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Nature Biotechnology
Resumen/Descripción – provisto por la editorial en inglés
Nature Biotechnology is a monthly journal covering the science and business of biotechnology. It publishes new concepts in technology/methodology of relevance to the biological, biomedical, agricultural and environmental sciences as well as covers the commercial, political, ethical, legal, and societal aspects of this research. The first function is fulfilled by the peer-reviewed research section, the second by the expository efforts in the front of the journal. We provide researchers with news about business; we provide the business community with news about research developments.Palabras clave – provistas por la editorial
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Disponibilidad
| Institución detectada | Período | Navegá | Descargá | Solicitá |
|---|---|---|---|---|
| No detectada | desde jul. 2012 / hasta dic. 2023 | Nature.com |
Información
Tipo de recurso:
revistas
ISSN impreso
1087-0156
ISSN electrónico
1546-1696
Editor responsable
Springer Nature
País de edición
Reino Unido
Fecha de publicación
1996-
Cobertura temática
Tabla de contenidos
Epicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease
Anna B. Meier
; Dorota Zawada; Maria Teresa De Angelis; Laura D. Martens; Gianluca Santamaria; Sophie Zengerle; Monika Nowak-Imialek; Jessica Kornherr; Fangfang Zhang; Qinghai Tian; Cordula M. Wolf; Christian Kupatt; Makoto Sahara; Peter Lipp; Fabian J. Theis; Julien Gagneur; Alexander Goedel; Karl-Ludwig Laugwitz; Tatjana Dorn; Alessandra Moretti
<jats:title>Abstract</jats:title><jats:p>The epicardium, the mesothelial envelope of the vertebrate heart, is the source of multiple cardiac cell lineages during embryonic development and provides signals that are essential to myocardial growth and repair. Here we generate self-organizing human pluripotent stem cell-derived epicardioids that display retinoic acid-dependent morphological, molecular and functional patterning of the epicardium and myocardium typical of the left ventricular wall. By combining lineage tracing, single-cell transcriptomics and chromatin accessibility profiling, we describe the specification and differentiation process of different cell lineages in epicardioids and draw comparisons to human fetal development at the transcriptional and morphological levels. We then use epicardioids to investigate the functional cross-talk between cardiac cell types, gaining new insights into the role of IGF2/IGF1R and NRP2 signaling in human cardiogenesis. Finally, we show that epicardioids mimic the multicellular pathogenesis of congenital or stress-induced hypertrophy and fibrotic remodeling. As such, epicardioids offer a unique testing ground of epicardial activity in heart development, disease and regeneration.</jats:p>
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible
A relay velocity model infers cell-dependent RNA velocity
Shengyu Li; Pengzhi Zhang; Weiqing Chen; Lingqun Ye; Kristopher W. Brannan; Nhat-Tu Le; Jun-ichi Abe; John P. Cooke; Guangyu Wang
<jats:title>Abstract</jats:title><jats:p>RNA velocity provides an approach for inferring cellular state transitions from single-cell RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal kinetics from all cells in an scRNA-seq experiment, resulting in unpredictable performance in experiments with multi-stage and/or multi-lineage transition of cell states where the assumption of the same kinetic rates for all cells no longer holds. Here we present cellDancer, a scalable deep neural network that locally infers velocity for each cell from its neighbors and then relays a series of local velocities to provide single-cell resolution inference of velocity kinetics. In the simulation benchmark, cellDancer shows robust performance in multiple kinetic regimes, high dropout ratio datasets and sparse datasets. We show that cellDancer overcomes the limitations of existing RNA velocity models in modeling erythroid maturation and hippocampus development. Moreover, cellDancer provides cell-specific predictions of transcription, splicing and degradation rates, which we identify as potential indicators of cell fate in the mouse pancreas.</jats:p>
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
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Genetic medicines aim straight for the heart
Cormac Sheridan
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible
Data sharing in the age of deep learning
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible
Exploring tRNAs and their modifications and crosstalk using Nano-tRNAseq
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible
Xenotransplantation: how close are we?
Kathryn Aschheim; Laura DeFrancesco
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible
Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing
Morghan C. Lucas; Leszek P. Pryszcz; Rebeca Medina; Ivan Milenkovic; Noelia Camacho; Virginie Marchand; Yuri Motorin; Lluís Ribas de Pouplana; Eva Maria Novoa
<jats:title>Abstract</jats:title><jats:p>Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to <jats:italic>Saccharomyces cerevisiae</jats:italic> tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.</jats:p>
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible
DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins
Yu-Hang Xing; Rui Dong; Lukuo Lee; Shruthi Rengarajan; Nicolò Riggi; Gaylor Boulay; Miguel N. Rivera
<jats:title>Abstract</jats:title><jats:p>Intrinsically disordered regions (IDRs) in DNA-associated proteins are known to influence gene regulation, but their distribution and cooperative functions in genome-wide regulatory programs remain poorly understood. Here we describe DisP-seq (disordered protein precipitation followed by DNA sequencing), an antibody-independent chemical precipitation assay that can simultaneously map endogenous DNA-associated disordered proteins genome-wide through a combination of biotinylated isoxazole precipitation and next-generation sequencing. DisP-seq profiles are composed of thousands of peaks that are associated with diverse chromatin states, are enriched for disordered transcription factors (TFs) and are often arranged in large lineage-specific clusters with high local concentrations of disordered proteins and different combinations of histone modifications linked to regulatory potential. We use DisP-seq to analyze cancer cells and reveal how disordered protein-associated islands enable IDR-dependent mechanisms that control the binding and function of disordered TFs, including oncogene-dependent sequestration of TFs through long-range interactions and the reactivation of differentiation pathways upon loss of oncogenic stimuli in Ewing sarcoma.</jats:p>
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible
The scverse project provides a computational ecosystem for single-cell omics data analysis
Isaac Virshup; Danila Bredikhin; Lukas Heumos; Giovanni Palla; Gregor Sturm; Adam Gayoso; Ilia Kats; Mikaela Koutrouli; Philipp Angerer; Volker Bergen; Pierre Boyeau; Maren Büttner; Gokcen Eraslan; David Fischer; Max Frank; Justin Hong; Michal Klein; Marius Lange; Romain Lopez; Mohammad Lotfollahi; Malte D. Luecken; Fidel Ramirez; Jeffrey Regier; Sergei Rybakov; Anna C. Schaar; Valeh Valiollah Pour Amiri; Philipp Weiler; Galen Xing; Bonnie Berger; Dana Pe’er; Aviv Regev; Sarah A. Teichmann; Francesca Finotello; F. Alexander Wolf; Nir Yosef; Oliver Stegle; Fabian J. Theis;
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible
Challenges and solutions to advancing heath equity with medical devices
Kushal T. Kadakia; Vinay K. Rathi; Reshma Ramachandran; James L. Johnston; Joseph S. Ross; Sanket S. Dhruva
Palabras clave: Biomedical Engineering; Molecular Medicine; Applied Microbiology and Biotechnology; Bioengineering; Biotechnology.
Pp. No disponible