Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres

Nanopore long-read genome sequencing is emerging as a potential approach for the study of genomes including long repetitive elements like telomeres. Here, we report extensive basecalling induced errors at telomere repeats across nanopore datasets, sequencing platforms, basecallers, and basecalling models. We found that telomeres which are represented by (TTAGGG)n and (CCCTAA)n repeats in many organisms were frequently miscalled (~40-50% of reads) as (TTAAAA)n, or as (CTTCTT)n and (CCCTGG)n repeats respectively in a strand-specific manner during nanopore sequencing. We showed that this miscalling is likely caused by the high similarity of current profiles between telomeric repeats and these repeat artefacts, leading to mis-assignment of electrical current profiles during basecalling. We further demonstrated that tuning of nanopore basecalling models, and selective application of the tuned models to telomeric reads led to improved recovery and analysis of telomeric regions, with little detected negative impact on basecalling of other genomic regions. Our study thus highlights the importance of verifying nanopore basecalls in long, repetitive, and poorly defined regions of the genome, and showcases how such artefacts in regions like telomeres can potentially be resolved by improvements in nanopore basecalling models.

Validity, reliability and viability of pre-school educators’ use of early years toolbox early numeracy

There is need and opportunity for assessments that support quick and playful – yet also accurate, rigorous and developmentally sensitive – appraisals of early numeracy. Ideally, these should be accessible to those who have opportunity to support children’s learning development and ultimately shift children’s trajectories. The iPad-based Early Years Toolbox (EYT) Early Numeracy assessment was developed and evaluated to determine its validity and reliability, and appropriateness of use by researchers and preschool educators. Results from two studies with 246 children aged 3–5 years indicated the following: construct validity and internal consistency, concurrent validity with established measures, developmental sensitivity, test–retest reliability and highly comparable results whether used by a researcher or an educator. This yields a brief and playful assessment of early numeracy and a potential approach to develop broad-use early years assessments.

Nanotechnology-Based Weapons: A Potential Approach for COVID-19

In the last few decades, viral infections have caused a greater number of health constraints worldwide. This havoc has created challenges for the healthcare system. Since the pandemic began, COVID-19 has killed more than 2.5 million people across the world. We are still witnessing deaths daily due to the deadly virus SARS-CoV-2 which is the causative agent for COVID-19. Thus, there is an increasing concern about finding an apt way to control the spread of this virus. Recently, the application of nanotechnology-based approaches has emerged as a ground-breaking step in the medical sector owing to their potential for accurate diagnosis and specific treatment in a wide range of health problems, including viral diseases. Therefore, the implementation of nanotechnology can be an articulate strategy to confront the rising distress of COVID-19. The present review particularly emphasizes the perception of several nanoformulation-based approaches as an appropriate means to safeguard mankind against COVID-19.