Palaeo-sea-level and palaeo-ice-sheet databases: problems, strategies, and perspectives

Sea-level and ice-sheet databases have driven numerous advances in understanding the Earth system. We describe the challenges and offer best strategies that can be adopted to build self-consistent and standardised databases of geological and geochemical information used to archive palaeo-sea-levels and palaeo-ice-sheets. There are three phases in the development of a database: (i) measurement, (ii) interpretation, and (iii) database creation. Measurement should include the objective description of the position and age of a sample, description of associated geological features, and quantification of uncertainties Interpretation of the sample may have a subjective component, but it should always include uncertainties and alternative or contrasting interpretations, with any exclusion of existing interpretations requiring a full justification. During the creation of a database, an approach based on accessibility, transparency, trust, availability, continuity, completeness, and communication of content (ATTAC³) must be adopted. It is essential to consider the community that creates and benefits from a database. We conclude that funding agencies should not only consider the creation of original data in specific research question-oriented projects, but also include the possibility of using part of the funding for IT -related and database creation tasks, which are essential to guarantee accessibility and maintenance of the collected data

PURA syndrome : clinical delineation and genotype-phenotype study in 32 individuals with review of published literature

Background De novo mutations in PURA have recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia. Objectives T o delineate the clinical spectrum of PURA syndrome and study genotype-phenotype correlations. Methods Diagnostic or research-based exome or Sanger sequencing was performed in individuals with ID. We systematically collected clinical and mutation data on newly ascertained PURA syndrome individuals, evaluated data of previously reported individuals and performed a computational analysis of photographs. We classified mutations based on predicted effect using 3D in silico models of crystal structures of Drosophila-derived Pur-alpha homologues. Finally, we explored genotypephenotype correlations by analysis of both recurrent mutations as well as mutation classes. Results We report mutations in PURA (purine-rich element binding protein A) in 32 individuals, the largest cohort described so far. Evaluation of clinical data, including 22 previously published cases, revealed that all have moderate to severe ID and neonatal-onset symptoms, including hypotonia (96%), respiratory problems (57%), feeding difficulties (77%), exaggerated startle response (44%), hypersomnolence (66%) and hypothermia (35%). Epilepsy (54%) and gastrointestinal (69%), ophthalmological (51%) and endocrine problems (42%) were observed frequently. Computational analysis of facial photographs showed subtle facial dysmorphism. No strong genotype-phenotype correlation was identified by subgrouping mutations into functional classes. Conclusion We delineate the clinical spectrum of PURA syndrome with the identification of 32 additional individuals. The identification of one individual through targeted Sanger sequencing points towards the clinical recognisability of the syndrome. Genotype-phenotype analysis showed no significant correlation between mutation classes and disease severity.Peer reviewe

NEXMIF encephalopathy:an X-linked disorder with male and female phenotypic patterns

Purpose Pathogenic variants in the X-linked gene NEXMIF (previously KIAA2022) are associated with intellectual disability (ID), autism spectrum disorder, and epilepsy. We aimed to delineate the female and male phenotypic spectrum of NEXMIF encephalopathy. Methods Through an international collaboration, we analyzed the phenotypes and genotypes of 87 patients with NEXMIF encephalopathy. Results Sixty-three females and 24 males (46 new patients) with NEXMIF encephalopathy were studied, with 30 novel variants. Phenotypic features included developmental delay/ID in 86/87 (99%), seizures in 71/86 (83%) and multiple comorbidities. Generalized seizures predominated including myoclonic seizures and absence seizures (both 46/70, 66%), absence with eyelid myoclonia (17/70, 24%), and atonic seizures (30/70, 43%). Males had more severe developmental impairment; females had epilepsy more frequently, and varied from unaffected to severely affected. All NEXMIF pathogenic variants led to a premature stop codon or were deleterious structural variants. Most arose de novo, although X-linked segregation occurred for both sexes. Somatic mosaicism occurred in two males and a family with suspected parental mosaicism. Conclusion NEXMIF encephalopathy is an X-linked, generalized developmental and epileptic encephalopathy characterized by myoclonic-atonic epilepsy overlapping with eyelid myoclonia with absence. Some patients have developmental encephalopathy without epilepsy. Males have more severe developmental impairment. NEXMIF encephalopathy arises due to loss-of-function variants

Genetic and phenotypic spectrum associated with IFIH1 gain-of-function

IFIH1 gain-of-function has been reported as a cause of a type I interferonopathy encompassing a spectrum of autoinflammatory phenotypes including Aicardi–Goutières syndrome and Singleton Merten syndrome. Ascertaining patients through a European and North American collaboration, we set out to describe the molecular, clinical and interferon status of a cohort of individuals with pathogenic heterozygous mutations in IFIH1. We identified 74 individuals from 51 families segregating a total of 27 likely pathogenic mutations in IFIH1. Ten adult individuals, 13.5% of all mutation carriers, were clinically asymptomatic (with seven of these aged over 50 years). All mutations were associated with enhanced type I interferon signaling, including six variants (22%) which were predicted as benign according to multiple in silico pathogenicity programs. The identified mutations cluster close to the ATP binding region of the protein. These data confirm variable expression and nonpenetrance as important characteristics of the IFIH1 genotype, a consistent association with enhanced type I interferon signaling, and a common mutational mechanism involving increased RNA binding affinity or decreased efficiency of ATP hydrolysis and filament disassembly rate

The direct effect of platelets on EPCs functional properties and its comparison to the platelets’ indirect effect.

<p><b>A.</b> The average number of colonies per field ± SE in EPCs cultured with vs. without platelets, p<0.05, n = 13 (Wilcoxon matched-pairs signed-rank test). The capacity to form colonies was higher in EPCs cultured with platelets compared to EPCs cultured alone. <b>B.</b> Culture viability expressed as OD (560 nm) ± SE in EPCs cultured with vs. without platelets, p<0.05, n = 11 (Wilcoxon matched-pairs signed-rank test). EPCs cultured with platelets have enhanced culture viability. <b>C.</b> FACS analysis of the average number of Tie-2 expressing cells ± SE in EPCs cultured with vs. without platelets, p<0.05, n = 7 (Wilcoxon matched-pairs signed-rank test. A higher percent of Tie-2 expressing cells appear in EPCs cultured with platelets compared to EPCs cultured alone. D–F Direct vs indirect effect of platelets on EPCs ability to form colonies (D), culture viability (E) and the expression of Tie-2(F), for n = 13 or 11 or 7 respectively, p = NS for all. There was no significant difference in any of the tested parameters in EPCs incubated with platelets directly vs. indirectly.</p

bFGF inhibition and its effect on EPCs differentiation.

<p><b>A.</b> The average number of colonies per field ± SE in EPCs cultured with platelets compared to EPCs cultured with platelets and FGF inhibitor or alone, P<0.05, n = 23 (Friedman test followed by Wilcoxon matched-pairs signed-rank test) The ability to form colonies was higher in EPCs cultured with platelets compared to EPCs cultured alone or with platelets and FGF inhibitor. <b>B–C.</b> FACS analysis of the average number of VE-cadherin (A) and Tie-2 (B) expressing cells ± SE, p<0.05, n = 11 for A, p<0.05 n = 10 for B. EPCs cultured with platelets have a higher proportion of Tie-2 and VE-cadherin expressing cells compared to EPCs cultured alone or with platelets and bFGF inhibitor.</p

The indirect effect of platelets on EPCs’ functional properties.

<p><b>A.</b> The average number of colonies per field ± SE in EPCs cultured with vs. without platelets, p<0.05, n = 13 (Wilcoxon matched-pairs signed-rank test). The capacity to form colonies was higher in EPCs cultured with platelets compared to EPCs cultured alone<b>. B.</b> Culture viability expressed as OD (560 nm) ± SE in EPCs cultured with vs. without platelets, p<0.05, n = 11 (Wilcoxon matched-pairs signed-rank test). EPCs cultured with platelets have enhanced culture viability. <b>C.</b> FACS analysis of the average number of Tie-2 expressing cells ± SE in EPCs cultured with vs. without platelets, p<0.05, n = 7 (Wilcoxon matched-pairs signed-rank test. A higher percent of Tie-2 expressing cells appear in EPCs cultured with platelets compared to EPCs cultured alone. <b>D.</b> Representative EPC colonies with platelets (right) compared to EPCs cultured alone (left). <b>E.</b> FACS analysis representative figure of Tie-2 expressing cells.</p

PDGF and FGF protein levels on EPC-PLT supernatant and relative PDGF B/C mRNA levels in EPCs following co incubation with platelets.

<p><b>A–B.</b> PDGF(A) and FGF(B) levels expressed as pg/ml ± SE in supernatants of EPCs cultured with vs. without platelets, n = 11, p<0.05 for A, n = 5 p = NS for B (Wilcoxon matched-pairs signed-rank test). PDGF levels were significantly higher in EPCs cultured with platelets compared to EPCs cultured alone. There were no significant differences in FGF levels between the two groups. <b>C–D.</b> PDGFC(C) and PDGFB(D) relative expression appears as AU ± SE in EPCs cultured with vs. without platelets, n = 6 p<0.05 for A, n = 8, p = NS for B (Wilcoxon matched-pairs signed-rank test). PDGFC mRNA levels were significantly higher in EPCs cultured with platelets compared to EPCs cultured alone (C). There were no significant differences in PDGFB levels between the two groups (D).</p

PDGF inhibition and its effect on EPCs functional properties.

<p><b>A.</b> The average number of colonies per field ± SE in EPCs cultured with platelets compared to EPCs cultured with platelets and PDGF inhibitor or alone, n = 23, p<0.05, p<0.001. (Friedman test followed by Wilcoxon matched-pairs signed-rank test) The ability to form colonies was higher in EPCs cultured with platelets compared to EPCs cultured alone or with platelets and PDGF inhibitor. <b>B.</b> Culture viability expressed as OD (560 nm) ± SE in EPCs cultured with platelets compared to EPCs cultured with platelets and PDGF inhibitor or alone p<0.05, n = 11(Friedman test followed by Wilcoxon matched-pairs signed-rank test). EPCs cultured with platelets had greater culture viability compared to EPCs cultured with platelets and PDGF inhibitor or alone<b>. C–D</b> FACS analysis expressed as the average number of VE-cadherin (C) and Tie-2(D) expressing cells ± SE in EPCs cultured with platelets compared to EPCs cultured with platelets and PDGF inhibition or alone, p<0.05, n = 8 for C, p<0.05, n = 11 for D (Friedman test followed by Wilcoxon matched-pairs signed-rank test)<b>.</b> EPCs cultured with platelets have a higher percent of VE-cadherin (C) and Tie-2(D) expressing cells compared to EPCs cultured alone or with platelets and PDGF inhibitor. <b>E.</b> Representative EPC colonies with platelets (center) compared to EPCs cultured alone (left) or with platelets and PDGF inhibitor (right). <b>F.</b> FACs analysis representative figure of VE-cadherin expressing cells in EPCs cultured with platelets with or without PDGF inhibitor.</p