Description and evaluation of aerosol in UKESM1 and HadGEM3-GC3.1 CMIP6 historical simulations

We document and evaluate the aerosol schemes as implemented in the physical and Earth system models, HadGEM3-GC3.1 (GC3.1) and UKESM1, which are contributing to the 6th Coupled Model Intercomparison Project (CMIP6). The simulation of aerosols in the present-day period of the historical ensemble of these models is evaluated against a range of observations. Updates to the aerosol microphysics scheme are documented as well as differences in the aerosol representation between the physical and Earth system configurations. The additional Earth-system interactions included in UKESM1 leads to differences in the emissions of natural aerosol sources such as dimethyl sulfide, mineral dust and organic aerosol and subsequent evolution of these species in the model. UKESM1 also includes a stratospheric-tropospheric chemistry scheme which is fully coupled to the aerosol scheme, while GC3.1 employs a simplified aerosol chemistry mechanism driven by prescribed monthly climatologies of the relevant oxidants. Overall, the simulated speciated aerosol mass concentrations compare reasonably well with observations. Both models capture the negative trend in sulfate aerosol concentrations over Europe and the eastern United States of America (US) although the models tend to underestimate the sulfate concentrations in both regions. Interactive emissions of biogenic volatile organic compounds in UKESM1 lead to an improved agreement of organic aerosol over the US. Simulated dust burdens are similar in both models despite a 2-fold difference in dust emissions. Aerosol optical depth is biased low in dust source and outflow regions but performs well in other regions compared to a number of satellite and ground-based retrievals of aerosol optical depth. Simulated aerosol number concentrations are generally within a factor of 2 of the observations with both models tending to overestimate number concentrations over remote ocean regions, apart from at high latitudes, and underestimate over Northern Hemisphere continents. Finally, a new primary marine organic aerosol source is implemented in UKESM1 for the first time. The impact of this new aerosol source is evaluated. Over the pristine Southern Ocean, it is found to improve the seasonal cycle of organic aerosol mass and cloud droplet number concentrations relative to GC3.1 although underestimations in cloud droplet number concentrations remain. This paper provides a useful characterization of the aerosol climatology in both models facilitating the understanding of the numerous aerosol-climate interaction studies that will be conducted as part of CMIP6 and beyond

Functional genomics analysis of Phelan-McDermid syndrome 22q13 region during human neurodevelopment

Phelan-McDermid syndrome (PMS) is a neurodevelopmental disorder characterized by varying degrees of intellectual disability, severely delayed language development and specific facial features, and is caused by a deletion within chromosome 22q13.3. SHANK3, which is located at the terminal end of this region, has been repeatedly implicated in other neurodevelopmental disorders and deletion of this gene specifically is thought to cause much of the neurologic symptoms characteristic of PMS. However, it is still unclear to what extent SHANK3 deletions contribute to the PMS phenotype, and what other genes nearby are causal to the neurologic disease. In an effort to better understand the functional landscape of the PMS region during normal neurodevelopment, we assessed RNA-sequencing (RNA-seq) expression data collected from post-mortem brain tissue from developmentally normal subjects over the course of prenatal to adolescent age and analyzed expression changes of 65 genes on 22q13. We found that the majority of genes within this region were expressed in the brain, with ATNX10, MLC1, MAPK8IP2, and SULT4A1 having the highest overall expression. Analysis of the temporal profiles of the highest expressed genes revealed a trend towards peak expression during the early post-natal period, followed by a drop in expression later in development. Spatial analysis revealed significant region specific differences in the expression of SHANK3, MAPK8IP2, and SULT4A1. Region specific expression over time revealed a consistently unique gene expression profile within the cerebellum, providing evidence for a distinct developmental program within this region. Exon-specific expression of SHANK3 showed higher expression within exons contributing to known brain specific functional isoforms. Overall, we provide an updated roadmap of the PMS region, implicating several genes and time periods as important during neurodevelopment, with the hope that this information can help us better understand the phenotypic heterogeneity of PMS.Pattern Recognition and Bioinformatic

Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism.

BackgroundAutism spectrum disorder (ASD) involves complex genetics interacting with the perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome.ResultsWe use whole genome bisulfite sequencing in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene, LOC105373085, renamed NHIP. Out of 134 differentially methylated regions associated with ASD in placental samples, a cluster at 22q13.33 corresponds to a 118-kb hypomethylated block that replicates in two additional cohorts. Within this locus, NHIP is functionally characterized as a nuclear peptide-encoding transcript with high expression in brain, and increased expression following neuronal differentiation or hypoxia, but decreased expression in ASD placenta and brain. NHIP overexpression increases cellular proliferation and alters expression of genes regulating synapses and neurogenesis, overlapping significantly with known ASD risk genes and NHIP-associated genes in ASD brain. A common structural variant disrupting the proximity of NHIP to a fetal brain enhancer is associated with NHIP expression and methylation levels and ASD risk, demonstrating a common genetic influence.ConclusionsTogether, these results identify and initially characterize a novel environmentally responsive ASD risk gene relevant to brain development in a hitherto under-characterized region of the human genome

Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism

Abstract Background Autism spectrum disorder (ASD) involves complex genetics interacting with the perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome. Results We use whole genome bisulfite sequencing in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene, LOC105373085, renamed NHIP. Out of 134 differentially methylated regions associated with ASD in placental samples, a cluster at 22q13.33 corresponds to a 118-kb hypomethylated block that replicates in two additional cohorts. Within this locus, NHIP is functionally characterized as a nuclear peptide-encoding transcript with high expression in brain, and increased expression following neuronal differentiation or hypoxia, but decreased expression in ASD placenta and brain. NHIP overexpression increases cellular proliferation and alters expression of genes regulating synapses and neurogenesis, overlapping significantly with known ASD risk genes and NHIP-associated genes in ASD brain. A common structural variant disrupting the proximity of NHIP to a fetal brain enhancer is associated with NHIP expression and methylation levels and ASD risk, demonstrating a common genetic influence. Conclusions Together, these results identify and initially characterize a novel environmentally responsive ASD risk gene relevant to brain development in a hitherto under-characterized region of the human genome.http://deepblue.lib.umich.edu/bitstream/2027.42/173873/1/13059_2022_Article_2613.pd

SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research

The Simons Foundation Autism Research Initiative (SFARI) has launched SPARKForAutism. org, a dynamic platform that is engaging thousands of individuals with autism spectrum disorder (ASD) and connecting them to researchers. By making all data accessible, SPARK seeks to increase our understanding of ASD and accelerate new supports and treatments for ASD