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10.1111/gcb.15577 | 35,724,816 | Abstract Human activity is affecting every ecosystem on Earth, with terrestrial biodiversity decreasing rapidly. Human influences materialize in the form of numerous, jointly acting factors, yet the experimental study of such joint impacts is not well developed. We identify the absence of a systematic ordering system o... | 10.1038/s41558-023-01628-1 | This article presents an approach for classifying global change factors that affect terrestrial ecosystems and the soil. |
10.1126/science.aay2832 | 104,291,708 | Soils underpin terrestrial ecosystem functions, but they face numerous anthropogenic pressures. Despite their crucial ecological role, we know little about how soils react to more than two environmental factors at a time. Here, we show experimentally that increasing the number of simultaneous global change factors (up ... | 10.1038/s41558-023-01628-1 | This paper uses a lab-based experiment to show that increasing the number of global change factors leads to progressively lower biodiversity and soil processes. |
10.1038/s41467-022-31936-7 | 130,232,738 | Abstract Biodiversity is crucial for the provision of ecosystem functions. However, ecosystems are now exposed to a rapidly growing number of anthropogenic pressures, and it remains unknown whether biodiversity can still promote ecosystem functions under multifaceted pressures. Here we investigated the effects of soil ... | 10.1038/s41558-023-01628-1 | This paper reports that high soil biodiversity cannot protect soils from the effects of an increasing number of global change factors. |
10.1017/cbo9780511817649 | 45,369,274 | Nobel laureate Robert Fogel's compelling study, first published in 2004, examines health, nutrition and technology over the last three centuries and beyond. Throughout most of human history, chronic malnutrition has been the norm. During the past three centuries, however, a synergy between improvements in productive te... | 10.1038/s41576-018-0012-3 | This book by Robert Fogel, a recipient of the Nobel Prize in Economics, documents the remarkable changes in human stature that followed the nutritional and demographic transitions and the contributions made by these improvements in health to human economic development. |
10.1257/089533003772034943 | 20,541,536 | The global demographic transition began around 1800 in Europe with declining mortality followed by declining fertility, trends which spread around the world and continue in this century. At the aggregate level, population size greatly increased, growth accelerated and declined with many countries now shrinking, and age... | 10.1038/s41576-018-0012-3 | This is an excellent summary of the changes occurring across the demographic transition, including analyses of causes and consequences and yet-to-be-resolved uncertainties. |
10.1073/pnas.0904280106 | 20,626,338 | The tumor suppressor protein p53 plays an important role in maternal reproduction in mice through transcriptional regulation of leukemia inhibitory factor (LIF), a cytokine crucial for blastocyst implantation. To determine whether these observations could be extended to humans, a list of single-nucleotide polymorphisms... | 10.1038/s41576-018-0012-3 | This paper is among the first to find that the genetic variants that increase cancer risk may also confer benefits to fertility by improving the ability of zygotes to implant in the endometrium to initiate pregnancy. |
10.1073/pnas.1612113114 | 42,570,817 | Epidemiological and genetic association studies show that genetics play an important role in the attainment of education. Here, we investigate the effect of this genetic component on the reproductive history of 109,120 Icelanders and the consequent impact on the gene pool over time. We show that an educational attainme... | 10.1038/s41576-018-0012-3 | This paper leverages Icelandic genomic data to estimate the direction of selection on educational attainment in a contemporary population: it is negative |
10.1073/pnas.0906199106 | 81,309,102 | Our aims were to demonstrate that natural selection is operating on contemporary humans, predict future evolutionary change for specific traits with medical significance, and show that for some traits we can make short-term predictions about our future evolution. To do so, we measured the strength of selection, estimat... | 10.1038/s41576-018-0012-3 | This is one of the papers that ignited interest in researching evolution in contemporary human populations. |
10.1126/science.aag0776 | 125,088,765 | Identifying genes under recent selection Evolutionary analyses aim to identify recent genetic changes that are likely to have been subject to selection. Field et al. present a method to identify such changes, the singleton density score, which they applied to over 3000 human genomes. Over the past ∼100 generations (200... | 10.1038/s41576-018-0012-3 | This paper proposes the singleton density score (SDS), a new measure to infer signatures of recent selection from contemporary genomes |
10.1126/science.aaz7015 | 132,927,464 | Another benefit of dietary fiber The gut microbiome can modulate the immune system and influence the therapeutic response of cancer patients, yet the mechanisms underlying the effects of microbiota are presently unclear. Spencer et al . add to our understanding of how dietary habits affect microbiota and clinical outco... | 10.1038/s41589-022-01017-3 | This study suggests that high dietary fiber intake improves responsiveness to immunotherapy via interplay with microbiota-derived production of the SCFA propionate |
10.1126/sciadv.abm8433 | 130,255,009 | Precise microscale patterning is a prerequisite to incorporate the emerging colloidal metal halide perovskite nanocrystals into advanced, integrated optoelectronic platforms for widespread technological applications. Current patterning methods suffer from some combination of limitations in patterning quality, versatili... | 10.1038/s41578-022-00522-0 | This study reports a universal method for the photolithographic patterning of perovskite nanocrystals based on ultraviolet light, resulting in PeLEDs with a record efficiency |
10.1002/adom.202101642 | 132,917,175 | Abstract Light sources with high color purity are promising for revolutionizing traditional displays because of their wide achievable color gamut, high contrast ratio, and good color saturation. The demand for next‐generation displays has driven the development of the optoelectronic materials with narrow linewidth. Unt... | 10.1038/s41578-022-00522-0 | This study presents a self-emissive RGB micro-PeLED array driven by microelectrodes that can dynamically show colourful Arabic numbers |
10.1126/science.1194637 | 20,828,539 | Primitive Origins for Microglia Microglia are the resident macrophages of the central nervous system and are associated with neurodegeneration and brain inflammatory diseases. Although the developmental origins of other tissue macrophage populations are well established, the origins of microglia remain controversial. G... | 10.1038/s41583-018-0057-5 | References 7 and 8 identify microglia as originating from yolk-sac-derived primitive macrophages |
10.1084/jem.20180247 | 41,647,924 | Peripherally derived macrophages infiltrate the brain after bone marrow transplantation and during central nervous system (CNS) inflammation. It was initially suggested that these engrafting cells were newly derived microglia and that irradiation was essential for engraftment to occur. However, it remains unclear wheth... | 10.1038/s41583-018-0057-5 | This study shows that microglial populations can be replaced with peripherally derived macrophages that maintain a unique identity and distinct functional role in the CNS compared with microglia |
10.1182/blood.v91.10.3702 | 122,047,453 | Abstract The ets family transcription factor PU.1 is expressed in monocytes/macrophages, neutrophils, mast cells, B cells, and early erythroblasts, but not in T cells. We have recently shown that PU.1 gene disruption results in mice with no detectable monocytes/macrophages and B cells but T-cell development is retained... | 10.1038/s41583-018-0057-5 | This study demonstrates that PU.1 gene disruption affects a number of developmentally regulated haematopoietic processes and myeloid development |
10.1126/scitranslmed.aaf6295 | 41,622,095 | C3 deficiency protects against hippocampal neurodegeneration and cognitive decline in aged APP/PS1 mice despite abundant Aβ plaques. | 10.1038/s41583-018-0057-5 | References 91–93 provide evidence for the role of complement in synaptic elimination by microglia |
10.1073/pnas.1710311114 | 125,272,139 | Variants in the gene encoding the triggering receptor expressed on myeloid cells 2 (TREM2) were recently found to increase the risk for developing Alzheimer’s disease (AD). In the brain, TREM2 is predominately expressed on microglia, and its association with AD adds to increasing evidence implicating a role for the inn... | 10.1038/s41583-018-0057-5 | References 182 and 183 connect TREM2 and ApoE signalling with exacerbation of neuroinflammation and tauopathy |
10.1002/adma.201804598 | 83,327,531 | Abstract Soft robots are an interesting alternative for classic rigid robots in applications requiring interaction with organisms or delicate objects. Elastic inflatable actuators are one of the preferred actuation mechanisms for soft robots since they are intrinsically safe and soft. However, these pneumatic actuators ... | 10.1038/s41586-021-04138-2 | This article describes an approach for embedding hardware intelligence into a robot with multiple, non-linear soft actuators, which are programmed via their structural sequence and passive flow restrictors |
10.1126/scirobotics.abd7338 | 37,932,528 | Continued development of untethered insect-scale robots will require codesigned power and actuation strategies. | 10.1038/s41586-021-04138-2 | This brief article highlights emerging robotic technologies that make use of combined, codesigned power-actuation systems containing chemical fuels to achieve high energy densities and untethered movement |
10.1088/2399-7532/ab8e95 | 60,485,597 | Abstract The development of multifunctional materials and structures is receiving increasing interest for many applications and industries; it is a promising way to increase system-wide efficiency and improve the ability to meet environmental targets. However, quantifying the advantages of a multifunctional solution ov... | 10.1038/s41586-021-04138-2 | This work discusses how the advantages of multifunctional systems over monofunctional systems can be determined mathematically and used to make design decisions |
10.1038/s41586-022-04569-5 | 136,034,041 | Abstract There is strong evidence of brain-related abnormalities in COVID-19 1–13 . However, it remains unknown whether the impact of SARS-CoV-2 infection can be detected in milder cases, and whether this can reveal possible mechanisms contributing to brain pathology. Here we investigated brain changes in 785 participa... | 10.1038/s41591-022-02018-4 | This article describes structural brain abnormalities in patients with SARS-CoV-2 infection. |
10.1038/s41591-022-01689-3 | 136,423,212 | Abstract The cardiovascular complications of acute coronavirus disease 2019 (COVID-19) are well described, but the post-acute cardiovascular manifestations of COVID-19 have not yet been comprehensively characterized. Here we used national healthcare databases from the US Department of Veterans Affairs to build a cohort... | 10.1038/s41591-022-02018-4 | This article describes the range of cardiovascular disorders in the post-acute phase of SARS-CoV-2 infection. |
10.1063/1.479670 | 86,521,726 | An electron paramagnetic resonance (EPR) study of 3,4-fulleropyrrolidine-2-spiro-4′[2′,2′,6′,6′-tetramethyl]piperidine-1′-oxyl (1) was performed on the photoexcited quartet state in toluene glass. The spectrum of the |S,Ms〉=|3/2,±3/2〉⇔|3/2,±1/2〉 transitions was observed selectively by using a two-dimensional (2D) nutat... | 10.1038/s41570-022-00453-y | Derivation of the spin polarization starting from the triplet and doublet density matrices. |
10.1111/j.1399-0004.2009.01186_3.x | 20,317,823 | tRNA splicing endoluclease mutations cause pontocerebellar hypoplasia. Budde BS et al.. (2008) Nature Genetics 40: 1113–1118. | 10.1038/s41580-018-0034-x | This study provides the link between mutation in TSEN complex subunits and pontocerebellar hypoplasia |
10.1126/science.aan2755 | 83,281,206 | Molecular mechanisms behind ribosomopathies Ribosomopathies are t issuespecific disorders that result from mutations in ribosomal proteins or ribosome biogenesis factors. Such disorders include Diamond-Blackfan anemia, isolated congenital asplenia, and Treacher Collins syndrome. Mills and Green review the underlying me... | 10.1038/s41580-018-0034-x | This review article provides a comprehensive discussion of current models explaining the tissue-specificity phenotype of ribosomopathies |
10.1144/sp470.3 | 41,091,542 | Abstract In the Wilson cycle, there is a change from an opening to a closing ocean when subduction begins. Subduction initiation is commonly identified as a major problem in plate tectonics and is said to be nowhere observable, yet there are many young subduction zones at the west Pacific margins and in eastern Indones... | 10.1038/s41467-020-17522-9 | Surface-topographic gradients, new magmatism and/or crustal thickening might be important precursors to a new subduction zone, highlighting the importance to further study the various young subduction trenches |
10.1029/2009gc002871 | 45,474,579 | Recent diving with the JAMSTEC Shinkai 6500 manned submersible in the Mariana fore arc southeast of Guam has discovered that MORB‐like tholeiitic basalts crop out over large areas. These “fore‐arc basalts” (FAB) underlie boninites and overlie diabasic and gabbroic rocks. Potential origins include eruption at a spreadin... | 10.1038/s41467-020-17522-9 | Early basalts are, for the first time, found in the IBM subduction system and interpreted as the first magmatic product to erupt during SZI, and could therefore also be found for other SZI events |
10.1130/ges01661.1 | 103,773,826 | Abstract Boninites are rare, high-Si, high-Mg, low-Ti lavas that have considerable tectonic significance, especially for recognizing and interpreting episodes of subduction initiation in the geologic record. Formal identification and classification of boninites may be carried out using MgO-SiO2 and MgO-TiO2 diagrams to... | 10.1038/s41467-020-17522-9 | Boninites can be subdivided into low-Si, which are not only associated with SZI, and high-Si suites, which appear to be uniquely associated with SZI |
10.1146/annurev-earth-060115-012211 | 62,242,041 | We present a revised global plate motion model with continuously closing plate boundaries ranging from the Triassic at 230 Ma to the present day, assess differences among alternative absolute plate motion models, and review global tectonic events. Relatively high mean absolute plate motion rates of approximately 9–10 c... | 10.1038/s41467-020-17522-9 | The global plate reconstruction model that is easily accessible to non-specialists via the GPlates software and therefore used for version 1.0 of the SZI Database |
10.1038/s41586-019-1916-6 | 83,480,955 | Abstract The origin of eukaryotes remains unclear 1–4 . Current data suggest that eukaryotes may have emerged from an archaeal lineage known as ‘Asgard’ archaea 5,6 . Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owin... | 10.1038/s41579-020-00458-8 | This study is the first to culture a member of the Asgard archaea group, the closest prokaryotic relatives of the eukaryote nuclear lineage, providing key insights into the evolutionary process of eukaryogenesis |
10.1073/pnas.1905179116 | 83,399,021 | In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lac... | 10.1038/s41579-020-00458-8 | This study uses traditional enrichment techniques and single-cell sorting to isolate a novel Nanohaloarchaeota, belonging to the poorly characterized DPANN archaea group |
10.1073/pnas.1404753111 | 29,300,578 | Significance Obtaining cultures of microbes is essential for developing knowledge of bacterial genetics and physiology, but many microbes with potential biomedical significance identified from metagenomic studies have not yet been cultured due to the difficulty of identifying growth conditions, isolation, and character... | 10.1038/s41579-020-00458-8 | This study uses the microfluidic SlipChip device to culture the first member of the genus Ruminococcae , which has relevance for better understanding the human microbiome |
10.7554/elife.56998 | 83,070,448 | Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivati... | 10.1038/s41579-020-00458-8 | This study demonstrates a high-throughput droplet cultivation method that can isolate and grow large numbers of single cells from environmental samples anaerobically |
10.1126/science.aab1595 | 83,550,794 | A concentrated effort for battery safety Aqueous electrolytes are limited to run below 1.23 V to avoid degradation. Suo et al. smash through this limit with an aqueous salt solution containing lithium (Li) bis(trifluoromethane sulfonyl)imide to create an electrolyte that has an electrochemical window of 3 V (see the Pe... | 10.1038/s41578-020-0218-9 | This study reports the advantages of using a ‘water-in-salt’ electrolyte in Li-ion batteries; the same strategy could be applied to design a ‘solvent-in-ionic-liquid’ electrolyte |
10.1108/03090560910935451 | 45,417,054 | Purpose Trade in counterfeit goods is perceived as a substantial threat to various industries. No longer is the emergence of imitation products confined to branded luxury goods and final markets. Counterfeit articles are increasingly finding their way into other sectors, including the fast‐moving consumer goods, pharma... | 10.1038/s41570-017-0031 | This paper discusses the economic losses due to counterfeit goods. |
10.1126/science.1074376 | 41,503,623 | Modern cryptographic practice rests on the use of one-way functions, which are easy to evaluate but difficult to invert. Unfortunately, commonly used one-way functions are either based on unproven conjectures or have known vulnerabilities. We show that instead of relying on number theory, the mesoscopic physics of cohe... | 10.1038/s41570-017-0031 | This paper defines PUFs and demonstrates their use to generate a 1D barcode for data encryption purposes. |
10.1007/s10897-011-9462-x | 125,137,381 | Abstract Updated from their original publication in 2004, these cancer genetic counseling recommendations describe the medical, psychosocial, and ethical ramifications of counseling at‐risk individuals through genetic cancer risk assessment with or without genetic testing. They were developed by members of the Practice... | 10.1038/s41585-022-00580-7 | This paper highlights principles of genetic counselling that are important in clinical genetic evaluation practice regarding genetic testing for prostate cancer |
10.1126/science.aat8084 | 122,975,128 | Deep learning has been transforming our ability to execute advanced inference tasks using computers. Here we introduce a physical mechanism to perform machine learning by demonstrating an all-optical diffractive deep neural network (D 2 NN) architecture that can implement various functions following the deep learning–b... | 10.1038/s41586-020-2973-6 | An optical implementation using multiple optimized layers for all-optical image classification |
10.1038/s41598-018-30619-y | 18,945,377 | Abstract Convolutional neural networks (CNNs) excel in a wide variety of computer vision applications, but their high performance also comes at a high computational cost. Despite efforts to increase efficiency both algorithmically and with specialized hardware, it remains difficult to deploy CNNs in embedded systems du... | 10.1038/s41586-020-2973-6 | An optical implementation of a single CNN layer demonstrated for hybrid optical–electronic image classification |
10.1145/3197517.3201333 | 83,369,887 | In typical cameras the optical system is designed first; once it is fixed, the parameters in the image processing algorithm are tuned to get good image reproduction. In contrast to this sequential design approach, we consider joint optimization of an optical system (for example, the physical shape of the lens) together... | 10.1038/s41586-020-2973-6 | The first demonstration of end-to-end optimization of optics and image processing for a computational camera design with computer vision applications |
10.1146/annurev.biochem.75.101304.124125 | 26,728,189 | Genome sequencing projects have provided researchers with a complete inventory of the predicted proteins produced by eukaryotic and prokaryotic organisms. Assignment of functions to these proteins represents one of the principal challenges for the field of proteomics. Activity-based protein profiling (ABPP) has emerged... | 10.1038/s41573-022-00542-z | This review highlights the tools involved in ABPP and explains their corresponding applications |
10.1261/rna.075945.120 | 100,175,892 | A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative nonribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not com... | 10.1038/s41576-021-00326-y | The study reports the sensitive CRISPR-based depletion of unwanted bacterial sequences to improve targeted next-generation sequencing |
10.1126/science.aad9822 | 20,545,421 | How bacteria switch between tracks Bacterial riboswitches prevent the formation of full-length messenger RNA, and hence proteins, via transcriptional termination in response to metabolites. However, identifying riboswitches within the genome has previously required comparative analysis, which may miss species- and envi... | 10.1038/s41576-021-00326-y | The authors established Term-seq to map prokaryotic RNA 3′ ends at the genome-wide scale and, among other uses, applied the method to human oral microbiome samples |
10.1126/science.aat7148 | 20,344,003 | Many bacterial infections are hard to treat and tend to relapse, possibly due to the presence of antibiotic-tolerant persisters. In vitro, persister cells appear to be dormant. After uptake of Salmonella species by macrophages, nongrowing persisters also occur, but their physiological state is poorly understood. In thi... | 10.1038/s41576-021-00326-y | Dual RNA-seq of Salmonella -infected mouse macrophages linked the polarization towards the M2-like macrophage phenotype with the secreted bacterial effector protein SteE |
10.1128/msystems.00057-17 | 83,428,810 | The nutrients consumed by intracellular pathogens are mostly unknown. This is mainly due to the challenge of disentangling host and pathogen metabolism sharing the majority of metabolic pathways and hence metabolites. Here, we investigated the metabolic changes of Mycobacterium tuberculosis , the causative agent of tub... | 10.1038/s41576-021-00326-y | The study combined dual RNA-seq with host–pathogen metabolomics for a cell-culture model of M. tuberculosis infection and inferred a system-wide host–pathogen metabolic network |
10.1038/s41467-020-17094-8 | 122,544,946 | Abstract Studying emerging or neglected pathogens is often challenging due to insufficient information and absence of genetic tools. Dual RNA-seq provides insights into host-pathogen interactions, and is particularly informative for intracellular organisms. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), an ... | 10.1038/s41576-021-00326-y | Dual RNA-seq unveiled differences in the pathogenicity of two strains of the obligate intracellular pathogen O. tsutsugamushi in an infected cell-culture model |
10.1073/pnas.1613405114 | 28,039,812 | Pathogenic bacteria need to rapidly adjust their virulence and fitness program to prevent eradication by the host. So far, underlying adaptation processes that drive pathogenesis have mostly been studied in vitro, neglecting the true complexity of host-induced stimuli acting on the invading pathogen. In this study, we ... | 10.1038/s41576-021-00326-y | One of the first applications of dual RNA-seq to an in vivo setting, analysing host and bacterial gene expression during the infection of mouse Peyer’s patches with Y. pseudotuberculosis |
10.1038/s42003-020-1018-x | 18,802,416 | Abstract Streptococcus pneumoniae is a genetically diverse human-adapted pathogen commonly carried asymptomatically in the nasopharynx. We have recently shown that a single nucleotide polymorphism (SNP) in the raffinose pathway regulatory gene rafR accounts for a difference in the capacity of clonally-related strains t... | 10.1038/s41576-021-00326-y | The authors devised a comparative dual RNA-seq approach to identify the impact of a SNP in a Streptococcus raffinose utilization regulator gene on infection outcome in a mouse model |
10.1128/mbio.01193-19 | 80,619,952 | Dual RNA sequencing (RNA-seq) offers the promise of determining an interactome at a transcriptional level between a bacterium and the host but has yet to be done on any bacterial infection in human tissue. We performed dual RNA-seq and metabolomics analyses on wounded and infected sites following experimental infection... | 10.1038/s41576-021-00326-y | Combined dual RNA-seq and metabolomics study of punch biopsy samples from human volunteers inoculated with the bacterial skin pathogen H. ducreyi |
10.1038/s41467-019-11722-8 | 17,549,777 | Abstract Necrotizing soft tissue infections (NSTIs) are devastating infections caused by either a single pathogen, predominantly Streptococcus pyogenes , or by multiple bacterial species. A better understanding of the pathogenic mechanisms underlying these different NSTI types could facilitate faster diagnostic and mor... | 10.1038/s41576-021-00326-y | Comprehensive host–bacterial transcriptomic analysis of necrotizing soft-tissue biopsy samples from human patients with either S. pyogenes monomicrobial or polymicrobial infections |
10.1126/science.aao4277 | 62,174,010 | Spatial information from NICHE-seq Immune functions depend on the interactions of heterogeneous cells in a range of microenvironments in the body. Although information regarding immune cell function has been collected using single-cell RNA-sequencing methods, these techniques have traditionally lacked spatial informati... | 10.1038/s41576-021-00326-y | This study introduced NICHE-seq, which combines eukaryotic gene expression analysis at single-cell resolution with spatial information to dissect cellular and molecular aspects of infection niches |
10.1126/science.aba5257 | 82,812,273 | Single-cell RNA sequencing (scRNA-seq) has become an essential tool for characterizing gene expression in eukaryotes, but current methods are incompatible with bacteria. Here, we introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for Gram-negative and Gram-positive ... | 10.1038/s41576-021-00326-y | Pioneering study of bacterial scRNA-seq via ‘micro-SPLiT’ that was used to detect the transcriptome of >25,000 individual B. subtilis cells |
10.1038/s41467-020-17081-z | 20,181,343 | Abstract No method exists to measure large-scale translation of genes in uncultured organisms in microbiomes. To overcome this limitation, we develop MetaRibo-Seq, a method for simultaneous ribosome profiling of tens to hundreds of organisms in microbiome samples. MetaRibo-Seq was benchmarked against gold-standard Ribo... | 10.1038/s41576-021-00326-y | A sensitive protocol for the performance of MetaRibo-seq to globally profile bacterial translation in complex consortia such as the human faecal microbiota |
10.1002/dvg.20438 | 67,622,969 | Abstract In female mouse embryos, the paternal X chromosome (Xp) is preferentially inactivated during preimplantation development and trophoblast differentiation. This imprinted X‐chromosome inactivation (XCI) is partly due to an activating imprint on the maternal X chromosome (Xm), which is set during oocyte growth. H... | 10.1038/s41576-020-0245-9 | Together with reference 14, this study demonstrates the presence of germline DNA methylation-independent autosomal and X-chromosomal imprinting |
10.1101/gad.304113.117 | 61,061,486 | Maternal imprinting at the Xist gene is essential to achieve paternal allele-specific imprinted X-chromosome inactivation (XCI) in female mammals. However, the mechanism underlying Xist imprinting is unclear. Here we show that the Xist locus is coated with a broad H3K27me3 domain that is established during oocyte growt... | 10.1038/s41576-020-0245-9 | This study demonstrates that maternal Xist is repressed by oocyte H3K27me3, thus causing imprinted XCI |
10.1101/gad.495809 | 61,648,771 | Genomic imprinting requires the differential marking by DNA methylation of genes in male and female gametes. In the female germline, acquisition of methylation imprint marks depends upon the de novo methyltransferase Dnmt3a and its cofactor Dnmt3L, but the reasons why specific sequences are targets for Dnmt3a and Dnmt3... | 10.1038/s41576-020-0245-9 | This study demonstrates that transcription through a maternally methylated DMR is required for de novo DNA methylation during oogenesis |
10.1101/gad.320069.118 | 4,835,287 | Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation, causing parental origin-specific monoallelic gene expression. Zinc finger protein 57 (ZFP57) is critical for maintenance of this epigenetic memory during post-fertilization reprogramming, yet incomplete penetrance of ZFP57 mutati... | 10.1038/s41576-020-0245-9 | Together with reference 37, this study demonstrates that the KRAB-containing zinc finger proteins ZFP57 and ZFP445 maintain allelic DNA methylation specifically at ICRs during the global wave of DNA demethylation in early embryos |
10.1186/s13059-019-1896-8 | 75,839,981 | Abstract Background Genomic imprinting is essential for mammalian development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. So far, the detailed allele-specific chromatin organization of imprinted gene domains has mostly been lacking. Here, we explored the chromatin st... | 10.1038/s41576-020-0245-9 | This study investigates how allele-specific TAD formation is involved in imprinted gene activity |
10.1186/s13059-019-1833-x | 2,537,605 | Abstract Background Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on the parent of origin and is typically regulated by differential DNA methylation inherited from gametes. Imprinting is pervasive in murine extra-embryonic lineages, and uniquely, the... | 10.1038/s41576-020-0245-9 | Together with reference 70, this study demonstrates that maintenance of non-canonical imprinting in extra-embryonic cells involves a switch from allelic H3K27me3 to allelic DNA methylation |
10.1126/science.1194174 | 122,755,668 | Cloning Futures Cloning mammals by somatic cell nuclear transfer is a technique with many potential applications in regenerative medicine, agriculture, and pharmaceutics; however, it is inefficient because of the incidence of aberrant genomic reprogramming. Inoue et al. (p. 496 , published online 16 September) found th... | 10.1038/s41576-020-0245-9 | This study demonstrates that aberrant imprinted XCI is a major barrier in SCNT and that impeding Xist expression can greatly improve cloning efficiency |
10.1128/aac.02177-15 | 20,039,957 | ABSTRACT We are in a crisis of bacterial resistance. For economic reasons, most pharmaceutical companies are abandoning antimicrobial discovery efforts, while, in health care itself, infection control and antibiotic stewardship programs have generally failed to prevent the spread of drug-resistant bacteria. At this poi... | 10.1038/s41579-021-00578-9 | Together with Drusano et al. (2016), this article reviews state-of-the-art approaches to antimicrobial dosing and suppression of resistance |
10.1152/ajpcell.00281.2013 | 18,707,742 | Do you know the sex of your cells? Not a question that is frequently heard around the lab bench, yet thanks to recent research is probably one that should be asked. It is self-evident that cervical epithelial cells would be derived from female tissue and prostate cells from a male subject (exemplified by HeLa and LnCaP... | 10.1038/s41586-019-1657-6 | This review demonstrates that the sex of cells used in experiments can influence the biology of the cell and provides a table outlining the sex of cell lines that have appeared in Am. J. Physiol. Cell Physiol in recent years |
10.1089/gg.2016.29002.nom | 60,095,052 | This article provides an overview of the current research on gender in human-robot interaction (HRI) including a discussion of the effects of gender characteristics in robotics design (robot gender), gender differences on interaction with robots (human gender), and some interaction effects between the two. The article ... | 10.1038/s41586-019-1657-6 | This paper presents an overview of research on the role of sex and gender in the context of human–robot interaction research and summarizes the cutting-edge research in this area from an engineering perspective |
10.1038/s41598-017-09298-8 | 31,966,135 | Abstract Sequentially hermaphroditic fish change sex from male to female (protandry) or vice versa (protogyny), increasing their fitness by becoming highly fecund females or large dominant males, respectively. These life-history strategies present different social organizations and reproductive modes, from near-random ... | 10.1038/s41586-019-1657-6 | This paper demonstrates that the direction of sex change in sequentially hermaphroditic fish is a critical variable determining demographic stability and resilience, with considerable implications concerning the resilience of these populations to anthropogenic disturbances, such as overfishing |
10.1084/jem.20150496 | 41,626,456 | We examine the features, origin, turnover, and gene expression of pancreatic macrophages under steady state. The data distinguish macrophages within distinct intrapancreatic microenvironments and suggest how macrophage phenotype is imprinted by the local milieu. Macrophages in islets of Langerhans and in the interacina... | 10.1038/s41574-019-0286-3 | This study provides a comprehensive view of the origin, phenotype, turnover and gene expression of macrophages in exocrine pancreas and the islets |
10.2337/db06-1650 | 104,241,365 | Activation of the innate immune system in obesity is a risk factor for the development of type 2 diabetes. The aim of the current study was to investigate the notion that increased numbers of macrophages exist in the islets of type 2 diabetes patients and that this may be explained by a dysregulation of islet-derived i... | 10.1038/s41574-019-0286-3 | This study provides clear evidence showing an increase in the number of macrophages in the islets of humans with T2DM and animal models of obesity and T2DM |
10.2337/dc14-0396 | 104,112,988 | OBJECTIVE This article examines the foundation of β-cell failure in type 2 diabetes (T2D) and suggests areas for future research on the underlying mechanisms that may lead to improved prevention and treatment. RESEARCH DESIGN AND METHODS A group of experts participated in a conference on 14–16 October 2013 cosponsored ... | 10.1038/s41574-019-0286-3 | This paper briefly summarizes recent knowledge on the mechanisms underlying β cell failure in T2DM |
10.1073/pnas.1515954112 | 103,788,794 | Beta cells from nondiabetic mice transfer secretory vesicles to phagocytic cells. The passage was shown in culture studies where the transfer was probed with CD4 T cells reactive to insulin peptides. Two sets of vesicles were transferred, one containing insulin and another containing catabolites of insulin. The passage... | 10.1038/s41574-019-0286-3 | This study shows evidence that intra-islet macrophages take up intact insulin-containing vesicles from β-cells |
10.1073/pnas.1321347111 | 83,387,270 | Significance Here, we show how, mechanistically, inflammation-recruited macrophages may stimulate beta-cell proliferation in the pancreas, and specifically identify that TGFβ1 and EGF, which are secreted by M2 macrophages, induce SMAD7 expression in beta cells. SMAD7 not only activates cell cycle activators but also in... | 10.1038/s41574-019-0286-3 | This study reveals that M2-like macrophages and the SMAD7 pathway can increase β-cell mass |
10.2337/db05-1430 | 60,486,383 | High glucose concentrations have a dual effect on β-cell turnover, inducing proliferation in the short-term and apoptosis in the long-term. Hyperglycemia leads to β-cell production of interleuking (IL)-1β in human pancreatic islets. Fas, a death receptor regulated by IL-1β, is involved in glucose-induced β-cell apoptos... | 10.1038/s41574-019-0286-3 | This study shows an improvement in β-cell proliferation by a low concentration of IL-1β |
10.1158/0008-5472.can-15-2402 | 20,790,415 | Abstract Many cancers feature cellular hierarchies that are driven by tumor-initiating cancer stem cells (CSC) and rely on complex interactions with the tumor microenvironment. Standard cell culture conditions fail to recapitulate the original tumor architecture or microenvironmental gradients and are not designed to r... | 10.1038/s41578-019-0135-y | The method used in this paper to derive and culture patient cells and matrix minimally disturbed cell–matrix interactions, preserved tumour cell heterogeneity and resulted in an accurate recapitulation of patient tumour response in an orthotopic xenograft culture |
10.1126/science.aay1813 | 62,452,592 | Targeting the cross-talk between tumor-initiating cells (TICs) and the niche microenvironment is an attractive avenue for cancer therapy. We show here, using a mouse model of squamous cell carcinoma, that TICs play a crucial role in creating a niche microenvironment that is required for tumor progression and drug resis... | 10.1038/s41568-021-00363-z | A mechanism by which tumour-initiating cells create a favourable environment that fosters tumour growth is demonstrated here |
10.4049/jimmunol.1490019 | 62,181,422 | Abstract The ability of IL-2 to expand T cells with maintenance of functional activity has been translated into the first reproducible effective human cancer immunotherapies. The administration of IL-2 can lead to durable, complete, and apparently curative regressions in patients with metastatic melanoma and renal canc... | 10.1038/s41568-021-00363-z | This work provides an overview of the treatment of patients with cancer with recombinant IL-2, the first interleukin approved for cancer therapy |
10.1073/pnas.1108174108 | 20,811,717 | A moiré pattern is formed when two copies of a periodic pattern are overlaid with a relative twist. We address the electronic structure of a twisted two-layer graphene system, showing that in its continuum Dirac model the moiré pattern periodicity leads to moiré Bloch bands. The two layers become more strongly coupled ... | 10.1038/s41586-021-04173-z | This reference theoretically shows the presence of flat bands in t-BLG and predicts the magic angle of 1.05° |
10.1126/science.aay5533 | 20,689,173 | The quantum anomalous Hall (QAH) effect combines topology and magnetism to produce precisely quantized Hall resistance at zero magnetic field. We report the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal boron nitride. The effect is driven by intrinsic strong interactions, which polarize t... | 10.1038/s41586-021-04173-z | This reference reports the observation of an intrinsic QAH state (that is, without magnetic dopants) in t-BLG aligned to hBN |
10.1038/s41467-020-16239-z | 104,385,682 | Abstract Cigarette smoke first interacts with the lung through the cellularly diverse airway epithelium and goes on to drive development of most chronic lung diseases. Here, through single cell RNA-sequencing analysis of the tracheal epithelium from smokers and non-smokers, we generate a comprehensive atlas of epitheli... | 10.1038/s41577-020-00477-9 | This study used scRNA-seq to evaluate the impact of cigarette smoking on each airway cell type in the human tracheal epithelium |
10.1073/pnas.0911934107 | 62,084,623 | The upper respiratory tract is continually assaulted with harmful dusts and xenobiotics carried on the incoming airstream. Detection of such irritants by the trigeminal nerve evokes protective reflexes, including sneezing, apnea, and local neurogenic inflammation of the mucosa. Although free intra-epithelial nerve endi... | 10.1038/s41577-020-00477-9 | This article shows how chemosensory cells in the airways mediate reflex reactions to irritants, including bacterial quorum-sensing molecules, describing a mechanism by which bacterial population densities are limited by the local epithelial inflammatory response |
10.1126/science.aad7969 | 125,074,963 | Neuroendocrine cells as air sensors Liters of air pass through the lung every minute. Signals in the atmospheric environment are processed into physiological outputs, including the immune response. Branchfield et al. show that rare airway cells called pulmonary neuroendocrine cells (PNECs) sense and respond to airborne... | 10.1038/s41577-020-00477-9 | This article describes how PNECs act as rheostats to enable the lungs to sense and respond to changes in the inhaled environment |
10.1126/sciimmunol.aav5581 | 29,303,998 | Tissue-resident memory T cells (T RM ) maintain immunity in diverse sites as determined in mouse models, whereas their establishment and role in human tissues have been difficult to assess. Here, we investigated human lung T RM generation, maintenance, and function in airway samples obtained longitudinally from human l... | 10.1038/s41577-020-00477-9 | This study demonstrates that donor T RM cells persisted around the airways of lung transplant recipients for over 1 year |
10.1126/sciimmunol.aav7638 | 62,630,943 | Group 2 innate lymphoid cells (ILC2s) are enriched in mucosal tissues (e.g., lung) and respond to epithelial cell–derived cytokines initiating type 2 inflammation. During inflammation, ILC2 numbers are increased in the lung. However, the mechanisms controlling ILC2 trafficking and motility within inflamed lungs remain ... | 10.1038/s41577-020-00477-9 | This study shows that extracellular matrix influences cell dynamics in vivo and in vitro, changing the course of inflammation |
10.1126/science.aaa1975 | 62,566,030 | Build the builders before the brain Humans are much smarter than mice—key to this is the relative thickness of the human brain's neocortex. Florio et al. combed through genes expressed in the progenitor cells that build the neocortex and zeroed in on one gene found in humans but not in mice. The gene, which seems to di... | 10.1038/s41583-018-0112-2 | This seminal study demonstrates the importance of a gene that emerged in the recent evolutionary human lineage for the proliferation of cortical progenitor cells and neurogenesis; its overexpression in mice induces cortical folding |
10.1126/science.1074192 | 4,697,166 | Transgenic mice expressing a stabilized β-catenin in neural precursors develop enlarged brains with increased cerebral cortical surface area and folds resembling sulci and gyri of higher mammals. Brains from transgenic animals have enlarged lateral ventricles lined with neuroepithelial precursor cells, reflecting an ex... | 10.1038/s41583-018-0112-2 | This is the first study to demonstrate that folding of cortical tissue (albeit only the neuroepithelium) can be induced in mice in vivo and that demonstrates the central role of progenitor cell proliferation in this process |
10.1115/1.4001683 | 42,639,691 | During human brain development, the cerebral cortex undergoes substantial folding, leading to its characteristic highly convoluted form. Folding is necessary to accommodate the expansion of the cerebral cortex; abnormal cortical folding is linked to various neurological disorders, including schizophrenia, epilepsy, aut... | 10.1038/s41583-018-0112-2 | This paper demonstrates the absence of net tension between opposite walls of cortical gyri, neither during development nor in the adult cortex, thus refuting the long-standing axon tension hypothesis proposed by Van Essen |
10.1126/science.1244193 | 20,529,953 | Not Too Much, Not Too Little The microRNA miR128 is expressed in brain neurons of the mouse. Lek Tan et al. (p. 1254 ) now find that miR128 is crucial to stable brain function. Mice deficient in miR128 developed hyperactivity and were susceptible to fatal seizures, whereas overexpression of miR128 correlated with reduc... | 10.1038/s41576-020-00309-5 | This article illustrates an essential postnatal miRNA requirement mir-128-2 −/− mice are hyperactive as juveniles before severe seizures and death in 2–3 months |
10.1126/science.aaf8995 | 38,411,935 | Intraneuronal control of protein expression In cells and tissues, mRNA copy numbers far exceed the number of micro RNAs (miRNAs). How then can a miRNA effectively regulate translation of a particular target mRNA? Sambandan et al. used high-resolution in situ hybridization to detect precursor miRNA in rat neuronal dendr... | 10.1038/s41576-020-00309-5 | This study reveals subcellularly localized maturation and activity of mir-181a in neuronal dendrites and spines following local stimulation |
10.1073/pnas.1706879114 | 79,842,340 | Bacterial communities colonize epithelial surfaces of most animals. Several factors, including the innate immune system, mucus composition, and diet, have been identified as determinants of host-associated bacterial communities. Here we show that the early branching metazoan Hydra is able to modify bacterial quorum-sen... | 10.1038/s41579-019-0186-5 | This study demonstrates that Hydra , a genus of metazoans, modify the autoinducers of the primary bacterial colonizer of hydra, Curvibacter spp., and in so doing alter their quorum-sensing behaviours |
10.1186/s13059-016-1012-2 | 83,282,709 | Abstract Background The success of the CRISPR/Cas9 genome editing technique depends on the choice of the guide RNA sequence, which is facilitated by various websites. Despite the importance and popularity of these algorithms, it is unclear to which extent their predictions are in agreement with actual measurements. Res... | 10.1038/s41587-020-0490-7 | This study provides one of the first systematic comparisons of on- and off-target scoring algorithms, notable in part for its organization of external data |
10.1101/003327 | 28,996,862 | Abstract Technological advancement has opened the door to systematic genetics in mammalian cells. Genome-scale loss-of-function screens can assay fitness defects induced by partial gene knockdown, using RNA interference, or complete gene knockout, using new CRISPR techniques. These screens can reveal the basic blueprin... | 10.1038/s41587-020-0490-7 | This study established a gold-standard set of genes for benchmarking the performance of genome-wide screens based on expected viability outcomes |
10.1038/s42003-020-01430-1 | 100,648,887 | Abstract Restless legs syndrome (RLS) is a common neurological sensorimotor disorder often described as an unpleasant sensation associated with an urge to move the legs. Here we report findings from a meta-analysis of genome-wide association studies of RLS including 480,982 Caucasians (cases = 10,257) and a follow up s... | 10.1038/s41572-021-00311-z | Second large-scale (>10,000 cases in discovery stage) GWAS meta-analysis for RLS, which increased the number of identified risk loci and used Mendelian randomization analyses for functional interpretation |
10.1002/mds.27287 | 41,113,149 | Abstract Background: To better understand the role of iron homeostasis dysregulation in restless legs syndrome, we compared serum hepcidin and ferritin levels in drug‐free patients with primary restless legs syndrome and healthy controls and studied the relationship between hepcidin level and restless legs syndrome sev... | 10.1038/s41572-021-00311-z | This is the first ssociation between high hepcidin levels and RLS that emphasizes the complex peripheral iron metabolism deregulation in RLS |
10.1002/ana.25104 | 123,398,796 | Objective The first aim was to demonstrate a previously hypothesized increased sensitivity of corticostriatal glutamatergic terminals in the rodent with brain iron deficiency (BID), a pathogenetic model of restless legs syndrome (RLS). The second aim was to determine whether these putative hypersensitive terminals coul... | 10.1038/s41572-021-00311-z | This is the first article showing compelling evidence for an adenosinergic dysfunction in RLS |
10.1002/mds.28668 | 81,238,971 | ABSTRACT Background New pharmacological targets are needed for restless legs syndrome. Preclinical data suggest that a hypoadenosinergic state plays an important pathogenetic role. Objective The objective of this study was to determine whether inhibitors of equilibrative nucleoside transporters, for example, dipyridamo... | 10.1038/s41572-021-00311-z | Main clinical evidence showing the involvement of adenosinergic mechanisms in the pathophysiology of RLS and the therapeutic effects of dipyridamole in RLS. |
10.1002/mds.28224 | 37,874,852 | Abstract Objective The objective of this study was to assess the rotigotine effect on the nocturnal blood pressure (BP) dip by 24‐hour ambulatory BP monitoring and on endothelial function in patients with restless legs syndrome (RLS) compared with placebo. Methods In this double‐blind, placebo‐controlled trial, 76 adul... | 10.1038/s41572-021-00311-z | This was the first study showing that rotigotine increased the percentage of blood pressure dipper profiles in patients with RLS |
10.1126/sciadv.abf4408 | 19,074,776 | Intratumoral heterogeneity is a driver of breast cancer progression, but the nature of the clonal interactive network involved in this process remains unclear. Here, we optimized the use of optical barcoding to visualize and characterize 31 cancer subclones in vivo. By mapping the clonal composition of thousands of met... | 10.1038/s41568-022-00500-2 | This study uses optical barcoding to map clonal fate and interactions of 31 breast cancer clones in vitro and in vivo, in multiple organs and in response to targeted therapy |
10.1038/ncomms6871 | 62,657,201 | Abstract Genomic and phenotypic analyses indicate extensive intra- as well as intertumoral heterogeneity in primary human malignant cell populations despite their clonal origin. Cellular DNA barcoding offers a powerful and unbiased alternative to track the number and size of multiple subclones within a single human tum... | 10.1038/s41568-022-00500-2 | This study is one of the first to use genetic barcoding to investigate the frequency of tumour-initiating cells in retransplantation experiments using PDXs |
10.1038/s41586-020-2969-2 | 125,121,535 | Abstract Most deaths from cancer are explained by metastasis, and yet large-scale metastasis research has been impractical owing to the complexity of in vivo models. Here we introduce an in vivo barcoding strategy that is capable of determining the metastatic potential of human cancer cell lines in mouse xenografts at ... | 10.1038/s41568-022-00500-2 | This study uses the multiplexing capability of genetic barcoding to generate a ‘metastasis map’ for 500 cancer cell lines |
10.1038/s41467-022-30008-0 | 143,279,066 | Abstract While multiplexing samples using DNA barcoding revolutionized the pace of biomedical discovery, multiplexing of live imaging-based applications has been limited by the number of fluorescent proteins that can be deconvoluted using common microscopy equipment. To address this limitation, we develop visual barcod... | 10.1038/s41568-022-00500-2 | In this study, fluorescent proteins targeted to specific locations are used to increase the multiplexing potential of optical barcoding |
10.1126/science.aax6624 | 41,565,073 | How early-life colonization and subsequent exposure to the microbiota affect long-term tissue immunity remains poorly understood. Here, we show that the development of mucosal-associated invariant T (MAIT) cells relies on a specific temporal window, after which MAIT cell development is permanently impaired. This imprin... | 10.1038/s41579-022-00780-3 | This study identifies that crosstalk between non-classical immune cells and the microbiota is important for tissue development and wound healing. |
10.1126/scitranslmed.aal4651 | 103,727,935 | Genomic and functional analyses of staphylococcal strain specificity reveal roles for microbes in human atopic dermatitis pathogenesis. | 10.1038/s41579-022-00780-3 | This study is one of the first to identify that S. epidermidis , akin to S. aureus , can expand in some lesional atopic dermatitis sites. |
10.1371/journal.ppat.1009304 | 2,645,033 | S . epidermidis is a substantial component of the human skin microbiota, but also one of the major causes of nosocomial infection in the context of implanted medical devices. We here aimed to advance the understanding of S . epidermidis genotypes and phenotypes conducive to infection establishment. Furthermore, we inve... | 10.1038/s41579-022-00780-3 | This study utilizes patient-matched isolates to demonstrate S. epidermidis genetic flexibility and adaptation to various environments. |
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