Brief Report: Attenuated Emotional Suppression of the Attentional Blink in Autism Spectrum Disorder: Another Non-Social Abnormality?

Twenty-five individuals with Autism Spectrum Disorder and 25 typically developed individuals participated in an Attentional Blink paradigm to determine whether emotional words would capture attention similarly in the two groups. Whilst the emotionality of words facilitated attention in typical comparison participants, this effect was attenuated in the ASD group. The magnitude of the emotional modulation of attention in ASD also correlated significantly with participants’ VIQ, which was not observed for the comparison group. Together these observations replicate and extend the findings of Corden et al. (J Autism Develop Disord 38:1072–1080, 2008) and implicate abnormalities in emotional processes outside the broader context of social cognition in ASD. We discuss our findings in relation to possible abnormalities in amygdala function that may underlie the disorder

Infertility treatment outcome in sub groups of obese population

<p>Abstract</p> <p>Background</p> <p>Obesity is a common disorder with a negative impact on IVF treatment outcome. It is not clear whether morbidly obese women (BMI >= 35 kg/m2) respond to treatment differently as compared to obese women (BMI = 30–34.9 kg/m2) in IVF. Our aim was to compare the outcome of IVF or ICSI treatments in obese patients to that in morbidly obese patients.</p> <p>Methods</p> <p>This retrospective cohort study was conducted in a tertiary care centre. Patients inclusion criteria were as follows; BMI ≥ 30, age 20–40 years old, first cycle IVF/ICSI treatment with primary infertility and long follicular pituitary down regulation protocol.</p> <p>Results</p> <p>A total of 406 obese patients (group A) and 141 morbidly obese patients (group B) satisfied the inclusion criteria. Average BMI was 32.1 ± 1.38 kg/m2 for group A versus 37.7 ± 2.99 kg/m²for group B. Patient age, cause of infertility, duration of stimulation, fertilization rate, and number of transferred embryos were similar in both groups. Compared to group A, group B had fewer medium size and mature follicles (14 vs. 16), fewer oocytes collected (7 vs. 9) and required higher doses of HMG (46.2 vs. 38.5 amps). There was also a higher cancellation rate in group B (28.3% vs. 19%) and lower clinical pregnancy rate per started cycle (19.9% vs. 28.6%).</p> <p>Conclusion</p> <p>In a homogenous infertile and obese patient population stratified according to their BMI, morbid obesity is associated with unfavorable IVF/ICSI cycle outcome as evidenced by lower pregnancy rates. It is recommended that morbidly obese patients undergo appropriate counseling before the initiation of this expensive and invasive therapy.</p

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development

The benefit of directly comparing autism and schizophrenia for revealing mechanisms of social cognitive impairment

Autism and schizophrenia share a history of diagnostic conflation that was not definitively resolved until the publication of the DSM-III in 1980. Though now recognized as heterogeneous disorders with distinct developmental trajectories and dissociative features, much of the early nosological confusion stemmed from apparent overlap in certain areas of social dysfunction. In more recent years, separate but substantial literatures have accumulated for autism and schizophrenia demonstrating that abnormalities in social cognition directly contribute to the characteristic social deficits of both disorders. The current paper argues that direct comparison of social cognitive impairment can highlight shared and divergent mechanisms underlying pathways to social dysfunction, a process that can provide significant clinical benefit by informing the development of tailored treatment efforts. Thus, while the history of diagnostic conflation between autism and schizophrenia may have originated in similarities in social dysfunction, the goal of direct comparisons is not to conflate them once again but rather to reveal distinctions that illuminate disorder-specific mechanisms and pathways that contribute to social cognitive impairment

GENCODE 2025: reference gene annotation for human and mouse

Data availability: A new GENCODE release is produced up to four times each year for both human and mouse. Each release is made freely available immediately upon release from the Ensembl website (https://www.ensembl.org) and the GENCODE webportal (https//www.gencodegenes.org), with a release on the UCSC Genome Browser shortly after that (https://genome.ucsc.edu/). GENCODE is currently the default annotation in both genome browsers, and is embedded in numerous genomics and clinical projects. The current human release is GENCODE 47, and the current mouse release is GENCODE M36 (October 2024). Additional information and previous releases can be found at https//www.gencodegenes.org. MANE annotations are available from the Ensembl and RefSeq NCBI websites and can be viewed on both the Ensembl and UCSC genome browsers. To expedite public access to updated annotation between releases, all annotation changes are made freely available within 24 h via the ‘GENCODE Annotation Updates’ Track Hub, accessed at both the Ensembl and UCSC genome browsers. GENCODE has been designated a Global Core Biodata Resource by the Global Biodata Coalition. GENCODE produces the human and mouse gene annotation for the Ensembl project, in collaboration with Ensembl. Human 47 and mouse M36 are contained within Ensembl release e113. Programmatic access to the GENCODE gene sets is possible via the extensive Ensembl Perl API and the language-agnostic Ensembl REST API (50). Programmatic access facilitates advanced genome-wide analysis such as retrieval of supporting features and associated gene trees. Examples of REST endpoint usage and starter scripts in different languages are at https://rest.ensembl.org. Other interfaces include the Ensembl FTP site (ftp://ftp.ensembl.org/pub/), which includes gene sets in GFF3, Genbank and GTF formats and full download of the complete Ensembl databases. GENCODE-specific training materials and GENCODE-focused workshops from the Ensembl Outreach team are available via the Ensembl Training portal (http://training.ensembl.org) and EMBL-EBI (https://www.ebi.ac.uk/training/on-demand), and are regularly presented at online and in-person training events. Further information on the results of the GENCODE CLS pipeline to produce a collection of full-length high-quality transcripts—including access to the human and mouse master tables of transcript models prior to full annotation—is available here: https://github.com/guigolab/gencode-cls-master-table. All raw transcriptomics data produced by GENCODE to support the CLS work have been uploaded to the ENCODE data repository (see https://www.encodeproject.org/about/data-access/) and will be made publicly available as part of a manuscript describing this work, currently in preparation. Our resources are freely available at our web portal, www.gencodegenes.org, and via the Ensembl (https://www.ensembl.org) and UCSC genome browsers (https://genome.ucsc.edu/).GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result. Meanwhile, we are incorporating data from state-of-the-art proteomics and Ribo-seq experiments to fine-tune our annotation of translated sequences, while further insights into function can be gained from multi-genome alignments that grow richer as more species’ genomes are sequenced. Such methodologies are combined into a fully integrated annotation workflow. However, the increasing complexity of our resources can present usability challenges, and we are resolving these with the creation of filtered genesets such as MANE Select and GENCODE Primary. The next challenge is to propagate annotations throughout multiple human and mouse genomes, as we enter the pangenome era. Our resources are freely available at our web portal www.gencodegenes.org, and via the Ensembl and UCSC genome browsers.National Human Genome Research Institute of the National Institutes of Health [U24HG007234, U24HG011451]; Wellcome Trust [WT222155/Z/20/Z]; European Molecular Biology Laboratory; National Science Center [2021/42/E/NZ2/00434 to B.U.-R.]. Funding for open access charge: National Institutes of Health

GENCODE: reference annotation for the human and mouse genomes in 2023

Data availability: No new data were generated or analysed in support of this research.Copyright © The Author(s) 2022. GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.National Human Genome Research Institute of the National Institutes of Health [U41HG007234, R01HG004037]; Wellcome Trust [WT222155/Z/20/Z]; European Molecular Biology Laboratory. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Funding for open access charge: National Institutes of Health

Regulation of nuclear import during differentiation; The IMP alpha gene family and spermatogenesis

Access to nuclear genes in eukaryotes is provided by members of the importin (IMP) superfamily of proteins, which are of alpha- or beta-types, the best understood nuclear import pathway being mediated by a heterodimer of an IMP alpha and IMP beta1. IMP alpha recognises specific targeting signals on cargo proteins, while IMP beta1 mediates passage into, and release within, the nucleus by interacting with other components of the transport machinery, including the monomeric guanine nucleotide binding protein Ran. In this manner, hundreds of different proteins can be targeted specifically into the nucleus in a tightly regulated fashion. The IMP alpha gene family has expanded during evolution, with only a single IMP alpha (Srp1p) gene in budding yeast, and three (IMP alpha1, 2/pendulin and 3) and five (IMP alpha1, -2, -3, -4 and -6) IMP alpha genes in Drosophila melanogaster and mouse respectively, which fall into three phylogenetically distinct groups. The fact that IMP alpha3 and IMP alpha2 are only present in metazoans implies that they emerged during the evolution of multicellular animals to perform specialised roles in particular cells and tissues. This review describes what is known of the IMP alpha gene family in mouse and in D. melanogaster, including a comparitive examination of their mRNA expression profiles in a highly differentiated tissue, the testis. The clear implication of their highly regulated synthesis during the course of spermatogenesis is that the different IMP alphas have distinct expression patterns during cellular differentiation, implying tissue/cell type-specific roles