source_doi stringlengths 13 57 | source_mag_paper_id int64 490k 157M | source_abstract stringlengths 8 10.7k | target_doi stringlengths 14 27 | target_summary stringlengths 42 889 |
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10.4049/jimmunol.174.6.3475 | 110,258,504 | Abstract The sequencing of the chicken MHC led to the identification of two open reading frames, designated B-NK and B-lec, that were predicted to encode C-type lectin domains. C-type lectin domains are not encoded in the MHC of any animal described to date; therefore, this observation was completely unexpected, partic... | 10.1038/s41577-018-0003-9 | This study proposes that the NKC and MHC were syntenic in the proto-MHC. |
10.4049/jimmunol.1401177 | 68,475,582 | Abstract The MHC is a large genetic region controlling Ag processing and recognition by T lymphocytes in vertebrates. Approximately 40% of its genes are implicated in innate or adaptive immunity. A putative proto-MHC exists in the chordate amphioxus and in the fruit fly, indicating that a core MHC region predated the e... | 10.1038/s41577-018-0003-9 | This study proposes that the ancestral MHC may have been focused on host recognition elements in the cytosol. |
10.1073/pnas.1005475107 | 98,194,328 | Adaptive immunity in jawless vertebrates is mediated by leucine-rich repeat proteins called “variable lymphocyte receptors” (VLRs). Two types of VLR (A and B) are expressed by mutually exclusive lymphocyte populations in lamprey. VLRB lymphocytes resemble the B cells of jawed vertebrates; VLRA lymphocytes are similar t... | 10.1038/s41577-018-0003-9 | This work demonstrates the potential for VLRA (lamprey TCR-equivalent) to bind to free antigen. |
10.1084/jem.178.3.815 | 4,319,890 | In Heterodontus, a phylogenetically primitive shark species, the variable (VH), diversity (DH), joining (JH) segments, and constant (CH) exons are organized in individual approximately 18-20-kb "clusters." A single large VH family with > 90% nucleic acid homology and a monotypic second gene family are identified... | 10.1038/s41577-018-0003-9 | This is the first description of somatic hypermutation of IgV genes in ectothermic vertebrates. |
10.1073/pnas.93.17.9096 | 58,560,849 | Proteasomes are the multi-subunit protease thought to play a key role in the generation of peptides presented by major histocompatibility complex (MHC) class I molecules. When cells are stimulated with interferon gamma, two MHC-encoded subunits, low molecular mass polypeptide (LMP) 2 and LMP7, and the MECL1 subunit enc... | 10.1038/s41577-018-0003-9 | This is the first study to demonstrate MHC paralogous regions, consistent with Ohno’s proposal of two genome-wide duplications early in vertebrate history. |
10.1126/science.1188934 | 41,091,077 | Biocatalytic Boost Enzymes tend to direct reactions toward specific products much more selectively than synthetic catalysts. Unfortunately, this selectivity has evolved for cellular purposes and may not promote the sorts of reactions chemists are seeking to enhance (see the Perspective by Lutz ). Siegel et al. (p. 309 ... | 10.1038/s41570-017-0016 | This paper offers a notable example of the use of a transaminase in the manufacture of sitagliptin. |
10.1111/acer.13546 | 60,314,558 | Background One mechanism by which alcoholic liver disease (ALD) progresses is oxidative stress and the generation of reactive oxygen species, among others due to the induction of cytochrome P‐4502E1 (CYP2E1). Experimental data underline the key role of CYP2E1 because ALD could be partially prevented in rats by the admi... | 10.1038/s41572-018-0014-7 | This article shows for the first time a correlation between CYP2E1 and fibrosis in a large cohort of alcoholic patients with various severities of ALD |
10.1111/acer.12704 | 125,082,096 | Alcoholic liver disease ( ALD ) is a leading cause of morbidity and mortality worldwide. Alcoholic fatty liver disease can progress to steatohepatitis, alcoholic hepatitis, fibrosis, and cirrhosis. Patients with alcohol abuse show quantitative and qualitative changes in the composition of the intestinal microbiome. Fur... | 10.1038/s41572-018-0014-7 | The paper describes in an excellent way the mechanisms by which gut microbiota contribute to the development of ALD |
10.3189/172756411795931651 | 61,937,191 | Abstract Snow distribution is a dominating factor in sea-ice mass balance in the Bellingshausen Sea, Antarctica, through its roles in insulating the ice and contributing to snow-ice production. the wind has long been qualitatively recognized to influence the distribution of snow accumulation on sea ice, but the relativ... | 10.1038/s41558-018-0286-7 | This analysis uses Antarctic field observations to quantify snow accumulation on level ice and inform a modelling investigation, which showed that about half of precipitation over sea ice could be lost to leads. |
10.1098/rsta.2014.0162 | 89,147,271 | We use a large ensemble of simulations from the Community Earth System Model to quantify simulated changes in the twentieth and twenty-first century Arctic surface shortwave heating associated with changing incoming solar radiation and changing ice conditions. For increases in shortwave absorption associated with albed... | 10.1038/s41558-018-0286-7 | A large ensemble from an Earth system model is used to quantify the simulated changes associated with changing solar radiation and ice conditions in the twentieth and twenty-first centuries. |
10.1101/gad.268151.115 | 61,620,559 | Polycomb-repressive complex 1 (PRC1) and PRC2 maintain repression at many developmental genes in mouse embryonic stem cells and are required for early development. However, it is still unclear how they are targeted and how they function. We show that the ability of RING1B, a core component of PRC1, to ubiquitinate hist... | 10.1038/s41576-022-00499-0 | This study, along with that of Pengelly et al (2015), shows that the bulk of ubiquitylation is dispensable for correct patterning of animals by generating ubiquitylation-deficient flies and mice |
10.1101/gad.265439.115 | 39,238,305 | Histone H2A monoubiquitylation (H2Aub) is considered to be a key effector in transcriptional repression by Polycomb-repressive complex 1 (PRC1). We analyzed Drosophila with a point mutation in the PRC1 subunit Sce that abolishes its H2A ubiquitylase activity or with point mutations in the H2A and H2Av residues ubiquity... | 10.1038/s41576-022-00499-0 | This study, along with that of Illingworth et al (2015), shows that the bulk of ubiquitylation is dispensable for correct patterning of animals by generating ubiquitylation-deficient flies and mice |
10.1101/gad.326488.119 | 41,665,581 | Mammalian development requires effective mechanisms to repress genes whose expression would generate inappropriately specified cells. The Polycomb-repressive complex 1 (PRC1) family complexes are central to maintaining this repression. These include a set of canonical PRC1 complexes, each of which contains four core pr... | 10.1038/s41576-022-00499-0 | This study, along with that of Tatavosian et al (2019), shows that the cPRC1 component CBX2 can phase separate, suggesting another potential way of physically regulating Polycomb domains |
10.1126/science.aal2512 | 101,658,648 | Polycomb steps to inactivate X XX females silence one of their X chromosomes. This involves a process whereby a noncoding RNA known as Xist coats one of the X chromosomes and recruits chromatin silencing factors. The Polycomb complexes PRC1 and PRC2 are also known to be involved in X chromosome inactivation. Almeida et... | 10.1038/s41576-022-00499-0 | Using livecell imaging and genetic mouse models, the authors show the specific roles of PCGF3 and PCGF5 in X chromosome-inactivation. |
10.1126/science.aai8236 | 124,485,254 | DNA sequence and inherited gene silencing Cell fate decisions require a gene's transcriptional status, whether on or off, to be stably and heritably maintained over multiple cell generations. For silenced genes, heterochromatin domains are associated with specific histone posttranslational modifications, and these hist... | 10.1038/s41576-022-00499-0 | This study, together with that of Laprell et al. (2017), demonstrates that existing H3K27me3 is not sufficient for self-maintenance and gene repression by inducing the deletion of DNA elements needed for de novo PcG recruitment |
10.1126/science.aai8266 | 104,344,301 | DNA sequence and inherited gene silencing Cell fate decisions require a gene's transcriptional status, whether on or off, to be stably and heritably maintained over multiple cell generations. For silenced genes, heterochromatin domains are associated with specific histone posttranslational modifications, and these hist... | 10.1038/s41576-022-00499-0 | This study, together with that of Coleman et al. (2017), demonstrates that existing H3K27me3 is not sufficient for self-maintenance and gene repression by inducing the deletion of DNA elements needed for de novo PcG recruitment |
10.1126/science.aan1121 | 20,363,473 | A multifactorial strategy establishes and maintains repressive chromatin marks in plants in response to environmental signals. | 10.1038/s41576-022-00499-0 | This study shows that the loss of Polycomb-mediated memory can be variable between cells within an organism |
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/s41576-018-0066-2 | Visualization of single-synapse stimulation-dependent local maturation of miRNA that then contributes to spatially restricted reduction in the translation of a target mRNA |
10.1126/science.1138659 | 83,017,798 | We tested the hypothesis that de novo copy number variation (CNV) is associated with autism spectrum disorders (ASDs). We performed comparative genomic hybridization (CGH) on the genomic DNA of patients and unaffected subjects to detect copy number variants not present in their respective parents. Candidate genomic reg... | 10.1038/s41576-018-0066-2 | A systematic analysis of copy number variants uncovers their association with ASD |
10.1128/jvi.01512-10 | 104,401,478 | ABSTRACT Epstein-Barr virus (EBV) infects cells in latent or lytic forms, but the role of lytic infection in EBV-induced lymphomas is unclear. Here, we have used a new humanized mouse model, in which both human fetal CD34 + hematopoietic stem cells and thymus/liver tissue are transplanted, to compare EBV pathogenesis a... | 10.1038/s41579-019-0249-7 | This study shows that EBV deficient in lytic gene expression does not efficiently establish lymphomas in HIS mice |
10.1073/pnas.1605884113 | 103,996,493 | Infection with Epstein–Barr virus (EBV) affects most humans worldwide and persists life-long in the presence of robust virus-specific T-cell responses. In both immunocompromised and some immunocompetent people, EBV causes several cancers and lymphoproliferative diseases. EBV transforms B cells in vitro and encodes at l... | 10.1038/s41579-019-0249-7 | This study and Murer et al. (2019) demonstrate that EBV miRNAs mainly serve the role of immune escape from CD8 + T cell responses |
10.1101/gr.201814.115 | 104,308,624 | Although human LINE-1 (L1) elements are actively mobilized in many cancers, a role for somatic L1 retrotransposition in tumor initiation has not been conclusively demonstrated. Here, we identify a novel somatic L1 insertion in the APC tumor suppressor gene that provided us with a unique opportunity to determine whether... | 10.1038/s41576-020-0251-y | This study resequenced all non-reference L1 elements in a colon cancer case to identify internal diagnostic SNPs and subsequently which elements are expressed in the sample |
10.1073/pnas.0601324103 | 122,575,071 | Despite being scarce in the human genome, active L1 retrotransposons continue to play a significant role in its evolution. Because of their recent expansion, many L1s are not fixed in humans, and, when present, their mobilization potential can vary among individuals. Previously, we showed that the great majority of ret... | 10.1038/s41576-020-0251-y | Seleme et al. (2006) and Sanchez-Luque et al. (2019) show that a given L1 locus can exhibit internal sequence variation leading to differences in retrotransposition activity between individuals. |
10.1093/bioinformatics/btv422 | 125,231,691 | Abstract Motivation: Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryot... | 10.1038/s41576-020-0251-y | TEtranscripts is the first application of the EM algorithm to TE RNA-seq analyses, and one of the most popular software packages dedicated to this task since its release |
10.1073/pnas.1307797110 | 122,347,617 | Significance Multiple Escherichia coli genome sequences have recently been made available by advances in DNA sequencing. Analysis of these genomes has demonstrated that the fraction of genes common to all E. coli strains in the species represents a small fraction of the entire E. coli gene pool. This observation raises... | 10.1038/s41579-020-00440-4 | This is the first study to focus on a strain-level study of E. coli using GEMs |
10.1038/s41467-019-13818-7 | 84,352,094 | Abstract Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flux models. ETFL is a hierarchical model formulation, fro... | 10.1038/s41579-020-00440-4 | This article describes an implementation of the ME models called ‘ETFL’, for ‘expression and thermodynamics flux models’ |
10.1038/msb.2013.52 | 125,291,100 | Growth is a fundamental process of life. Growth requirements are well‐characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive of events at the molecular scale and capable of explaining the high‐level behavior of the cell as a whole. Here, we ... | 10.1038/s41579-020-00440-4 | This study outlines the development of the first E. coli ME model |
10.1073/pnas.1705524114 | 122,345,931 | Significance How do bacteria adapt to the diverse thermal niches on earth? Evidence accumulates in the protein sequence and structural determinants of thermosensitivity and mechanisms by which molecular chaperones aid protein folding. However, a comprehensive understanding of how thermoadaptation is achieved at the sys... | 10.1038/s41579-020-00440-4 | As one of the three stress response extensions of the ME model, FoldME focuses on simulation of response to temperature stress |
10.1073/pnas.1905039116 | 20,865,415 | Catalysis using iron–sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage to metalloproteins caused by reactive oxygen species (ROS) can prevent cell growth and survival when unmanaged, thus eliciting an essential stress response that is universal and fundamental in... | 10.1038/s41579-020-00440-4 | As one of the three stress response extensions of the ME model, OxidizeME incorporates mechanisms involved in response to oxidative stress |
10.1111/imr.12534 | 20,822,327 | Summary Cell death is a fundamental biological phenomenon that is essential for the survival and development of an organism. Emerging evidence also indicates that cell death contributes to immune defense against infectious diseases. Pyroptosis is a form of inflammatory programmed cell death pathway activated by human a... | 10.1038/s41568-019-0123-y | This review provides an overview on the functions and mechanisms of inflammatory caspases and pyroptosis |
10.1073/pnas.97.2.734 | 124,127,286 | Proinflammatory cytokines, including IL-1 β and tumor necrosis factor- α (TNF- α ), promote cancer cell adhesion and liver metastases by up-regulating the expression of vascular cell adhesion molecule-1 (VCAM-1) on hepatic sinusoidal endothelium (HSE). In this study, hepatic metastasis after intrasplenically injected m... | 10.1038/s41568-019-0123-y | This article shows that IL-18 contributes to hepatic metastasis by increasing VCAM1 expression in HSECs |
10.1038/ncomms13007 | 80,232,001 | Abstract Obesity is associated with an increased risk of developing breast cancer and is also associated with worse clinical prognosis. The mechanistic link between obesity and breast cancer progression remains unclear, and there has been no development of specific treatments to improve the outcome of obese cancer pati... | 10.1038/s41568-019-0123-y | This study demonstrates that IL-1β production as a result of NLRC4 inflammasome activation in immune cells of the TME of obese mice acts on adipocytes to promote VEGF production and angiogenesis |
10.1002/adma.200305717 | 61,968,975 | The up‐conversion photoluminescence (PL) in films of polyfluorene (PF) doped with metallated porphyrins is reported for the first time. The dependence of the up‐conversion process on the pump laser intensity and wavelength, the central metal moiety of the dopants, and the temperature is presented. Up‐conversion emissio... | 10.1038/s41570-018-0057-z | This paper presents the rediscovery of the sTTA-UC phenomenon using PtOEP and fluorene molecules |
10.1002/anie.201309389 | 83,272,123 | Abstract Liposomes capable of generating photons of blue light in situ by triplet–triplet annihilation upconversion of either green or red light, were prepared. The red‐to‐blue upconverting liposomes were capable of triggering the photodissociation of ruthenium polypyridyl complexes from PEGylated liposomes using a cli... | 10.1038/s41570-018-0057-z | This is the first chemical demonstration that the light generated in situ by sTTA-UC in liposomes can be used to activate a PACT molecule |
10.1002/anie.201704430 | 105,377,628 | Abstract A strategy to expand anti‐Stokes shifting from the far‐red to deep‐blue region in metal‐free triplet–triplet annihilation upconversion (TTA‐UC) is presented. The method is demonstrated by in vivo titration of the photorelease of an anticancer prodrug. This new TTA system has robust brightness and the longest a... | 10.1038/s41570-018-0057-z | This is the first in vivo demonstration that sTTA-UC can be used to activate a photoactivated chemotherapeutic compound |
10.59117/20.500.11822/43142 | 151,371,163 | This new report builds on the previous Sick Water? report, starting with the premise that wastewater is an important and valuable resource that can also help avoid costs of pollution and biodiversity loss. It aims to inspire policy and decision makers to be proactive in leading transformational change in sustainable wa... | 10.1038/s41467-019-11693-w | This report was the first to use the term ‘blue carbon’ |
10.1890/110004 | 83,499,119 | Recent research has highlighted the valuable role that coastal and marine ecosystems play in sequestering carbon dioxide (CO 2 ). The carbon (C) sequestered in vegetated coastal ecosystems, specifically mangrove forests, seagrass beds, and salt marshes, has been termed “blue carbon”. Although their global area is one t... | 10.1038/s41467-019-11693-w | Identified key areas of uncertainly and specific actions needed to understand the role of vegetated coastal ecosystems as carbon sinks |
10.1126/science.211.4484.838 | 18,887,298 | Marine macrophyte biomass production, burial, oxidation, calcium carbonate dissolution, and metabolically accelerated diffusion of carbon dioxide across the air-sea interface may combine to sequester at least 10 9 tons of carbon per year in the ocean. This carbon sink may partially account for discrepancies in extant g... | 10.1038/s41467-019-11693-w | Seminal paper on the role of marine macrophytes in sequestering CO2; suggested that the role of seagrasses were overlooked |
10.5194/bg-2-1-2005 | 20,477,686 | Abstract. The carbon burial in vegetated sediments, ignored in past assessments of carbon burial in the ocean, was evaluated using a bottom-up approach derived from upscaling a compilation of published individual estimates of carbon burial in vegetated habitats (seagrass meadows, salt marshes and mangrove forests) to t... | 10.1038/s41467-019-11693-w | This paper showed that vegetated marine habitats are responsible for a previously unaccounted, 50% of C burial in ocean sediments |
10.1002/fee.1484 | 62,498,417 | To promote the sequestration of blue carbon, resource managers rely on best‐management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment‐level approaches. Drawing upon knowledge from a ... | 10.1038/s41467-019-11693-w | Proposed three key management actions for maximising blue carbon sequestration within existing coastal vegetated ecosystems |
10.1038/s41467-018-03168-1 | 123,191,700 | Abstract Here we report the discovery of two Tupanvirus strains, the longest tailed Mimiviridae members isolated in amoebae. Their genomes are 1.44–1.51 Mb linear double-strand DNA coding for 1276–1425 predicted proteins. Tupanviruses share the same ancestors with mimivirus lineages and these giant viruses present the ... | 10.1038/s41579-022-00754-5 | Isolation of tupanviruses (a novel sublineage in the Megamimivirinae ) and analysis of their infection mechanisms and host range and genomes that encoded for a complete set of 20 aminoacyl tRNA synthetases. |
10.1371/journal.pbio.3001430 | 134,143,517 | Large DNA viruses of the phylum Nucleocytoviricota have recently emerged as important members of ecosystems around the globe that challenge traditional views of viral complexity. Numerous members of this phylum that cannot be classified within established families have recently been reported, and there is presently a s... | 10.1038/s41579-022-00754-5 | Data-driven study in which all available Nucleocytoviricota isolate genomes and GVMAGs were used to establish a set of giant virus conserved genes and create a taxonomic framework of the phylum |
10.1126/science.1239181 | 104,096,091 | Zeus' Revenge Sediment-dwelling amoebae appear to have an unhappy affinity for huge viruses. Giant icosahedral Mimiviruses with genomes of the order of 1 megabase (Mb) were first identified in Acanthamoeba. Digging into antipodean sediments has once again been fruitful where Philippe et al. (p. 281 ; see the cover) dis... | 10.1038/s41579-022-00754-5 | Isolation of pandoravirus that represented a novel family of giant viruses with non-icosahedral virions, a nuclear infectious cycle and the largest viral genome known to date |
10.1073/pnas.1510795112 | 103,313,545 | Acanthamoeba species are infected by the largest known DNA viruses. These include icosahedral Mimiviruses, amphora-shaped Pandoraviruses, and Pithovirus sibericum , the latter one isolated from 30,000-y-old permafrost. Mollivirus sibericum , a fourth type of giant virus, was isolated from the same permafrost sample. It... | 10.1038/s41579-022-00754-5 | Recovery of a novel giant virus, pithovirus , from a 30,000-year-old permafrost sample through co-cultivation with amoeba |
10.1073/pnas.1007615107 | 62,610,653 | As major consumers of heterotrophic bacteria and phytoplankton, microzooplankton are a critical link in aquatic foodwebs. Here, we show that a major marine microflagellate grazer is infected by a giant virus, Cafeteria roenbergensis virus (CroV), which has the largest genome of any described marine virus (≈730 kb of do... | 10.1038/s41579-022-00754-5 | Isolation and characterization of a novel giant virus related to mimivirus together with its native host, the marine predatory flagellate Cafeteria roenbergensis |
10.1038/ismej.2013.59 | 41,509,647 | Abstract Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, ... | 10.1038/s41579-022-00754-5 | First study in which co-occurrence analysis was performed on metagenomic data to connect giant viruses to potential eukaryotic hosts. |
10.1038/s41586-020-1957-x | 123,192,277 | Abstract Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metag... | 10.1038/s41579-022-00754-5 | Recovery of more than 2,000 giant virus metagenome-assembled genomes from global metagenomic datasets, greatly expanding phylogenetic diversity, the repertoire of predicted metabolic traits for host reprogramming, and predicting connections between giant viruses and hosts in all major eukaryotic groups. |
10.1073/pnas.1907517116 | 123,013,226 | Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomic... | 10.1038/s41579-022-00754-5 | Discovery of a novel giant virus that groups with the Mesomimiviridae through co-sorting with its choanoflagellate host and experimental characterization that provided evidence for the function of the virus-encoded rhodopsin genes as a light-driven proton pump |
10.1126/science.278.5344.1800 | 121,819,081 | Sequence analysis of the 330-kilobase genome of the virus PBCV-1 that infects a chlorella-like green algae revealed an open reading frame, A98R, with similarity to several hyaluronan synthases. Hyaluronan is an essential polysaccharide found in higher animals as well as in a few pathogenic bacteria. Expression of the A... | 10.1038/s41579-022-00754-5 | First experimental characterization of a giant virus-encoded gene that plays a role in metabolic host reprogramming. |
10.1105/tpc.114.125641 | 42,537,748 | Abstract Marine viruses are major ecological and evolutionary drivers of microbial food webs regulating the fate of carbon in the ocean. We combined transcriptomic and metabolomic analyses to explore the cellular pathways mediating the interaction between the bloom-forming coccolithophore Emiliania huxleyi and its spec... | 10.1038/s41579-022-00754-5 | Experimental validation of metabolic host reprogramming by E. huxleyi virus in its coccolithophore host. |
10.1073/pnas.1912006116 | 125,112,204 | Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects ... | 10.1038/s41579-022-00754-5 | Phylogenetic analysis that provides evidence for the repeated transfer of DNA-dependent RNA polymerase between giant viruses and a proto-eukaryote, suggesting a major role of viruses in the evolution of cellular domains. |
10.1007/s11357-021-00495-y | 132,750,105 | Abstract A tiny fraction of people immunized with lipid nanoparticle (LNP)-enclosed mRNA (LNP-mRNA) vaccines develop allergic symptoms following their first or subsequent vaccinations, including anaphylaxis. These reactions resemble complement (C) activation-related pseudoallergy (CARPA) to i.v. administered liposomes,... | 10.1038/s41565-022-01071-x | Demonstrates in a pig model that injection of Comirnaty (Pfizer/BioNTech) vaccine causes hemodynamic changes in animals that are similar to the changes characteristic of infusion reactions to nanomedicines |
10.1084/jem.20070657 | 103,780,449 | Hypertension promotes atherosclerosis and is a major source of morbidity and mortality. We show that mice lacking T and B cells (RAG-1−/− mice) have blunted hypertension and do not develop abnormalities of vascular function during angiotensin II infusion or desoxycorticosterone acetate (DOCA)–salt. Adoptive transfer of... | 10.1038/s41577-018-0113-4 | This is one of the first studies to describe a role for the adaptive immune system in the development of hypertension |
10.1126/science.aar7201 | 103,810,326 | Bacterial involvement in autoimmunity The composition of the commensal microbiota is known to influence autoimmune disease development and persistence. Manfredo Vieira et al. identified a gut microbe, Enterococcus gallinarum , that translocates from the gut into the organs of mice with a genetic predisposition to lupus... | 10.1038/s41577-018-0113-4 | This study shows that, on a susceptible genetic background, the systemic translocation of gut pathobionts as a result of intestinal barrier dysfunction can trigger autoimmunity |
10.1126/science.1210713 | 104,407,395 | Light propagation can be controlled with plasmonic interfaces that introduce abrupt phase shifts along the optical path. | 10.1038/s41578-018-0061-4 | This paper derives the generalized Snell’s law, which provides the theoretical framework for many types of acoustic metasurfaces |
10.1063/1.4941338 | 41,749,850 | Conventional acoustic absorbers are used to have a structure with a thickness comparable to the working wavelength, resulting in major obstacles in real applications in low frequency range. We present a metasurface-based perfect absorber capable of achieving the total absorption of acoustic wave in an extremely low fre... | 10.1038/s41578-018-0061-4 | This study reports a metasurface-based sound absorber with near-perfect absorption at a frequency whose wavelength is over 200 times greater than the thickness of the absorber |
10.1126/science.1206923 | 125,113,991 | The mutational profile of head and neck cancer is complex and may pose challenges to the development of targeted therapies. | 10.1038/s41572-020-00224-3 | This was one of the first papers to describe NOTCH1 mutations in HNSCC |
10.1126/science.1208130 | 82,877,340 | The mutational profile of head and neck cancer is complex and may pose challenges to the development of targeted therapies. | 10.1038/s41572-020-00224-3 | This was one of the first papers to report whole-exome sequencing in HNSCC |
10.1002/hed.26016 | 58,746,124 | Abstract Background Second primary tumors (SPTs) are a common cause of reduced life expectancy in patients treated for head and neck cancer (HNC). This phenomenon forms an area to be addressed during posttreatment follow‐up. Methods We conducted a systematic review of literature following PRISMA guidelines, from 1979 t... | 10.1038/s41572-020-00224-3 | This paper underscores the high risk of developing second primary tumors in carcinogen-associated HNSCC |
10.1126/scitranslmed.aad7121 | 62,293,106 | A longitudinal study of intestinal microbiota in children and their mothers shows that antibiotics, cesarean section, and infant formula alter patterns of microbial acquisition and succession during the first 2 years of childhood. | 10.1038/s41575-022-00685-9 | This paper shows the profound effects of caesarean section and antibiotic exposure on how the early-life microbiome develops. |
10.1002/bies.202000163 | 84,481,881 | Abstract Worldwide, antibiotic use is increasing, but many infections against which antibiotics are applied are not even caused by bacteria. Over‐the‐counter and internet sales preclude physician oversight. Regional differences, between and within countries highlight many potential factors influencing antibiotic use. T... | 10.1038/s41575-022-00685-9 | This paper indicates the extensive variation in antibiotic use and the means to rationalize therapeutic approaches |
10.1210/jc.2015-2696 | 104,382,626 | Context and objective: Evidence that bacteria in the human gut may influence nutrient metabolism is accumulating. We investigated whether use of antibiotics influences the risk of developing type 2 diabetes and whether the effect can be attributed to specific types of antibiotics. Methods: We conducted a population-bas... | 10.1038/s41575-022-00685-9 | This was a large epidemiological study in Denmark linking prior antibiotic exposures, even years earlier, with the risk of developing T2DM |
10.1186/s13059-020-02051-x | 37,953,963 | Abstract We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using... | 10.1038/s41580-020-00288-9 | This study establishes a trifunctional multiplexed orthogonal genome editing system that performs cytosine base editing, adenine base editing and insertions and deletions in plants |
10.1002/ana.24385 | 40,790,928 | Objective To assess whether risk factors for Parkinson disease and dementia with Lewy bodies increase rate of defined neurodegenerative disease in idiopathic rapid eye movement (REM) sleep behavior disorder (RBD). Methods Twelve centers administered a detailed questionnaire assessing risk factors for neurodegenerative ... | 10.1038/s41572-018-0016-5 | This is the first multicentre study showing that patients with iRBD are at very high risk of neurodegenerative α-synucleinopathy with different risk factor profiles between converters and nonconverters |
10.1002/mds.23257 | 82,523,312 | Abstract The presence of either excessive tonic chin EMG activity during REM sleep, or excessive phasic submental or limb EMG twitching is required to diagnose REM sleep behavior disorder (RBD). The aim was to identify cut‐off values and to assess the sensitivity and specificity of these values taken separately or comb... | 10.1038/s41572-018-0016-5 | This is one of the first validated PSG studies to estimate the diagnostic value of a visual scoring method for the diagnosis of iRBD with establishment of cut-off values to be used in clinical and research settings |
10.1128/mr.55.3.371-394.1991 | 104,321,907 | The regulatory regions for 119 Escherichia coli promoters have been analyzed, and the locations of the regulatory sites have been cataloged. The following observations emerge. (i) More than 95% of promoters are coregulated with at least one other promoter. (ii) Virtually all sigma 70 promoters contain at least one regu... | 10.1038/s41576-020-0254-8 | This landmark review from the pre-genomics era stresses the importance of promoter architecture rather than sequence |
10.1073/pnas.72.3.784 | 125,081,002 | Escherichia coli RNA polymerase (EC 2.7.7.6), bound in a tight complex at an early T7 promoter, protects 41 to 43 base pairs of DNA from digestion by DNase. I. The protected DNA fragment contains both the binding site for RNA polymerase and the mRNA initiation point for the promoter. The sequence of the DNA fragment an... | 10.1038/s41576-020-0254-8 | This first promoter sequence analysis reveals that promoters contain instances of conserved sequence motifs |
10.1128/jb.141.2.973-976.1980 | 61,154,082 | In bacterial promoters subject to stringent control the heptanucleotide sequence spanning nucleotide positions −5 to +2 (defining the −10 region [D. Pribnow, J. Mol. Biol. 99: 419–443, 1975] as positions −12 to −6) is highly conserved. This conserved region, for which the best consensus sequence is [Formula: see text] ... | 10.1038/s41576-020-0254-8 | This study highlights the role of the discriminator sequence at bacterial promoters and lays the basis for work on detailed sequence rules |
10.1126/science.1227786 | 124,077,446 | The bacterial transcription initiation complex preorganizes promoter DNA for nucleotide binding and RNA synthesis. | 10.1038/s41576-020-0254-8 | Following earlier structures, this publication reveals new details about interactions by the transcription bubble during initiation |
10.1126/science.8248780 | 19,455,743 | A DNA sequence rich in (A+T), located upstream of the -10, -35 region of the Escherichia coli ribosomal RNA promoter rrnB P1 and called the UP element, stimulates transcription by a factor of 30 in vivo, as well as in vitro in the absence of protein factors other than RNA polymerase (RNAP). When fused to other promoter... | 10.1038/s41576-020-0254-8 | At the culmination of many publications describing the contributions of upstream sequences to promoter activity, this study presents a unified model |
10.1128/jb.90.4.946-957.1965 | 28,226,141 | Englesberg, Ellis (University of Pittsburgh, Pittsburgh, Pa.), Joseph Irr, Joseph Power, and Nancy Lee . Positive control of enzyme synthesis by gene C in the l -arabinose system. J. Bacteriol 90: 946–957. 1965.—The l -arabinose gene complex consists of genes D, A, B, and C, linked in that order between the markers thr... | 10.1038/s41576-020-0254-8 | This landmark paper undermines the belief that regulation must be due to repressors |
10.1146/annurev-micro-092412-155737 | 83,040,229 | Transcription initiation is the crucial focal point of gene expression in prokaryotes. The key players in this process, sigma factors (σs), associate with the catalytic core RNA polymerase to guide it through the essential steps of initiation: promoter recognition and opening, and synthesis of the first few nucleotides... | 10.1038/s41576-020-0254-8 | This is a must-read, beautifully written review of bacterial sigma factors, starting with their history |
10.1101/262964 | 74,017,809 | Abstract Current methods for genome-wide analysis of gene expression requires shredding original transcripts into small fragments for short-read sequencing. In bacteria, the resulting fragmented information hides operon complexity. Additionally, in-vivo processing of transcripts confounds the accurate identification of... | 10.1038/s41576-020-0254-8 | This study reports the identification of transcription units using long-read sequencing |
10.1073/pnas.1621224114 | 59,077,258 | Significance Retroviruses copy their RNA genome into complementary DNA, which is then inserted into the host chromosomal DNA as an obligatory part of their life cycle. Such integrated viral sequences, called proviruses, are passed to the infected cell progeny on cellular division. If germline cells are targeted, the pr... | 10.1038/s41579-019-0189-2 | This paper is the first to identify an ERV related to modern deltaretroviruses, the genus that includes human T-lymphotropic viruses and the bovine leukaemia virus |
10.1073/pnas.1814203116 | 70,931,323 | Human endogenous retrovirus-K (HERV-K) human mouse mammary tumor virus-like 2 (HML-2) is the most recently active endogenous retrovirus group in humans, and the only group with human-specific proviruses. HML-2 expression is associated with cancer and other diseases, but extensive searches have failed to reveal any repl... | 10.1038/s41579-019-0189-2 | This study uncovers multiple young ERVs in gorilla genomes related to human HERV-K(HML2), indicating recent activity in the gorilla lineage and raising the possibility that modern gorillas host an active HML-2 virus |
10.1038/ncomms13954 | 81,524,353 | Abstract Very little is known about the ancient origin of retroviruses, but owing to the discovery of their ancient endogenous viral counterparts, their early history is beginning to unfold. Here we report 36 lineages of basal amphibian and fish foamy-like endogenous retroviruses (FLERVs). Phylogenetic analyses reveal ... | 10.1038/s41579-019-0189-2 | This paper describes the discovery and analysis of foamy-virus-like ERVs in marine vertebrates and suggests retroviruses may have originated early during vertebrate evolution |
10.7554/elife.12704 | 102,860,069 | Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, co... | 10.1038/s41579-019-0189-2 | This paper describes the use of ERV loci to retrace the origins and global spread of an ancient gammaretrovirus among mammals between 15 million and 33 million years ago, spanning the late Oligocene and early Miocene epochs |
10.7554/elife.22519 | 80,641,848 | Endogenous retroviral sequences provide a molecular fossil record of ancient infections whose analysis might illuminate mechanisms of viral extinction. A close relative of gammaretroviruses, HERV-T, circulated in primates for ~25 million years (MY) before apparent extinction within the past ~8 MY. Construction of a nea... | 10.1038/s41579-019-0189-2 | This study uses ancestral node reconstruction to establish that an intact env gene in the human genome can mediate superinfection interference and may have functioned to restrict entry of an ancient exogenous virus. |
10.1073/pnas.1602336113 | 103,786,506 | Endogenous retroviruses (ERVs) have contributed to more than 8% of the human genome. The majority of these elements lack function due to accumulated mutations or internal recombination resulting in a solitary (solo) LTR, although members of one group of human ERVs (HERVs), HERV-K, were recently active with members that... | 10.1038/s41579-019-0189-2 | This study capitalizes on human genomic variation captured in databases, such as the 1000 Genomes Project, to detect and describe rare, unfixed HERV-K(HML-2) loci in the human population |
10.1101/gad.1762309 | 109,095,543 | At least 8% of the human genome was formed by integration of retroviral DNA sequences. Here we analyze the forces directing the accumulation of human endogenous retroviruses (HERVs) by comparing de novo HERV integration targeting with the distribution of fixed HERV elements in the human genome. All known genomic HERVs ... | 10.1038/s41579-019-0189-2 | This study describes the first global analysis of integration site preferences for an ancient, reconstituted endogenous retrovirus (HERV–Kcon), enabling direct comparison of integration site preferences to the locations of fixed HERV-K(HML2) loci in the human genome |
10.1073/pnas.1714590114 | 100,639,927 | Syncytins are envelope genes from endogenous retroviruses that have been captured during evolution for a function in placentation. They have been found in all placental mammals in which they have been searched, including marsupials. Placental structures are not restricted to mammals but also emerged in some other verte... | 10.1038/s41579-019-0189-2 | This paper gives the first description of a syncytin in a nonmammalian species |
10.1073/pnas.1702204114 | 83,110,096 | Capture of retroviral envelope genes is likely to have played a role in the emergence of placental mammals, with evidence for multiple, reiterated, and independent capture events occurring in mammals, and be responsible for the diversity of present day placental structures. Here, we uncover a full-length endogenous ret... | 10.1038/s41579-019-0189-2 | This paper describes the discovery and functional characterization of an unusual ERV-encoded Env expressed as a secreted protein in placental tissues and in the blood of pregnant women |
10.7554/elife.35989 | 83,023,109 | Recent work suggests extensive adaptation of transposable elements (TEs) for host gene regulation. However, high numbers of integrations typical of TEs, coupled with sequence divergence within families, have made systematic interrogation of the regulatory contributions of TEs challenging. Here, we employ CARGO, our rec... | 10.1038/s41579-019-0189-2 | This study uses a modified CRISPR system to induce or silence multiple HERV-K(HML2) LTRs in parallel, revealing long-range effects on expression of hundreds of genes |
10.1073/pnas.0703637104 | 123,167,785 | The evolutionary forces that establish and hone target gene networks of transcription factors are largely unknown. Transposition of retroelements may play a role, but its global importance, beyond a few well described examples for isolated genes, is not clear. We report that LTR class I endogenous retrovirus (ERV) retr... | 10.1038/s41579-019-0189-2 | This paper and that of Chuong et al. (2016) reveal that co-option of ERV LTRs contributed to concerted evolution of interferon-regulated gene networks and many p53 regulated genes, respectively |
10.1126/science.aan4187 | 62,333,589 | Taking the PERVs out of pigs With the severe shortage of organs needed for transplants, xenotransplantation (transplantation of nonhuman organs to humans) offers an alternative source. Some pig organs have similar size and function to those of humans. The challenge is that the pig genome harbors porcine endogenous retr... | 10.1038/s41579-019-0189-2 | This paper describes the parallel inactivation of two dozen related porcine ERV (PERV) loci in a single fetal fibroblast cell using a customized CRISPR–Cas9 protocol followed by nuclear transfer to create a line of pigs free of functional PERV loci. |
10.1136/oemed-2019-106008 | 38,717,098 | Objectives This study provides an overview of the influence of occupational risk factors on the global burden of disease as estimated by the occupational component of the Global Burden of Disease (GBD) 2016 study. Methods The GBD 2016 study estimated the burden in terms of deaths and disability-adjusted life years (DAL... | 10.1038/s41572-021-00257-2 | An important study that used data from the GBD 2016 study to provide global, regional, and national estimates for prevalence and years of life lived with disability for migraine and TTH |
10.1093/eurpub/ckz185.161 | 81,991,270 | Abstract Background The Nordic countries - Norway, Sweden, Finland, Iceland, Denmark - combine liberal and open-market economies with public welfare and universal health services. As separate countries with differences in culture and lifestyle, important health differences may exist between them. The aim of this study ... | 10.1038/s41572-021-00257-2 | Updated data from the GBD 2017 providing estimates for incidence, prevalence and years of life lived with disability for migraine and TTH in the United States |
10.1002/ejp.748 | 40,291,982 | Abstract Background and Objective Tension‐type headache ( TTH ) imposes a heavy burden on the global population but remains incompletely understood and poorly managed. Databases and Data Treatment Here, we review current knowledge of peripheral factors involved in the mechanism of TTH and make recommendations for the t... | 10.1038/s41572-021-00257-2 | A review on peripheral and muscular factors involved in the pathophysiology of TTH and implications for the treatment of episodic TTH |
10.1046/j.1468-2982.2000.00070.x | 83,051,647 | The aim of the present thesis was to investigate the pathophysiology of chronic tension-type headache with special reference to central mechanisms. Increased tenderness to palpation of pericranial myofascial tissues is the most apparent abnormality in patients with tension-type headache. A new piece of equipment, a so-... | 10.1038/s41572-021-00257-2 | A comprehensive review on the important role and mechansms of central sensitization in the pathophysiology of CTTH |
10.1111/ene.14268 | 125,060,845 | Abstract Background The frequent use of medication to treat migraine attacks can lead to an increase in migraine frequency and is called medication‐overuse headache (MOH). Methods Based on the available literature in this guideline, the first step in patient management is education and counselling. Results Patients wit... | 10.1038/s41572-021-00257-2 | An important guideline on the management of MOH, a complication of primary headaches including migraine and TTH |
10.1353/bhm.2002.0022 | 125,195,437 | The influenza pandemic of 1918-20 is recognized as having generally taken place in three waves, starting in the northern spring and summer of 1918. This pattern of three waves, however, was not universal: in some locations influenza seems to have persisted into or returned in 1920. The recorded statistics of influenza ... | 10.1038/s41591-022-01910-3 | A Review article that revises the estimated mortality from the 1918 IAV pandemic. |
10.1371/journal.ppat.1009453 | 104,220,574 | There is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have n... | 10.1038/s41576-021-00408-x | This paper presents a retrospective analysis of HCoV-229E sequences and plasma samples that shows that human coronaviruses can evolve over several years to resist antibody neutralization, providing a potential mechanism for recurrent human coronavirus infections |
10.1101/2020.09.15.298067 | 80,151,703 | Abstract SARS-CoV-2, the causative agent of COVID-19, is responsible for over 24 million infections and 800,000 deaths since its emergence in December 2019. There are few therapeutic options and no approved vaccines. Here we examine the properties of highly potent human monoclonal antibodies (hu-mAbs) in a mouse adapte... | 10.1038/s41576-021-00408-x | This study demonstrates the likely importance of SARS-CoV-2 neutralizing mAb Fc-effector functions in an animal model |
10.1093/cid/ciab646 | 135,269,469 | Abstract Recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may pose a threat to immunity. A systematic landscape of neutralizing antibodies against emerging variants is needed. We systematically searched for studies that evaluated neutralizing antibody titers induced by previous inf... | 10.1038/s41576-021-00408-x | This paper presents a systematic review and meta-analysis of in vitro neutralization studies of SARS-CoV-2 variants by convalescent and vaccinee plasma |
10.1101/2021.06.06.446826 | 83,029,839 | Emergence of SARS-CoV-2 variants, including the globally successful B.1.1.7 lineage, suggests viral adaptations to host selective pressures resulting in more efficient transmission. Although much effort has focused on Spike adaptation for viral entry and adaptive immune escape, B.1.1.7 mutations outside Spike likely co... | 10.1038/s41576-021-00408-x | This systems biology study shows that in contrast to earlier SARS-CoV-2 variants, the alpha variant may owe its increased transmissibility and virulence to its antagonism of cellular innate immunity |
10.1073/pnas.90.10.4495 | 103,664,053 | Erythropoietin regulates the proliferation and differentiation of erythroid precursor cells. Its effect is mediated by the erythropoietin receptor (EPOR), a member of a large family of cytokine receptors. The EPOR gene has recently been cloned, sequenced, and characterized. As shown experimentally, its intracellular C-... | 10.1038/s41576-021-00400-5 | This article describes a study of the family of Eero Mäntyranta that identified a familial mutation that caused benign erythrocytosis and hence, improved VO 2 max |
10.1161/circ.142.suppl_3.16685 | 57,037,917 | Introduction: Hypertrophic (HCM) and dilated (DCM) cardiomyopathies are leading causes of sudden death and heart failure requiring transplantation in young individuals. While some cases have a monogenic underlying cause, the majority remain unexplained. Objective: To better understand the contribution of common genetic... | 10.1038/s41576-021-00400-5 | This article describes a large GWAS of both cardiac function and dilated versus hypertrophic cardiomyopathy risk, which highlights the possibility of antagonist pleiotropy for genes that aid cardiac function during reproductive ages and then cause elevated risk later in life |
10.1038/s41598-018-24735-y | 38,272,830 | Abstract We performed a large genome-wide association study to discover genetic variation associated with muscular strength, and to evaluate shared genetic aetiology with and causal effects of muscular strength on several health indicators. In our discovery analysis of 223,315 individuals, we identified 101 loci associ... | 10.1038/s41576-021-00400-5 | This article reports the largest GWAS to date of hand-grip strength that provides evidence for brain–muscle association |
10.1038/s41467-021-23579-x | 135,540,329 | Abstract Exercise training prevents multiple diseases, yet the molecular mechanisms that drive exercise adaptation are incompletely understood. To address this, we create a computational framework comprising data from skeletal muscle or blood from 43 studies, including 739 individuals before and after exercise or train... | 10.1038/s41576-021-00400-5 | This article accompanies the online ExtraMeta ( ) resource, and highlights the changes to gene expression that occur with endurance exercise |
10.1073/pnas.0909285106 | 103,923,092 | The impact of globalization on the emergence and spread of pathogens is an important veterinary and public health issue. Staphylococcus aureus is a notorious human pathogen associated with serious nosocomial and community-acquired infections. In addition, S. aureus is a major cause of animal diseases including skeletal... | 10.1038/s41576-018-0032-z | This paper describes a host-jump event for Staphylococcus aureus and reports the identification of MGEs associated with adaptation to poultry. |
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