Top 25 Life and Biological Sciences Articles of 2022

Top 25 Articles

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  Engineered helicase replaces thermocycler in DNA amplification while retaining desired PCR characteristics

  PCR is an essential method for the amplification and manipulation of nucleic acids, but the requirement for a thermocycler limits access. Here, authors engineer a helicase to replace the heating step of PCR with enzymatic unwinding, allowing the isothermal amplification of fragments up to 6 kb.

  • Momčilo Gavrilov
  • Joshua Y. C. Yang
  • Taekjip Ha

  ArticleOpen Access23 Oct 2022 Nature Communications
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  Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms

  Transitions between hermaphroditic and separate sexes are relatively understudied in animals compared to pants. Here, Wang et al. reconstruct the evolution of separate sexes in the flatworms and complex changes of sex chromosomes in the roundworms.

  • Yifeng Wang
  • Robin B. Gasser
  • Qi Zhou

  ArticleOpen Access10 Jun 2022 Nature Communications
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  The gut microbiota and depressive symptoms across ethnic groups

  Here, by studying a multi-ethnic cross-sectional urban cohort (N = 3211, 6 ethnic groups), the authors show that depressive symptom levels are related to the gut microbiota taxonomic characteristics but that these are largely invariant across ethnic groups.

  • Jos A. Bosch
  • Max Nieuwdorp
  • Anja Lok

  ArticleOpen Access6 Dec 2022 Nature Communications
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  Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms

  Here, the authors perform large-scale high-resolution Parkinson’s disease metagenomics analyses, revealing widespread dysbiosis characterized by overabundance of pathogens, immunogens, toxicants, and curli, reduction in neuroprotective and antiinflammatory molecules, and dysregulated neuroactive signaling.

  • Zachary D. Wallen
  • Ayse Demirkan
  • Haydeh Payami

  ArticleOpen Access15 Nov 2022 Nature Communications
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  Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon

  Genetic code redundancies are considered inconsequential to protein structure. This study uncovers a dependence between local amino acid conformation in folded proteins and the identity of the codon from which that amino acid was translated.

  • Aviv A. Rosenberg
  • Ailie Marx
  • Alex M. Bronstein

  ArticleOpen Access20 May 2022 Nature Communications
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  De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution

  Current methods to reanalyze bulk RNA-seq at spatially resolved single-cell resolution have limitations. Here, the authors develop Bulk2Space, a spatial deconvolution algorithm using single-cell and spatial transcriptomics as references, providing new insights into spatial heterogeneity within bulk tissue.

  • Jie Liao
  • Jingyang Qian
  • Xiaohui Fan

  ArticleOpen Access30 Oct 2022 Nature Communications
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  Exceptional preservation and foot structure reveal ecological transitions and lifestyles of early theropod flyers

  The shape of bird toe pads and foot scales can be used to infer their behaviour. Here, the authors examine fossil evidence of toe pads and scales, in addition to claws and bones, from birds and close relatives, illustrating diverse lifestyles and ecological roles among early theropod flyers.

  • Michael Pittman
  • Phil R. Bell
  • Thomas G. Kaye

  ArticleOpen Access20 Dec 2022 Nature Communications
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  Common evolutionary origin of acoustic communication in choanate vertebrates

  Here, the authors record acoustic communication in 53 species commonly considered non-vocal and reconstruct acoustic communication as originating 407 million years ago.

  • Gabriel Jorgewich-Cohen
  • Simon William Townsend
  • Marcelo R. Sánchez-Villagra

  ArticleOpen Access25 Oct 2022 Nature Communications
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  Calcium-mediated rapid movements defend against herbivorous insects in Mimosa pudica

  Mimosa pudica moves its leaves within seconds of being touched or wounded. Here the authors show that such movements are triggered by rapid changes in Ca²⁺ and action and variation potentials and provide evidence that rapid movements help protect the plant from insect attacks.

  • Takuma Hagihara
  • Hiroaki Mano
  • Masatsugu Toyota

  ArticleOpen Access14 Nov 2022 Nature Communications
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  Evolutionary transition from a single RNA replicator to a multiple replicator network

  Long-term experimental evolution shows that a single polymerase-encoding RNA replicator can evolve into a complex replicator network, shedding light on how a molecular replicator could have developed complexity before the emergence of life.

  • Ryo Mizuuchi
  • Taro Furubayashi
  • Norikazu Ichihashi

  ArticleOpen Access18 Mar 2022 Nature Communications
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  Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism

  Extensive lysosomal damage can result in cell death but how limited protease leakage affects cytoplasmic organelles in viable cells is not well understood. Here the authors show that limited lysosomal damage leads to changes in the mitochondrial proteome and the modulation of macrophage immunometabolism.

  • Claudio Bussi
  • Tiaan Heunis
  • Maximiliano G. Gutierrez

  ArticleOpen Access28 Nov 2022 Nature Communications
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  Payload distribution and capacity of mRNA lipid nanoparticles

  Lipid nanoparticles (LNPs) are effective vehicles to deliver mRNA vaccines and therapeutics but assessing the mRNA packaging characteristics in LNPs is challenging. Here, the authors report that mRNA and lipid contents in LNP formulations can be quantitatively examined by multi-laser cylindrical illumination confocal spectroscopy at the single-nanoparticle level.

  • Sixuan Li
  • Yizong Hu
  • Hai-Quan Mao

  ArticleOpen Access23 Sep 2022 Nature Communications
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  Improved prediction of protein-protein interactions using AlphaFold2

  Predicting the structure of protein complexes is extremely difficult. Here, authors apply AlphaFold2 with optimized multiple sequence alignments to model complexes of interacting proteins, enabling prediction of both if and how proteins interact with state-of-art accuracy.

  • Patrick Bryant
  • Gabriele Pozzati
  • Arne Elofsson

  ArticleOpen Access10 Mar 2022 Nature Communications
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  Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

  The accuracy of AlphaFold decreases with the number of protein chains and the available GPU memory limits the size of protein complexes that can be predicted. Here, the authors show that complexes with 10–30 chains can be assembled from predicted subcomponents using Monte Carlo tree search.

  • Patrick Bryant
  • Gabriele Pozzati
  • Arne Elofsson

  ArticleOpen Access12 Oct 2022 Nature Communications
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  Microbiome differential abundance methods produce different results across 38 datasets

  Many microbiome differential abundance methods are available, but it lacks systematic comparison among them. Here, the authors compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups, and show ALDEx2 and ANCOM-II produce the most consistent results.

  • Jacob T. Nearing
  • Gavin M. Douglas
  • Morgan G. I. Langille

  ArticleOpen Access17 Jan 2022 Nature Communications
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  Deep phenotyping and lifetime trajectories reveal limited effects of longevity regulators on the aging process in C57BL/6J mice

  Lifespan can be affected by both physiological ageing and specific sets of pathologies associated with old age. Here the authors report a resource of large-scale cross-sectional phenotyping of aging male mice at different time points to analyse a large set of phenotypes and molecular markers, including during genetic and diet interventions affecting lifespan.

  • Kan Xie
  • Helmut Fuchs
  • Dan Ehninger

  ArticleOpen Access11 Nov 2022 Nature Communications
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  Structure-based discovery of small molecules that disaggregate Alzheimer’s disease tissue derived tau fibrils in vitro

  Evidence suggests that fibrous aggregates of protein tau may be the proximal cause of Alzheimer’s disease. Here, using atomic structures of tau fibrils from brains of people with Alzheimer’s disease, the authors have found small-molecule drug leads that disaggregate tau fibrils in vitro.

  • Paul M. Seidler
  • Kevin A. Murray
  • David S. Eisenberg

  ArticleOpen Access16 Sep 2022 Nature Communications
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  The intestinal clock drives the microbiome to maintain gastrointestinal homeostasis

  Here, Heddes et al. demonstrate a major role for the intestinal circadian clock in driving microbiome dynamics. Microbiota transfer from intestinal clock-deficient mice promotes altered intestinal phenotypes, highlighting the importance of functional intestinal clocks for gastrointestinal homeostasis of the host.

  • Marjolein Heddes
  • Baraa Altaha
  • Silke Kiessling

  ArticleOpen Access14 Oct 2022 Nature Communications
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  A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues

  Identification of senescent cells in vivo remains a challenging task. Here the authors present and validate a senescence gene set called SenMayo enriched in human and murine aged tissues.

  • Dominik Saul
  • Robyn Laura Kosinsky
  • Sundeep Khosla

  ArticleOpen Access16 Aug 2022 Nature Communications
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  Caffeine blocks SREBP2-induced hepatic PCSK9 expression to enhance LDLR-mediated cholesterol clearance

  Caffeine may reduce cardiovascular disease risk, but the underlying mechanisms for these effects are incompletely understood. Here the authors report that caffeine inhibits the activation of the transcription factor SREBP2 to promote LDLc clearance through the PCSK9-LDLR axis.

  • Paul F. Lebeau
  • Jae Hyun Byun
  • Richard C. Austin

  ArticleOpen Access9 Feb 2022 Nature Communications
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  Tissue-specific impacts of aging and genetics on gene expression patterns in humans

  Age is a risk factor for many diseases, but the impact of aging on molecular phenotypes is not fully understood. Here, the authors quantify the relative contributions of genetics and aging to gene expression patterns across 27 tissues in humans, showing that age and genetics each play distinct roles in shaping expression phenotypes.

  • Ryo Yamamoto
  • Ryan Chung
  • Peter H. Sudmant

  ArticleOpen Access3 Oct 2022 Nature Communications
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  Altered glycolysis triggers impaired mitochondrial metabolism and mTORC1 activation in diabetic β-cells

  Chronic hyperglycemia impairs insulin secretion from pancreatic beta cells in diabetes. Here, the authors reveal that a glucose metabolite is responsible and show lowering glucose metabolism during hyperglycemia prevents loss of beta-cell function.

  • Elizabeth Haythorne
  • Matthew Lloyd
  • Frances M. Ashcroft

  ArticleOpen Access14 Nov 2022 Nature Communications
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  Perspectives in machine learning for wildlife conservation

  Animal ecologists are increasingly limited by constraints in data processing. Here, Tuia and colleagues discuss how collaboration between ecologists and data scientists can harness machine learning to capitalize on the data generated from technological advances and lead to novel modeling approaches.

  • Devis Tuia
  • Benjamin Kellenberger
  • Tanya Berger-Wolf

  PerspectiveOpen Access9 Feb 2022 Nature Communications
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  Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data

  Cell types are typically identified in single cell transcriptomic data by manual annotation of cell clusters using established marker genes. Here the authors present a fully-automated computational platform that can quickly and accurately distinguish between cell types.

  • Aleksandr Ianevski
  • Anil K. Giri
  • Tero Aittokallio

  ArticleOpen Access10 Mar 2022 Nature Communications
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  Host-dependent resistance of Group A Streptococcus to sulfamethoxazole mediated by a horizontally-acquired reduced folate transporter

  There is increasing evidence for metabolic processes mediating antimicrobial resistance. Here, the authors present a mechanism of sulfamethoxazole resistance in Group A Streptococcus that is dependent on acquiring end products of the host folate biosynthesis pathway.

  • M. Kalindu D. Rodrigo
  • Aarti Saiganesh
  • Timothy C. Barnett

  ArticleOpen Access30 Nov 2022 Nature Communications