Petabyte-scale innovations at the European Nucleotide Archive

Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets. Sequence repositories, which provide the feed for these data sets into the worldwide computational infrastructure, are challenged by the impact of these data volumes. The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis, interpretation and visualization of petabyte-scale data sets. We present here our new repository for next generation sequence data, a brief summary of contents of the ENA and provide details of major developments to submission pipelines, high-throughput rule-based validation infrastructure and data integration approaches

Phenotypic expression and outcomes in individuals with rare genetic variants of hypertrophic cardiomyopathy

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is caused by rare variants in sarcomere-encoding genes, but little is known about the clinical significance of these variants in the general population. OBJECTIVES: The goal of this study was to compare lifetime outcomes and cardiovascular phenotypes according to the presence of rare variants in sarcomere-encoding genes among middle-aged adults. METHODS: This study analyzed whole exome sequencing and cardiac magnetic resonance imaging in UK Biobank participants stratified according to sarcomere-encoding variant status. RESULTS: The prevalence of rare variants (allele frequency <0.00004) in HCM-associated sarcomere-encoding genes in 200,584 participants was 2.9% (n = 5,712; 1 in 35), and the prevalence of variants pathogenic or likely pathogenic for HCM (SARC-HCM-P/LP) was 0.25% (n = 493; 1 in 407). SARC-HCM-P/LP variants were associated with an increased risk of death or major adverse cardiac events compared with controls (hazard ratio: 1.69; 95% confidence interval [CI]: 1.38-2.07; P < 0.001), mainly due to heart failure endpoints (hazard ratio: 4.23; 95% CI: 3.07-5.83; P < 0.001). In 21,322 participants with both cardiac magnetic resonance imaging and whole exome sequencing, SARC-HCM-P/LP variants were associated with an asymmetric increase in left ventricular maximum wall thickness (10.9 ± 2.7 mm vs 9.4 ± 1.6 mm; P < 0.001), but hypertrophy (≥13 mm) was only present in 18.4% (n = 9 of 49; 95% CI: 9%-32%). SARC-HCM-P/LP variants were still associated with heart failure after adjustment for wall thickness (hazard ratio: 6.74; 95% CI: 2.43-18.7; P < 0.001). CONCLUSIONS: In this population of middle-aged adults, SARC-HCM-P/LP variants have low aggregate penetrance for overt HCM but are associated with an increased risk of adverse cardiovascular outcomes and an attenuated cardiomyopathic phenotype. Although absolute event rates are low, identification of these variants may enhance risk stratification beyond familial disease

Improvements to services at the European Nucleotide Archive

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe’s primary nucleotide sequence archival resource, safeguarding open nucleotide data access, engaging in worldwide collaborative data exchange and integrating with the scientific publication process. ENA has made significant contributions to the collaborative nucleotide archival arena as an active proponent of extending the traditional collaboration to cover capillary and next-generation sequencing information. We have continued to co-develop data and metadata representation formats with our collaborators for both data exchange and public data dissemination. In addition to the DDBJ/EMBL/GenBank feature table format, we share metadata formats for capillary and next-generation sequencing traces and are using and contributing to the NCBI SRA Toolkit for the long-term storage of the next-generation sequence traces. During the course of 2009, ENA has significantly improved sequence submission, search and access functionalities provided at EMBL–EBI. In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services

Stretchable Gold Nanomembrane Electrode with Ionic Hydrogel Skin-Adhesive Properties

Skin has a dynamic surface and offers essential information through biological signals originating from internal organs, blood vessels, and muscles. Soft and stretchable bioelectronics can be used in wearable machines for long-term stability and to continuously obtain distinct bio-signals in conjunction with repeated expansion and contraction with physical activities. While monitoring bio-signals, the electrode and skin must be firmly attached for high signal quality. Furthermore, the signal-to-noise ratio (SNR) should be high enough, and accordingly, the ionic conductivity of an adhesive hydrogel needs to be improved. Here, we used a chitosan-alginate-chitosan (CAC) triple hydrogel layer as an interface between the electrodes and the skin to enhance ionic conductivity and skin adhesiveness and to minimize the mechanical mismatch. For development, thermoplastic elastomer Styrene-Ethylene-Butylene-Styrene (SEBS) dissolved in toluene was used as a substrate, and gold nanomembranes were thermally evaporated on SEBS. Subsequently, CAC triple layers were drop-casted onto the gold surface one by one and dried successively. Lastly, to demonstrate the performance of our electrodes, a human electrocardiogram signal was monitored. The electrodes coupled with our CAC triple hydrogel layer showed high SNR with clear PQRST peaks

Injection-on-Skin Granular Adhesive for Interactive Human–Machine Interface

Realization of interactive human–machine interfaces (iHMI) is improved with development of soft tissue-like strain sensors beyond hard robotic exosuits, potentially allowing cognitive behavior therapy and physical rehabilitation for patients with brain disorders. Here, this study reports on a strain-sensitive granular adhesive inspired by the core–shell architectures of natural basil seeds for iHMI as well as human–metaverse interfacing. The granular adhesive sensor consists of easily fragmented hydropellets as a core and tissue-adhesive catecholamine layers as a shell, satisfying great on-skin injectability, ionic-electrical conductivity, and sensitive resistance changes through reversible yet robust cohesion among the hydropellets. Particularly, it is found that the ionic-electrical self-doping of the catecholamine shell on hydrosurfaces leads to a compact ion density of the materials. Based on these physical and electrical properties of the sensor, it is demonstrated that successful iHMI integration with a robot arm in both real and virtual environments enables robotic control by finger gesture and haptic feedback. This study expresses benefits of using granular hydrogel-based strain sensors for implementing on-skin writable bioelectronics and their bridging into the metaverse world. © 2023 Wiley-VCH GmbH.11Nsciescopu

The Promotion of Human Neural Stem Cells Adhesion Using Bioinspired Poly(norepinephrine) Nanoscale Coating

The establishment of versatile biomaterial interfaces that can facilitate cellular adhesion is crucial for elucidating the cellular processes that occur on biomaterial surfaces. Furthermore, biomaterial interfaces can provide physical or chemical cues that are capable of stimulating cellular behaviors by regulating intracellular signaling cascades. Herein, a method of creating a biomimetic functional biointerface was introduced to enhance human neural stem cell (hNSC) adhesion. The hNSC-compatible biointerface was prepared by the oxidative polymerization of the neurotransmitter norepinephrine, which generates a nanoscale organic thin layer, termed poly(norepinephrine) (pNE). Due to its adhesive property, pNE resulted in an adherent layer on various substrates, and pNE-coated biointerfaces provided a highly favorable microenvironment for hNSCs, with no observed cytotoxicity. Only a 2-hour incubation of hNSCs was required to firmly attach the stem cells, regardless of the type of substrate. Importantly, the adhesive properties of pNE interfaces led to micropatterns of cellular attachment, thereby demonstrating the ability of the interface to organize the stem cells. This highly facile surface-modification method using a biomimetic pNE thin layer can be applied to a number of suitable materials that were previously not compatible with hNSC technology