phase microglia partially regain inflammatory gene sets and increase expression of genes associated with proliferation. Together, the data presented here indicate that microglia obtain different features at different stages of crEAE and a particularly mixed phenotype in the chronic stage. Understanding the properties of microglia that are present at the chronic phase of EAE will help to understand the role of microglia in secondary progressive MS, to better aid the development of therapies for this phase of the disease

Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS

Genomic technologies such as next-generation sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole-genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)11 short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS-affected families and identified a core ancestral haplotype, estimated to have arisen in Europe more than twenty-five thousand years ago. WGS of the four RFC1-negative CANVAS-affected families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type, and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders