Search

A cross-reactive antibody and T cell response is identified in a large portion of patients with multisystem inflammatory syndrome in children.

The role of the nuclear lamina (NL) in chromatin architecture is still poorly understood. Here, the authors provide evidence that disruption of the NL in Drosophila cells leads to overall chromatin compaction and repositioning from the nuclear envelope, whereas lamina-associated regions become less compacted and transcription within them is increased.

This work presents Strainy, a long-read metagenome assembler that allows the identification of strain distributions and mutational patterns in environmental metagenomes.

The precise cell-type specific role of inhibitory interneurons in regulating sensory responses in the olfactory bulb is not known. Here, the authors report that removing GABAergic inhibition from one layer differentially affects response dynamics of the two main output cell types and changes odor mixture processing.

Complex structural variations and rearrangements in cancer are identified using long-read sequencing.

Applying thermal proteome profiling to acute B cell childhood leukemia cell lines combined with deep peptide fractionation and a graph-based clustering algorithm allows inference of functional proteoform groups and their association with drug response.

This Registered Report describes an extensive comparison of 22 near-infrared fluorescent proteins in vitro, in cultured mammalian cells, and in model animals, clarifying top performers in diverse biological settings.

This work introduces a wet lab and computational pipeline, Napu, for small variant calling and de novo assembly of Nanopore sequencing data, which leads to comparable performances to short-read sequencing and allows for large-scale long-read sequencing projects.

Several multi-cancer GWAS loci within the region encoding telomerase reverse transcriptase (TERT) have been identified. Here, the authors explore the locus within TERT intron 4, link it with a variable number tandem repeat (VNTR), and investigate its biological significance and role in cancer.

mBaoJin is a monomeric derivative of the bright and photostable green fluorescent protein StayGold. mBaoJin offers favorable photophysical properties for use in diverse protein tagging and subcellular labeling applications.

Long-read metagenomics offers a valuable approach for profiling bacterial communities. This work presents a long-read assembler, metaFlye, that specifically addresses the challenges of assembling metagenomes.

Which combination of current genome sequencing and assembly approaches results in high-quality, complete diploid genome assemblies is determined.

Magnetic resonance imaging combined with molecular reporters can visualise cellular functions in intact organisms. Here Mukherjeeet al. present a cellular imaging approach based on intracellular changes in water diffusion using human aquaporin 1 gene as a genetically encoded reporter for MRI.

Adipose stromal cells (ASC) have been shown to migrate to tumours and promote tumour growth. Using animal models and human tissue samples, the authors show here that ASC recruitment to prostate cancers is mediated by the chemokine CXCL1, which is secreted from tumour cells, and acts on CXCR1 on ASCs.

This work introduces a k-mer-based approach to customizing a pangenome reference, making it more relevant to a new sample of interest. This method enhances the accuracy of genotyping small variants and large structural variants.

Mammalian genomes are scattered with repetitive sequences, but their biology remains largely elusive. Here, the authors show that transcription can initiate from short tandem repetitive sequences, and that genetic variants linked to human diseases are preferentially found at repeats with high transcription initiation level.

A fluorescence-based sensor of PKA activity has increased brightness, dynamic range and signal-to-noise ratio over related sensors and is useful for visualizing kinase activity in HeLa cells, primary neurons and the cortex of awake mice.

What happens to histones during transcription is not well understood. Atomic force microscopy snapshots of RNA polymerase II (Pol II)-nucleosome complexes before, during and after transcription show the presence of looped transcriptional intermediates. In addition, a fraction of transcribed histones are remodeled to hexasomes, and the size of this fraction depends on the elongation rate of Pol II.

Metagenome sequencing can now distinguish closely related microbes using long reads and haplotype phasing.

A multiplex de Bruijn graph algorithm allows high-accuracy genome assembly from long, high-fidelity reads.

Regulatory T cells need to express a diverse T-cell-receptor repertoire to control pathogenic self-reactive T cells; here it is shown that repertoire diversification depends on the intronic Foxp3 enhancer CNS3 acting at the regulatory T-cell-precursor stage to induce T-cell-receptor responsiveness to low-strength signals.

Organoid avatars of colorectal cancer and its microenvironment model immune interactions and drug efficacy.

The PEPPER-Margin-DeepVariant pipeline achieves highly accurate variant calling using nanopore and other long-read sequencing data.

Flye improves the speed and accuracy of genome assembly by using repeat graphs to resolve repeat regions.

Sequence assemblies for the genomes of 16 widely used inbred laboratory mouse strains highlight considerable strain-specific haplotype variation and allow for the identification of regions with the greatest sequence diversity between strains.

Individual microbes in metagenomic samples are sequenced by assembly of barcoded short reads

An organic carbon decomposition model, calibrated with laboratory incubations, indicates a greater production rate of CO₂-C equivalents from waterlogged (compared to drained) permafrost soils, when the higher global warming potential of methane is factored in.

This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.

Trigonelline is identified as a human metabolite that can be used for NAD⁺ synthesis and is shown to improve muscle function in aged worms and mice.

Adam Rubin, Brook Barajas, Mayra Furlan-Magaril and colleagues studied dynamic chromatin across the genome of differentiating human skin keratinocytes, identifying both stable and reorganizing classes of transcriptional enhancers.

This Perspective describes the development and capabilities of SciPy 1.0, an open source scientific computing library for the Python programming language.

Using a high throughput, random bacterial peptide display approach applied to patient serum samples, Haynes, Kamath, Bozekowski et al identify the antigens and epitopes that elicit a SARS-CoV-2 humoral response. They identify differences depending on disease severity and further in silico analysis suggests decreased epitope signal for Q677P but not for D614G mutant SARSCoV-2 strains.

Integration of chemogenetics with quantitative behavioral assays and whole brain activity mapping reveal how distinct cerebellar regions influence activity during flexible behavioral learning. Integration of chemogenetics with quantitative behavioral assays and whole brain activity mapping reveal how distinct cerebellar regions influence activity during flexible behavioral learning