Experimental organisms

  • Article |

    Differences in the mechanical properties of individual cardiomyocytes drive their segregation into compact versus trabecular layer, thereby transforming the myocardium in a developing heart from a simple epithelium into an intricately patterned tissue with distinct cell fates.

    • Rashmi Priya
    • , Srinivas Allanki
    •  & Didier Y. R. Stainier
  • Article |

    Single-cell RNA sequencing and spatial transcriptomics reveal that the somitogenesis clock is active in mouse gastruloids, which can be induced to generate somites with the correct rostral–caudal patterning.

    • Susanne C. van den Brink
    • , Anna Alemany
    •  & Alexander van Oudenaarden
  • Article |

    Identification and characterization, using a comprehensive embryonic phenotyping pipeline, of 410 lethal alleles during the generation of the first 1,751 of 5,000 unique gene knockouts produced by the International Mouse Phenotyping Consortium.

    • Mary E. Dickinson
    • , Ann M. Flenniken
    •  & Stephen A. Murray
  • Letter |

    Mitochondria have essential functions within cells, and their dysfunction is linked to various disorders; here, the fatty acid stearic acid (C18:0), which is a dietary component, and the transferrin receptor (TFR1) are shown to regulate mitochondrial function.

    • Deniz Senyilmaz
    • , Sam Virtue
    •  & Aurelio A. Teleman
  • Article |

    In mouse, an axonal connectivity map showing the wiring patterns across the entire brain has been created using an EGFP-expressing adeno-associated virus tracing technique, providing the first such whole-brain map for a vertebrate species.

    • Seung Wook Oh
    • , Julie A. Harris
    •  & Hongkui Zeng
  • Letter |

    Mouse androgenetic haploid embryonic stem cell lines can be established by transferring sperm into an enucleated oocyte; the cells maintain haploidy and stable growth over 30 passages, express pluripotent markers, are able to differentiate into all three germ layers, contribute to germlines of chimaeras when injected into blastocysts and can produce fertile progeny that carry genetic modifications to the next generation.

    • Wei Li
    • , Ling Shuai
    •  & Qi Zhou
  • Letter |

    Sequencing of the Arabidopsis thaliana root microbiome shows that its composition is strongly influenced by location, inside or outside the root, and by soil type.

    • Derek S. Lundberg
    • , Sarah L. Lebeis
    •  & Jeffery L. Dangl
  • Letter |

    A genomic map of nearly 300,000 potential cis-regulatory sequences determined from diverse mouse tissues and cell types reveals active promoters, enhancers and CCCTC-binding factor sites encompassing 11% of the mouse genome and significantly expands annotation of mammalian regulatory sequences.

    • Yin Shen
    • , Feng Yue
    •  & Bing Ren
  • Letter |

    Novel protein-coding genes can arise either from pre-existing genes or de novo; here it is shown that functional genes emerge de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences.

    • Anne-Ruxandra Carvunis
    • , Thomas Rolland
    •  & Marc Vidal
  • Article |

    Genetic programs homologous to three vertebrate signalling centres are present in the hemichordate Saccoglossus kowalevskii and may be components of a complex, ancient genetic regulatory scaffold for deuterostome body patterning that degenerated in amphioxus and ascidians, but was retained to pattern divergent structures in hemichordates and vertebrates.

    • Ariel M. Pani
    • , Erin E. Mullarkey
    •  & Christopher J. Lowe
  • Article |

    Historical and contemporary data of whitefish radiations from pre-alpine European lakes and reconstruction of changes in whitefish genetic species differentiation through time show that species diversity may have evolved in response to ecological opportunity, and that eutrophication, by diminishing this opportunity, has driven extinctions through speciation reversal and demographic decline.

    • P. Vonlanthen
    • , D. Bittner
    •  & O. Seehausen
  • Article
    | Open Access

    A new resource for the analysis of population genomics and quantitative traits, the Drosophila melanogaster Genetic Reference Panel is presented.

    • Trudy F. C. Mackay
    • , Stephen Richards
    •  & Richard A. Gibbs
  • Article |

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

    • Brenton R. Graveley
    • , Angela N. Brooks
    •  & Susan E. Celniker
  • Article |

    As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study presents a genome-wide chromatin landscape of the fruitfly, based on 18 histone modifications. Nine prevalent chromatin states are described. Integrating these analyses with other data types reveals individual characteristics of different genomic elements. The work provides a resource of unprecedented scale for future experimental investigations.

    • Peter V. Kharchenko
    • , Artyom A. Alekseyenko
    •  & Peter J. Park
  • Letter |

    For two hundred years, scientists have noticed that the appearance of embryos in related species converge in their appearance mid-way in development, diverging thereafter. But is this 'phylotypic stage' real, and how is it connected with the genetic basis of development? Here, a method linking the genes transcribed at various stages of development (the transcriptome) with the evolutionary history of those genes is used. Genes transcribed in the phylotypic stage are, in evolutionary terms, the oldest and most conserved. This suggests that the phylotypic stage does represent the body plans of related species at their most unadorned, selection having sculpted the earlier and later stages of embryonic form to suit the particulars of each creature.

    • Alex T. Kalinka
    • , Karolina M. Varga
    •  & Pavel Tomancak
  • Letter |

    Acid sensing has so far been demonstrated in the gustatory system only. Now, fruitfly olfactory sensory neurons selectively activated by acidic compounds have been identified. Acid sensing also requires the transmembrane protein IR64a, expressed in those neurons as well as neurons involved in the detection of non acidic odorants. Although the IR64a protein isn't sufficient by itself to determine acid recognition, the requirement for IR64a in acid recognition is the first function for a member of this recently discovered family of putative odorant receptors — the ionotropic receptor family.

    • Minrong Ai
    • , Soohong Min
    •  & Greg S. B. Suh
  • Letter |

    Until now, studies of evolution in the laboratory have primarily been carried out in asexual systems with small genomes, such as bacteria and yeast. Here, however, whole-genome resequencing data are presented from fruitfly populations that have experienced over 600 generations of laboratory selection for accelerated development. The results suggest that unconditionally advantageous alleles rarely arise, are associated with small net fitness gains, or cannot fix because selection coefficients change over time.

    • Molly K. Burke
    • , Joseph P. Dunham
    •  & Anthony D. Long
  • Letter |

    When double-strand breaks occur in DNA, the broken ends must undergo processing to prepare them for repair. Here, and in an accompanying study, this processing reaction has now been replicated in vitro using yeast proteins. Processing minimally requires the activities of a helicase, a nuclease and a single-strand-binding protein, although the reaction is enhanced by the addition of three factors that help to target the core complex and stimulate the unwinding activity.

    • Hengyao Niu
    • , Woo-Hyun Chung
    •  & Patrick Sung
  • Letter |

    It is shown here that the methylation of histone proteins regulates lifespan in Caenorhabditis elegans. Deficiencies in members of the ASH-2 complex, which trimethylates histone H3 at lysine 4 (H3K4), extend worm lifespan. Meanwhile, the H3K4 demethylase RBR-2 is required for normal lifespan. These findings are consistent with the idea that an excess of H3K4 trimethylation reduces longevity. The extension of lifespan caused by ASH-2 deficiency requires an intact adult germline and the continuous production of mature eggs.

    • Eric L. Greer
    • , Travis J. Maures
    •  & Anne Brunet
  • Letter |

    Before mating, a yeast cell must detect a partner cell that is close enough and expresses sufficiently large amounts of a sex pheromone. The mating decision is an all-or-none, switch-like response to pheromone concentration. It is now shown that this decision involves the competition of one kinase and one phosphatase enzyme for multiple phosphorylation sites on a 'scaffold' protein. The results should prompt a re-evaluation of the role of related signalling molecules that have been implicated in cancer.

    • Mohan K. Malleshaiah
    • , Vahid Shahrezaei
    •  & Stephen W. Michnick
  • Letter |

    Complex heritable traits — such as human height and many human diseases — are caused by multiple genetic loci, each with small effects. It is hard to identify such loci, however, because of a lack of statistical power. Now, a method has been developed to overcome this problem. The method has been applied to chemical resistance traits and mitochondrial function in yeast, and has identified loci for each of these phenotypes.

    • Ian M. Ehrenreich
    • , Noorossadat Torabi
    •  & Leonid Kruglyak
  • Letter |

    How large groups of animals move in a coordinated way has defied complete explanation. Inability to track each member of a flock has hampered understanding of the behavioural rules governing flocks of birds. This, however, has been achieved for a small group of homing pigeons fitted with lightweight GPS loggers. A well–defined hierarchy is revealed — the average position of a pigeon within the flock strongly correlates with is position in the social hierarchy (a kind of airborne pecking order).

    • Máté Nagy
    • , Zsuzsa Ákos
    •  & Tamás Vicsek
  • Letter |

    Self-fertilisation (selfing) in plants is prevented mainly by the self-incompatibility recognition system, which consists of male and female specificity genes and modifier genes. Selfing does occur in Arabidopsis plants, but it is not known how it arose. Here it is reported that selfing in Arabidopsis results from a geographically widespread, 213-base-pair inversion within the male specificity gene. When this inversion is returned to its original orientation, selfing is prevented once more.

    • Takashi Tsuchimatsu
    • , Keita Suwabe
    •  & Kentaro K. Shimizu
  • Letter
    | Open Access

    The genome of the zebra finch — a songbird and a model for studying the vertebrate brain, behaviour and evolution — has been sequenced. Comparison with the chicken genome, the only other bird genome available, shows that genes that have neural function and are implicated in the cognitive processing of song have been evolving rapidly in the finch lineage. Moreover, vocal communication engages much of the transcriptome of the zebra finch brain.

    • Wesley C. Warren
    • , David F. Clayton
    •  & Richard K. Wilson
  • Letter |

    Making haploid plants — which inherit chromosomes from only one parent — is useful for genetic research and also, crucially, for plant breeding. A new method for generating haploid Arabidopsis plants is now described, involving the manipulation of a single centromeric protein, CENH3. When cenh3 null plants are crossed with wild-type plants, the mutant chromosomes are eliminated, producing haploid progeny.

    • Maruthachalam Ravi
    •  & Simon W. L. Chan
  • Letter |

    Zebrafish are able to replace lost heart muscle efficiently, and are used as a model to understand why natural heart regeneration — after a heart attack, for instance — is blocked in mammals. Here, and in an accompanying paper, genetic fate-mapping approaches reveal which cell population contributes prominently to cardiac muscle regeneration after an injury approximating myocardial infarction. The results show that cardiac muscle regenerates through activation and expansion of existing cardiomyocytes, without involving a stem-cell population.

    • Kazu Kikuchi
    • , Jennifer E. Holdway
    •  & Kenneth D. Poss
  • Letter |

    Zebrafish are able to replace lost heart muscle efficiently, and are used as a model to understand why natural heart regeneration — after a heart attack, for instance — is blocked in mammals. Here, and in an accompanying paper, genetic fate-mapping approaches reveal which cell population contributes prominently to cardiac muscle regeneration after an injury approximating myocardial infarction. The results show that cardiac muscle regenerates through activation and expansion of existing cardiomyocytes, without involving a stem-cell population.

    • Chris Jopling
    • , Eduard Sleep
    •  & Juan Carlos Izpisúa Belmonte
  • Letter |

    Here, large-scale genome-wide association studies were carried out with the naturally occurring inbred lines of Arabidopsis thaliana, which can be genotyped once and phenotyped repeatedly. The results range from significant associations, usually corresponding to single genes, to findings that are more difficult to interpret, because confounding by complex genetics and population structure makes it hard to distinguish true associations from false.

    • Susanna Atwell
    • , Yu S. Huang
    •  & Magnus Nordborg
  • Letter |

    Male pregnancy is restricted to seahorses, pipefishes and their relatives, in which young are nurtured in the male's brood pouch. It is now clear that the brood pouch has a further function. Studies of Gulf pipefish show that males can selectively abort embryos from females perceived as less attractive, saving resources for more hopeful prospects later. This is the only known example of post-copulatory sexual conflict in a sex-reversed species.

    • Kimberly A. Paczolt
    •  & Adam G. Jones
  • Letter |

    Evidence for hominin activity on Flores, Indonesia, has been thought to go back at least 800,000 years, as shown by fission-track dating at Mata Menge in the Soa Basin. However, new research at another locality in the Soa Basin uses the more accurate technique of 40Ar/39Ar dating to show that hominins were living on Flores at least a million years ago.

    • Adam Brumm
    • , Gitte M. Jensen
    •  & Michael Storey
  • Letter |

    An extensive genome-wide survey of over 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf, was conducted to shed light on the process of dog diversification. The results reveal that much of genome diversity came from Middle Eastern progenitors, combined with interbreeding with local wolf populations, and that recent evolution involved limited genetic variation to create the phenotypic diversity of modern dogs.

    • Bridgett M. vonHoldt
    • , John P. Pollinger
    •  & Robert K. Wayne