A fate for organic acids, formaldehyde and methanol in cloud water: their biotransformation by micro-organisms

International audienceThe interactions between microbial and chemical contents of cloud water were investigated. First, we observe that the bulk cloud water solution provides a substantial environment where bacteria can develop significantly. Then, a total number of 60 microbial strains originating from seven distinct samples of cloud water and affiliated to various taxonomic groups were looked for their ability to degrade some of the main atmospheric carboxylic compounds: formate, acetate, lactate, succinate, formaldehyde and methanol. Biodegradation tests show that all these compounds can be transformed when used as single carbonaceous substrates, with activities depending on both the strain and the compound. The highest capacities of biodegradation are observed towards formaldehyde, formate and acetate, which are also the more concentrated compounds typically measured in cloud water. Hence, analyses by 1H NMR permitted to establish for instance that compounds like pyruvate or fumarate can be produced and released in the media in relation to the transformation of lactate or succinate. In addition, utilization of 13C labelled formaldehyde showed that it can be transformed through many metabolic pathways, similar to those induced by photochemistry and leading to the production of formate and/or methanol. These results suggest that microorganisms of cloud water can have various behaviours towards the chemical compounds present in the atmosphere: they can represent either a sink or source for organic carbon, and may have to be considered as actors of cloud chemistry

Brain size regulations by cbp haploinsufficiency evaluated by in-vivo MRI based volumetry

The Rubinstein-Taybi Syndrome (RSTS) is a congenital disease that affects brain development causing severe cognitive deficits. In most cases the disease is associated with dominant mutations in the gene encoding the CREB binding protein (CBP). In this work, we present the first quantitative analysis of brain abnormalities in a mouse model of RSTS using magnetic resonance imaging (MRI) and two novel self-developed automated algorithms for image volumetric analysis. Our results quantitatively confirm key syndromic features observed in RSTS patients, such as reductions in brain size (-16.31%, p < 0.05), white matter volume (-16.00%, p < 0.05), and corpus callosum (-12.40%, p < 0.05). Furthermore, they provide new insight into the developmental origin of the disease. By comparing brain tissues in a region by region basis between cbp(+/-) and cbp(+/+) littermates, we found that cbp haploinsufficiency is specifically associated with significant reductions in prosencephalic tissue, such us in the olfactory bulb and neocortex, whereas regions evolved from the embryonic rhombencephalon were spared. Despite the large volume reductions, the proportion between gray-, white-matter and cerebrospinal fluid were conserved, suggesting a role of CBP in brain size regulation. The commonalities with holoprosencephaly and arhinencephaly conditions suggest the inclusion of RSTS in the family of neuronal migration disorders.We are grateful to Begona Fernandez for her excellent technical assistance. We would like to thank S. Sawiak (Wolfson Imaging Centre, University of Cambridge, Cambridge, United Kingdom) for the mouse brain tissue probability maps and the SPMmouse plug-in, and to N. Kovacevic (Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada) for the atlas of the mouse brain. Supported by grants from the Spanish MINECO to S.C. (BFU 2012-39958) and MINECO and FEDER to D.M. (TEC 2012-33778) and from MINECO (SAF2011-22855) and Generalitat Valenciana (Prometeo/2012/005) to A.B. The Instituto de Neurociencias is "Centre of Excellence Severo Ochoa".Ateca Cabarga, JC.; Cosa, A.; Pallares, V.; Lopez-Atalaya, JP.; Barco, A.; Canals, S.; Moratal Pérez, D. (2015). Brain size regulations by cbp haploinsufficiency evaluated by in-vivo MRI based volumetry. Scientific Reports. 5. https://doi.org/10.1038/srep16256S5Rubinstein, J. H. & Taybi, H. Broad thumbs and toes and facial abnormalities. A possible mental retardation syndrome. Am J Dis Child 105, 588–608 (1963).Van Belzen, M., Bartsch, O., Lacombe, D., Peters, D. J. & Hennekam, R. C. Rubinstein-Taybi syndrome (CREBBP, EP300). Eur J Hum Genet. 19, preceeding 118–120 (2011).Hennekam, R. C. Rubinstein-Taybi syndrome. Eur J Hum Genet. 14, 981–985 (2006).Wiley, S., Swayne, S., Rubinstein, J. H., Lanphear, N. E. & Stevens, C. A. Rubinstein-Taybi syndrome medical guidelines. Am J Med Genet A. 119A, 101–110 (2003).Michail, J., Matsoukas, J. & Theodorou, S. Pouce bot arqué en forte abduction-extension et autres symptomes concomitants. Rev Chir Orthop 43, 142–146 (1957).Barco A. The Rubinstein-Taybi syndrome: modeling mental impairment in the mouse. Genes Brain Behav 6, 32–39 (2007).Lopez-Atalaya, J. P., Valor, L. M. & Barco, A. Epigenetic factors in intellectual disability: the Rubinstein-Taybi syndrome as a paradigm of neurodevelopmental disorder with epigenetic origin. Prog Mol Biol Transl Sci. 128, 139–176 (2014).Petrij, F., Giles, R. H., Dauwerse, H. G., Saris, J. J., Hennekam, R. C. M., Masuno, M., Tommerup, N., Van Ommen, G. J. B., Goodman, R. H., Peters, D. J. M. & Breuning, M. H. Rubinstein-Taybi syndrome caused by mutations in the transcriptional co-activator CBP. Nature 376, 348–351 (1995).Zimmermann, N., Acosta, A. M., Kohlhase, J. & Bartsch, O. Confirmation of EP300 gene mutations as a rare cause of Rubinstein-Taybi syndrome. Eur J Hum Genet. 15, 837–842 (2007).Bartholdi, D. et al. Genetic heterogeneity in Rubinstein-Taybi syndrome: delineation of the phenotype of the first patients carrying mutations in EP300. J Med Genet. 44, 327–333 (2007).Roelfsema, J. H. et al. Genetic heterogeneity in Rubinstein-Taybi syndrome: mutations in both the CBP and EP300 genes cause disease. Am J Hum Genet. 76, 572–580 (2005).Tanaka, Y., Naruse, I., Maekawa, T., Masuya, H., Shiroishi, T. & Ishii, S. Abnormal skeletal patterning in embryos lacking a single Cbp allele: a partial similarity with Rubinstein-Taybi syndrome. Proc Natl Acad Sci USA 94, 10215–10220 (1997).López-Atalaya, J. P. et al. CBP is required for environmental enrichment-induced neurogenesis and cognitive enhancement. EMBO J 30, 4287–4298 (2011).Wang, J. et al. CBP histone acetyltransferase activity regulates embryonic neural differentiation in the normal and Rubinstein-Taybi syndrome brain. Dev Cell. 18, 114–125 (2010).Marzuillo, P. et al. Brain magnetic resonance in the routine management of Rubinstein-Taybi syndrome (RTS) can prevent life-threatening events and neurological deficits. Am J Med Genet A. 164A, 2129–2132 (2014).de Kort, E., Conneman, N. & Diderich, K. A case of Rubinstein-Taybi syndrome and congenital neuroblastoma. Am J Med Genet A. 164A, 1332–1333 (2014).Lee, J. S. et al. Clinical and mutational spectrum in Korean patients with Rubinstein-Taybi syndrome: the spectrum of brain MRI abnormalities. Brain Dev. 37, 402–408 (2015).Marzuillo, P. et al. Novel cAMP binding protein-BP (CREBBP) mutation in a girl with Rubinstein-Taybi syndrome, GH deficiency, Arnold Chiari malformation and pituitary hypoplasia. BMC Med Genet. 14, 28 (2013). 10.1186/1471-2350-14-28.Li, Z. et al. Phenotypic expansion of the interstitial 16p13.3 duplication: a case report and review of the literature. Gene. 531, 502–505 (2013).Demeer, B. et al. Duplication 16p13.3 and the CREBBP gene: confirmation of the phenotype. Eur J Med Genet. 56, 26–31 (2013).Kumar, S., Suthar, R., Panigrahi, I. & Marwaha, R. K. Rubinstein-Taybi syndrome: Clinical profile of 11 patients and review of literature. Indian J Hum Genet. 18, 161–166 (2012).Giussani, C. et al. The association of neural axis and craniovertebral junction anomalies with scoliosis in Rubinstein-Taybi syndrome. Childs Nerv Syst. 28, 2163–2168 (2012).Parsley, L., Bellus, G., Handler, M. & Tsai, A. C. Identical twin sisters with Rubinstein-Taybi syndrome associated with Chiari malformations and syrinx. Am J Med Genet A. 155A, 2766–2770 (2011).Thienpont, B. et al. Duplications of the critical Rubinstein-Taybi deletion region on chromosome 16p13.3 cause a novel recognisable syndrome. J Med Genet. 47, 155–161 (2010).Kim, S. H., Lim, B. C., Chae, J. H., Kim, K. J. & Hwang, Y. S. A case of Rubinstein-Taybi Syndrome with a CREB-binding protein gene mutation. Korean J Pediatr. 53, 718–721 (2010).Wójcik, C. et al. Rubinstein-Taybi syndrome associated with Chiari type I malformation caused by a large 16p13.3 microdeletion: a contiguous gene syndrome? Am J Med Genet A. 152A, 479–483 (2010).Wachter-Giner, T., Bieber, I., Warmuth-Metz, M., Bröcker, E. B. & Hamm, H. Multiple pilomatricomas and gliomatosis cerebri--a new association? Pediatr Dermatol. 26, 75–78 (2009).Verstegen, M. J., van den Munckhof, P., Troost, D. & Bouma, G. J. Multiple meningiomas in a patient with Rubinstein-Taybi syndrome. Case report. J Neurosurg. 102, 167–168 (2005).Agarwal, R., Aggarwal, R., Kabra, M. & Deorari, A. K. Dandy-Walker malformation in Rubinstein-Taybi syndrome: a rare association. Clin Dysmorphol. 11, 223–224 (2002).Ihara, K., Kuromaru, R., Takemoto, M. & Hara, T. Rubinstein-Taybi syndrome: a girl with a history of neuroblastoma and premature thelarche. Am J Med Genet. 83, 365–366 (1999).Sener, R. N. Rubinstein-Taybi syndrome: cranial MR imaging findings. Comput Med Imaging Graph 19, 417–418 (1995).Robinson, T. W., Stewart, D. L. & Hersh, J. H. Monozygotic twins concordant for Rubinstein-Taybi syndrome and implications for genetic counseling. Am J Med Genet. 45, 671–673 (1993).Guion-Almeida, M. L. & Richieri-Costa, A. Callosal agenesis, iris coloboma and megacolon in a Brazilian boy with Rubinstein-Taybi syndrome. Am J Med Genet. 43, 929–931 (1992).Albanese, A. et al. [Role of diagnostic imaging in Rubinstein-Taybi syndrome. personal experience with 8 cases]. Radiol Med. 81, 253–261 (1991).Rubinstein, J. H. Broad thumb-hallux (Rubinstein-Taybi) syndrome 1957-1988. Am J Med Genet Suppl. 6, 3–16 (1990).Hennekam, R. C., Stevens, C. A. & Van de Kamp, J. J. Etiology and recurrence risk in Rubinstein-Taybi syndrome. Am J Med Genet Suppl. 6, 56–64 (1990).Bonioli, E., Bellini, C. & Di Stefano, A. Unusual association: Dandy-Walker-like malformation in the Rubinstein-Taybi syndrome. Am J Med Genet. 33, 420–421 (1989).Beluffi, G., Pazzaglia, U. E., Fiori, P., Pricca, P. & Poznanski, A. K. [Oto-palato-digital syndrome. Clinico-radiological study]. Radiol Med. 74, 176–184 (1987).Cantani, A. & Gagliesi, D. Rubinstein-Taybi syndrome. Review of 732 cases and analysis of the typical traits. Eur Rev Med Pharmacol Sci. 2, 81–87 (1998).Viosca, J., Lopez-Atalaya, J. P., Olivares, R., Eckner, R. & Barco, A. Syndromic features and mild cognitive impairment in mice with genetic reduction on p300 activity: Differential contribution of p300 and CBP to Rubinstein-Taybi syndrome etiology. Neurobiol Dis. 37, 186–194 (2010).Martínez-Martínez, M. A., Pacheco-Torres, J., Borrell, V. & Canals, S. Phenotyping the central nervous system of the embryonic mouse by magnetic resonance microscopy. Neuroimage. 97, 95–106 (2014).Heikkinen, T. et al. Characterization of neurophysiological and behavioral changes, MRI brain volumetry and 1H MRS in zQ175 knock-in mouse model of Huntington’s disease. PLoS One. 7, e50717 (2012), 10.1371/journal.pone.0050717.Alarcón, J. M. et al. Chromatin acetylation, memory and LTP are impaired in CBP+/− mice: a model for the cognitive deficit in Rubinstein-Taybi syndrome and its amelioration. Neuron. 42, 947–959 (2004).Smith, S. M. et al. Advances in functional and structural MR image analysis and implementation as FSL. Neuroimage 23 Supp 1, S208–19 (2004).Smith, S. M. Fast robust automated brain extraction. Hum Brain Mapp 17, 143–155 (2002).Ashburner, J. & Friston, K. J. Unified segmentation. Neuroimage 26, 839–851 (2005).Sawiak, S. J., Wood, N. I., Williams, G. B., Morton, A. J. & Carpenter, T. A. Voxel-based morphometry in the R6/2 transgenic mouse reveals differences between genotypes not seen with manual 2D morphometry. Neurobiol Dis 33, 20–27 (2009).Kovačević, N. et al. A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability. Cereb Cortex 15, 639–645 (2005).Zacharoff, L. et al. Cortical metabolites as biomarkers in the R6/2 model of Huntington’s disease. J Cereb Blood Flow Metab. 32, 502–514 (2012).Petryk, A., Graf, D. & Marcucio, R. Holoprosencephaly: signaling interactions between the brain and the face, the environment and the genes and the phenotypic variability in animal models and humans. Wiley Interdiscip Rev Dev Biol. 4, 17–32 (2015).Solomon, B. D., Gropman, A. & Muenke, M. Holoprosencephaly Overview. In: GeneReviews (eds Pagon, R. A. et al.), Seattle (WA): University of Washington, Seattle; 1993-2014, 2000 Dec 27 [Updated 2013 Aug 29]. Available from: http://www.ncbi.nlm.nih.gov/books/NBK1530/ [Date of access: September 4, 2015].Mazzone, D., Milana, A., Praticò, G. & Reitano, G. Rubinstein-Taybi syndrome associated with Dandy-Walker cyst. 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A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

A hierarchical architecture for a distributed management of P2P networks and services

We propose a management architecture for the P2P model which respects its distributed nature while building a hierarchical structure. This architecture enables the distribution of management functions, avoids an excessive centralization of the manager role and fits the dy- namic of the P2P model well. The architecture is evaluated through an implementation in the Pastry framework

Genome sequencing identify chromosome 9 inversions disrupting ENG in 2 unrelated HHT families

International audienceHereditary hemorrhagic telangiectasia (HHT), also known as Rendu-Osler-Weber disease, is a dominant inherited vascular disorder. The clinical diagnosis is based on the Curaçao criteria and pathogenic variants in the ENG and ACVRL1 genes are responsible for most cases of HHT.Four families with a negative targeted gene panel and selected by a multidisciplinary team were selected and whole-genome sequencing was performed according to the recommendations of the French National Plan for Genomic Medicine. Structural variations were confirmed by standard molecular cytogenetic analysis (FISH).In two families with a definite diagnosis of HHT, we identified two different paracentric inversions of chromosome 9, both disrupting the ENG gene. These inversions are considered as pathogenic and causative for the HHT phenotype of the patients.This is the first time structural variations are reported to cause HHT. As such balanced events are often missed by exon-based sequencing (panel, exome), structural variations may be an under-recognized cause of HHT. Genome sequencing for the detection of these events could be suggested for patients with a definite diagnosis of HHT and in whom no causative pathogenic variant was identified

Desigualdades sócio-espaciais da adequação das informações de nascimentos e óbitos do Ministério da Saúde, Brasil, 2000-2002 Socio-spatial inequalities in the adequacy of Ministry of Health data on births and deaths at the municipal level in Brazil, 2000-2002

Neste trabalho, analisam-se as desigualdades sócio-espaciais da adequação das informações de nascimentos (SINASC) e óbitos (SIM) do Ministério da Saúde para o cálculo da mortalidade infantil por município. A análise foi realizada de acordo com o porte populacional do município e região geográfica no período 2000-2002, considerando-se cinco indicadores: coeficiente geral de mortalidade padronizado por idade; razão entre nascidos vivos informados e estimados; desvio médio relativo do coeficiente de mortalidade; desvio médio relativo da taxa de natalidade; percentual de óbitos sem definição da causa básica de morte. Os critérios de adequação foram estabelecidos estatisticamente nas Unidades da Federação com informações consideradas adequadas. Os resultados mostram desigualdades sócio-espaciais importantes: o percentual de adequação é maior no Centro-Sul e entre os municípios de maior porte populacional. Em relação aos três aspectos estudados, o SINASC teve a melhor avaliação. Quanto ao SIM, além de reduzir a subnotificação, é preciso melhorar a qualidade do preenchimento da causa de óbito, para que as informações possam orientar adequadamente os programas de saúde voltados para a redução das iniqüidades da mortalidade infantil no Brasil.<br>This study analyzed socio-spatial inequalities in the adequacy of Ministry of Health data systems on live births (SINASC) and deaths (SIM) for estimating infant mortality at the municipal level in Brazil. Data from 2000-2002 for all municipalities were analyzed according to population size and geographic region. Five indicators were considered: age-standardized mortality rate; ratio of reported-to-estimated live births; relative mean deviation of the mortality rate; relative mean deviation of the birth rate; and proportion of deaths with undetermined causes. Adequacy criteria were established statistically for eight Brazilian States in which vital statistics were adequate. The results showed important socio-spatial inequalities: in general, the proportion of adequate vital statistics was higher in the Central-South of the country and in larger municipalities. The live birth data system received the best evaluation for three items. The mortality data system requires both a reduction in underreporting and improved data on cause of death in order to orient health programs focused on decreasing inequalities in infant mortality in Brazil

RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features

Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males

Postzygotic inactivating mutations of RHOA cause a mosaic neuroectodermal syndrome

Hypopigmentation along Blaschko’s lines is a hallmark of a poorly defined group of mosaic syndromes whose genetic causes are unknown. Here we show that postzygotic inactivating mutations of RHOA cause a neuroectodermal syndrome combining linear hypopigmentation, alopecia, apparently asymptomatic leukoencephalopathy, and facial, ocular, dental and acral anomalies. Our findings pave the way toward elucidating the etiology of pigmentary mosaicism and highlight the role of RHOA in human development and disease