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Life Sciences
Biomedical Engineering/Biotechnology
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Article
Open AccessDeciphering spatial domains from spatial multi-omics with SpatialGlue
Advances in spatial omics technologies now allow multiple types of data to be acquired from the same tissue slice. To realize the full potential of such data, we need spatially informed methods for data integr...
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Author Correction: Prime editing using CRISPR-Cas12a and circular RNAs in human cells
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Prime editing using CRISPR-Cas12a and circular RNAs in human cells
Genome editing with prime editors based on CRISPR-Cas9 is limited by the large size of the system and the requirement for a G/C-rich protospacer-adjacent motif (PAM) sequence. Here, we use the smaller Cas12a p...
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Open AccessSequencing by avidity enables high accuracy with low reagent consumption
We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of step** along a DNA template and that of identifying each nucleotide within the template. Nucleotide identifica...
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A genetically encoded sensor measures temporal oxytocin release from different neuronal compartments
Oxytocin (OT), a peptide hormone and neuromodulator, is involved in diverse physiological and pathophysiological processes in the central nervous system and the periphery. However, the regulation and functiona...
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Exploring the value of a global gene drive project registry
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Open AccessRS-FISH: precise, interactive, fast, and scalable FISH spot detection
Fluorescent in-situ hybridization (FISH)-based methods extract spatially resolved genetic and epigenetic information from biological samples by detecting fluorescent spots in microscopy images, an often challe...
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MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells
Rigorously comparing gene expression and chromatin accessibility in the same single cells could illuminate the logic of how coupling or decoupling of these mechanisms regulates fate commitment. Here we present...
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Inferring gene expression from cell-free DNA fragmentation profiles
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles fr...
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Open AccessPopulation genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement
Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. ...
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Author Correction: A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis
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Open AccessImaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography
Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-...
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Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA
Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we de...
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Field trial demonstrating phytoremediation of the military explosive RDX by XplA/XplB-expressing switchgrass
The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a major component of munitions, is used extensively on military training ranges. As a result, widespread RDX pollution in groundwater and aquifers i...
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Genome-wide specificity of prime editors in plants
Although prime editors (PEs) have the potential to facilitate precise genome editing in therapeutic, agricultural and research applications, their specificity has not been comprehensively evaluated. To provide...
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High-efficiency prime editing with optimized, paired pegRNAs in plants
Prime editing (PE) applications are limited by low editing efficiency. Here we show that designing prime binding sites with a melting temperature of 30 °C leads to optimal performance in rice and that using tw...
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A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis
Complex biological processes such as embryogenesis require precise coordination of cell differentiation programs across both space and time. Using protein-fusion fluorescent reporters and four-dimensional live...
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Spatially resolved transcriptomics in neuroscience
One major challenge in neuroscience is to gain a systematic understanding of the extraordinary diversity of brain cell types and how they contribute to brain function. Spatially resolved transcriptomics holds ...
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A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells
Nine dogs with hemophilia A were treated with adeno-associated viral (AAV) gene therapy and followed for up to 10 years. Administration of AAV8 or AAV9 vectors expressing canine factor VIII (AAV-cFVIII) correc...
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Precise, predictable multi-nucleotide deletions in rice and wheat using APOBEC–Cas9
Short insertions and deletions can be produced in plant genomes using CRISPR–Cas editors, but reliable production of larger deletions in specific target sites has proven difficult to achieve. We report the dev...
