Search

Reproducibility is essential for the progress of research, yet achieving it remains elusive even in computational fields. Here, authors develop the rworkflows suite, making robust CI/CD workflows easy and freely accessible to all R package developers.

Removal of senescent cells rejuvenates lungs of aged mice. Here the authors show that elimination of senescent cells using either genetic or pharmacological means improves lung function and physical health in a mouse model of idiopathic pulmonary fibrosis (IPF), suggesting potential therapy for treatment of human IPF.

Cortex morphology varies with age, cognitive function, and in neurological and psychiatric diseases. Here the authors report 160 genome-wide significant associations with thickness, surface area and volume of the total cortex and 34 cortical regions from a GWAS meta-analysis in 22,824 adults.

Paul Pharoah, Joellen Schildkraut, Thomas Sellers and colleagues report a meta-analysis of genome-wide association studies for epithelial ovarian cancer and genotyping using the iCOGS array in 18,174 cases and 26,134 controls from 43 studies from the Ovarian Cancer Association Consortium. They identify three new ovarian cancer susceptibility loci, including one specific to the serous subtype, and their integrated molecular analysis of genes and regulatory regions at these loci suggests disease mechanisms.

Sequencing the transcriptomes of more than 100 species of alga yields new channelrhodopsins with promising properties for optogenetics. A far red–shifted channelrhodopsin, Chrimson, opens up new behavioral capabilities in Drosophila, and alongside a fast yet light-sensitive blue channelrhodopsin, Chronos, enables independent excitation of two neuronal populations in brain slices.

A study of SARS-CoV-2 variants examining their transmission, infectivity, and potential resistance to therapies provides insights into the biology of the Delta variant and its role in the global pandemic.

Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.

The X-ray crystal structure of the transmembrane portion of the human glucagon receptor, a class B G-protein-coupled receptor (GPCR), is solved in the presence of the antagonist MK-0893, with potential implications for the development of therapeutics that target other class B GPCRs.

Absorption lines of iron in the dayside atmosphere of an ultrahot giant exoplanet disappear after travelling across the nightside, showing that the iron has condensed during its travel.

An individual star at z = 1.49 is gravitationally lensed and highly magnified by a foreground galaxy cluster. Fluctuations in the star’s emission provide insight on the mass function of intracluster stars, compact objects and the presence of dark-matter subhaloes.

Very early observations of a type Ia supernova—from within one hour of explosion—show a red colour that develops and rapidly disappears. These data provide information on the initial explosion mechanism: surface nuclear burning on the white dwarf or extreme mixing of the nuclear burning process.

Peter Fraser and colleagues report a genome-wide analysis of transcription interactions involving the globin genes in mouse erythroid cells. They demonstrate that the transcription factor Klf1 mediates preferential co-associations between genes it regulates.

A retrobiosynthetic algorithm that relates known antibiotics by the similarities of their biosynthetic pathways to cluster them into distinct classes. Focusing on the telomycins helps to define the mechanism of action of this antibiotic class.

Spatial and temporal variations among individual human cell proteomes are comprehensively mapped across the cell cycle using proteomic imaging and transcriptomics.

A20, encoded by TNFAIP3, is a negative-feedback inhibitor of NF-κB. Grey and colleagues identify natural human variants of TNFAIP3, which lower A20 activity and increase autoinflammatory responses. These alleles were inherited by descendants of Denisovans who crossed the Wallace Line to inhabit Oceania.

Aminoadamantane compounds, delivered to cells via binding to viroporin channels, induce S-nitrosylation of the ACE2 protein, inhibiting binding to SARS-CoV-2 spike protein and viral infection.

By comparing neural responses to diverse visual stimuli measured with a standardized two-photon imaging pipeline, the authors reveal response specializations within the mouse visual cortex.

Photoabsorption is a fundamental process that leads to changes in the electron density in matter. Here, the authors show a direct measurement of the distribution of electron density when a cyclohexadine molecule is excited by pulsed UV radiation and probed by a time delayed X-ray pulse generated at LCLS.

The enzyme NEU1 negatively regulates lysosomal exocytosis in various cell types. Annunziata et al.show that mice deficient in NEU1 display Alzheimer’s disease-like pathology and that direct brain administration of NEU1 reduces pathology in an Alzheimer’s disease mouse model.

John Mattick and Yoshihide Hayashizaki and colleagues report the identifcation of tiny RNAs approximately 18 nucleotides in length that map near transcription start sites in human, chicken and Drosophila genomes. They call them transcription initiation RNAs (tiRNAs) and show that they associate with highly expressed transcripts and sites of RNA polymerase II binding.

A synthetic root microbial community rescues weak growth under low light and enhances immunity in Arabidopsis. Transcription factor MYC2 regulates both this coordination between rhizosphere and shoots and the growth/defence trade-off under low light conditions.

The authors examine present and past drivers of ungulate migratory behaviour, finding that current migratory ungulates are larger, more grass-dependent and live at higher latitudes on average than non-migrants, and that migration probably emerged after the rise of C₄ grasslands and increased seasonality towards the poles.

As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study uses RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages of the fruitfly. Among the results are scores of new genes, coding and non-coding transcripts, as well as splicing and editing events.

As modern humans migrated out of Africa, they encountered novel habitats. Here, Wedage et al. study the archaeological site of Fa-Hien Lena in Sri Lanka and show that the earliest human residents of the island practiced specialized hunting of small mammals, demonstrating ecological plasticity.

Novel antimalarial drugs are urgently needed to combat parasite drug resistance. Here, Vaidya et al. describe a new chemical class of potent antimalarial compounds that act by disrupting the parasite's sodium homeostasis.

Differentiating neutrophil functional states is difficult. Here the authors show, using single cell RNA-sequencing and trajectory analyses, that mouse neutrophils can be presented as a transcriptome continuum rather than discrete subsets, but are affected by inflammation to express distinct transcriptional states.

To reduce emissions, countries have committed to nationally determined contributions (NDCs). However, countries are also committed to the UN Sustainable Development Goals (SDGs) and this study looks at the synergies between meeting NDCs and SDGs.

Consolidated sediments in the Cascadia subduction zone may create conditions favourable for megathrust earthquake ruptures over long distances and close to the trench, according to analyses of seismic velocity of sediments from the region. Less-consolidated sediments instead may promote  aseismic slip of the plate boundary.

Most confirmed susceptibility variants for epithelial ovarian cancer lie in non-protein-coding sequences. Here Permuth-Wey and colleagues investigate variants in 3′ untranslated regions (UTRs) and uncover a new susceptibility locus.

Here, a combined experiment-theory framework based on different nano-imaging techniques and first-principle calculations is used to analyse the shapes of moiré patterns in twisted van der Waals structures, enabling an accurate description of the coupling between the atomically thin layers.

The daphnane diterpene orthoesters constitute a structurally fascinating family of natural products that exhibit remarkable and potent biological activities. A gateway strategy designed to provide general synthetic access to and biological evaluation of natural and non-natural daphnanes is described and used for yuanhuapin analogues.

Uniform processing and detailed annotation of human, worm and fly RNA-sequencing data reveal ancient, conserved features of the transcriptome, shared co-expression modules (many enriched in developmental genes), matched expression patterns across development and similar extent of non-canonical, non-coding transcription; furthermore, the data are used to create a single, universal model to predict gene-expression levels for all three organisms from chromatin features at the promoter.

Protein turnover underpins biology but is challenging to measure in vivo across the entire proteome. Here, the authors provide a comprehensive resource of protein turnover in mouse tissues and develop a visualization platform to analyze these data.

Could similar changes in SOD1 underlie both familial and sporadic ALS? Here, Bosco et al. find that wild-type SOD1 from sporadic ALS tissues shows conformational changes similar to those seen in familial ALS and that aberrant wild-type SOD1 can be pathogenic, potentially as a result of the same SOD1-dependent mechanism seen in familial ALS.

The authors investigate the broad-scale climatological and soil properties that co-vary with major axes of plant functional traits. They find that variation in plant size is attributed to latitudinal gradients in water or energy limitation, while variation in leaf economics traits is attributed to both climate and soil fertility including their interaction.

Analysis of plastic debris found in surface waters shows that lakes and reservoirs in densely populated and urbanized regions, as well as those with elevated deposition areas, are particularly vulnerable to plastic contamination.

Post-acute sequelae of SARS-CoV-2 (PASC) is still not well understood. Here the authors provide patient reported outcomes from 590 hospitalized COVID-19 patients and show association of PASC with higher respiratory SARS-CoV-2 load and circulating antibody titers, and in some an elevation in circulating fibroblast growth factor 21.

The huge amount of data generated in fields like neuroscience or finance calls for effective strategies that mine data to reveal underlying dynamics. Here Brunton et al.develop a data-driven technique to analyze chaotic systems and predict their dynamics in terms of a forced linear model.

Miniaturization of silicon transistors requires interconnects that can maintain low electrical resistivity. Here, resistivity is studied in anisotropic NbP as a function of crystal orientation as its size approaches the electron scattering length.

Transposable element (TE) bursts shape genome evolution but their origin remains unclear. Here, the authors show that a burst is restricted to only a few domesticated rice accessions and is associated with the acquisition of two TE variants, Ping16A and Ping16A_Stow, not the loss of TE silencing.

Humans have a capacity for hierarchical cognitive control—the ability to simultaneously control immediate actions while holding more abstract goals in mind. The authors show that neural oscillations establish dynamic communication networks within the frontal cortex and that these oscillations coordinate local neural activity with increasing cognitive control.

The interplay between amyloid and tau pathology in Alzheimer’s disease is still not well understood. Here, the authors show that amyloid-related increased in soluble p-tau is related to subsequent accumulation of tau aggregates and cognitive decline in early stage of the disease.

de Vries, Conomos, Singh and Nicholson et al. identify two additional loci associated with coronary artery calcification (ARSE and MMP16) via a genome-wide association study in 22,400 participants from multiple ancestral groups and prove that ARSE is a mediator of vascular smooth muscle cell calcification and phenotype switching.