Monogenic variants in dystonia: an exome-wide sequencing study

Background Dystonia is a clinically and genetically heterogeneous condition that occurs in isolation (isolated dystonia), in combination with other movement disorders (combined dystonia), or in the context of multisymptomatic phenotypes (isolated or combined dystonia with other neurological involvement). However, our understanding of its aetiology is still incomplete. We aimed to elucidate the monogenic causes for the major clinical categories of dystonia. Methods For this exome-wide sequencing study, study participants were identified at 33 movement-disorder and neuropaediatric specialty centres in Austria, Czech Republic, France, Germany, Poland, Slovakia, and Switzerland. Each individual with dystonia was diagnosed in accordance with the dystonia consensus definition. Index cases were eligible for this study if they had no previous genetic diagnosis and no indication of an acquired cause of their illness. The second criterion was not applied to a subset of participants with a working clinical diagnosis of dystonic cerebral palsy. Genomic DNA was extracted from blood of participants and whole-exome sequenced. To find causative variants in known disorder-associated genes, all variants were filtered, and unreported variants were classified according to American College of Medical Genetics and Genomics guidelines. All considered variants were reviewed in expert round-table sessions to validate their clinical significance. Variants that survived filtering and interpretation procedures were defined as diagnostic variants. In the cases that went undiagnosed, candidate dystonia-causing genes were prioritised in a stepwise workflow. Findings We sequenced the exomes of 764 individuals with dystonia and 346 healthy parents who were recruited between June 1, 2015, and July 31, 2019. We identified causative or probable causative variants in 135 (19%) of 728 families, involving 78 distinct monogenic disorders. We observed a larger proportion of individuals with diagnostic variants in those with dystonia (either isolated or combined) with coexisting non-movement disorder-related neurological symptoms (100 [45%] of 222;excepting cases with evidence of perinatal brain injury) than in those with combined (19 [19%] of 98) or isolated (16 [4%] of 388) dystonia. Across all categories of dystonia, 104 (65%) of the 160 detected variants affected genes which are associated with neurodevelopmental disorders. We found diagnostic variants in 11 genes not previously linked to dystonia, and propose a predictive clinical score that could guide the implementation of exome sequencing in routine diagnostics. In cases without perinatal sentinel events, genomic alterations contributed substantively to the diagnosis of dystonic cerebral palsy. In 15 families, we delineated 12 candidate genes. These include IMPDH2, encoding a key purine biosynthetic enzyme, for which robust evidence existed for its involvement in a neurodevelopmental disorder with dystonia. We identified six variants in IMPDH2, collected from four independent cohorts, that were predicted to be deleterious de-novo variants and expected to result in deregulation of purine metabolism. Interpretation In this study, we have determined the role of monogenic variants across the range of dystonic disorders, providing guidance for the introduction of personalised care strategies and fostering follow-up pathophysiological explorations

Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome

Purpose: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort. Methods: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. Results: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. Conclusion: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome

FRACTAL CHARACTERISTICS OF THE HORIZONTAL MOVEMENT OF WATER IN SOILS

Observed deviations from traditional concepts of soil-water movement are considered in terms of fractals. A connection is made between this movement and a Brownian motion, a random and self-affine type of fractal, to account for the soil-water diffusivity function having auxiliary time dependence for unsaturated soils. The position of a given water content is directly proportional to t(n), where t is time, and exponent n for distinctly unsaturated soil is less than the traditional 0.50. As water saturation is approached, n approaches 0.50. Macroscopic fractional Brownian motion is associated with n < 0.50, but shifts to regular Brownian motion for n = 0.50

Influência do tempo de contagem na determinação da densidade de nêutrons Influence of the counting time on neutron density determination

Com o objetivo de se estudar a influência do tempo de contagem na determinação da densidade de nêutrons moderados com uma sonda de nêutrons, num Latossolo localizado na área experimental do Departamento de Engenharia Rural, da Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Campus de Botucatu, SP, coletaram-se dados no interior de uma estufa de polietileno, a três profundidades no solo, 15, 30 e 45 cm, com tempos de contagem de 1, 4, 16, 32, 64, 128 e 256 s, com cinco repetições. Para avaliação da variabilidade entre as leituras, utilizaram-se métodos estatísticos descritivos: variância, desvio-padrão, valores de amplitude e coeficiente de variação. Para se determinar a influência do tempo de contagem no valor das leituras, utilizou-se o teste F e comparação entre médias através do teste de Tukey. Com exceção da profundidade de 45 cm, observou-se pequena variabilidade entre as leituras obtidas para cada tempo de contagem e uma significante variação entre as médias das leituras obtidas com curtos (1 e 4 s) e longos (tempos maiores de 16 s) tempos de contagem. O uso de longos tempos de contagem (maiores de 32 s) não ocasiona diferença significativa na magnitude das leituras.To study the influence of the neutron probe counting time on neutron density determination a study was carried out on a Latossol, under greenhouse conditions, at the Experimental Station of the Rural Engineering Department, UNESP in Botucatu-SP. Neutron probe data were collected, with five replicates, at three soil depths (15, 30 and 45 cm) with counting times of 1, 4, 16, 32, 128 and 256 s. To evaluate the variability among replicates, conventional statistics parameters were determined : variance, standard deviation, amplitude and coefficient of variation; to determine the influence of the counting time on neutron density determination, analyses of variance (F test) and comparisons of means (Tukey Test) were also conducted. The results showed small variability among readings for each counting time and significant variation among the reading means for the short (1 and 4 s) and long (longer than 16 s), counting times with the exception of the 45 cm soil depth. The use of long counting times (longer than 32 s) does not cause any significant difference on the readings magnitude

Eucalyptus ESTs corresponding to the protoporphyrinogen IX oxidase enzyme related to the synthesis of heme, chlorophyll, and to the action of herbicides

This work was aimed at locating Eucalyptus ESTs corresponding to the PROTOX or PPO enzyme (Protoporphyrinogen IX oxidase, E.C. 1.3.3.4) directly related to resistance to herbicides that promote oxidative stress, changing the functionality of this enzyme. PROTOX, which is the site of action of diphenyl-ether (oxyfluorfen, lactofen, fomesafen), oxadiazole (oxadiazon and oxadiargyl), and aryl triazolinone (sulfentrazone and carfentrazone) herbicides, acts on the synthesis route of porphyrins which is associated with the production of chlorophyll a, catalases, and peroxidases. One cluster and one single read were located, with e-values better than e-70, associated to PROTOX. The alignment results between amino acid sequences indicated that this enzyme is adequately represented in the ESTs database of the FORESTs project

Eucalyptus ESTs involved in the production of 9-cis epoxycarotenoid dioxygenase, a regulatory enzyme of abscisic acid production

Abscisic acid (ABA) regulates stress responses in plants, and genomic tools can help us to understand the mechanisms involved in that process. FAPESP, a Brazilian research foundation, in association with four private forestry companies, has established the FORESTs database (<A HREF="https://forests.esalq.usp.br">https://forests.esalq.usp.br</A>). A search was carried out in the Eucalyptus expressed sequence tag database to find ESTs involved with 9-cis epoxycarotenoid dioxygenase (NCED), the regulatory enzyme for ABA biosynthesis, using the basic local BLAST alignment tool. We found four clusters (EGEZLV2206B11.g, EGJMWD2252H08.g, EGBFRT3107F10.g, and EGEQFB1200H10.g), which represent similar sequences of the gene that produces NCED. Data showed that the EGBFRT3107F10.g cluster was similar to the maize (Zea mays) NCED enzyme, while EGEZLV2206B11.g and EGJMWD2252H08.g clusters were similar to the avocado (Persea americana) NCED enzyme. All Eucalyptus clusters were expressed in several tissues, especially in flower buds, where ABA has a special participation during the floral development process