Biological sciences articles within Nature

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  • News Feature |

    Experiments have revealed how single mutations can have huge effects that drive evolution. But small steps pave the way, finds Tanguy Chouard.

    • Tanguy Chouard

  • Letter |

    Here, iPS cell technology is used to study the mechanisms underlying dyskeratosis congenita in humans. Reprogramming restores telomere elongation in dyskeratosis congenita cells despite genetic lesions affecting telomerase. The reprogrammed cells were able to overcome a critical limitation in telomerase RNA component (TERC) levels to restore telomere maintenance and self-renewal, and multiple telomerase components are targeted by pluripotency-associated transcription factors.

    • Suneet Agarwal
    • , Yuin-Han Loh
    •  & George Q. Daley

  • Letter |

    Endogenous retroviruses (ERVs) are widely dispersed in mammalian genomes, and are silenced in somatic cells by DNA methylation. Here, an ERV silencing pathway independent of DNA methylation is shown to operate in embryonic stem cells. The pathway involves the histone H3K9 methyltransferase ESET and might be important for ERV silencing during the stages in embryogenesis when DNA methylation is reprogrammed.

    • Toshiyuki Matsui
    • , Danny Leung
    •  & Yoichi Shinkai

  • Letter |

    Plants and animals sense intruding pathogens by using proteins that recognize diverse microbe-associated molecular patterns (MAMPs) and initiate innate immune responses. Early signalling responses in the host include calcium influx, an oxidative burst and transcriptional reprogramming. Here, four calcium-dependent protein kinases are described that function as calcium sensors, act as convergence points for various MAMPs, and are crucial for transcriptional reprogramming and oxidative burst in plants.

    • Marie Boudsocq
    • , Matthew R. Willmann
    •  & Jen Sheen

  • Article |

    Local adaptations are often governed by several interacting genes scattered throughout the genome. Here a novel type of multi–locus genetic variation is described that has been maintained within a species over a vast period of time. A balanced unlinked gene network polymorphism is dissected that involves galactose utilization in a close relative of baker's yeast.

    • Chris Todd Hittinger
    • , Paula Gonçalves
    •  & Antonis Rokas

  • Article |

    The transcriptome of Helicobacter pylori, an important human pathogen involved in gastric ulcers and cancer, is presented. The approach establishes a model for mapping and annotating the primary transcriptomes of many living species.

    • Cynthia M. Sharma
    • , Steve Hoffmann
    •  & Jörg Vogel

  • News |

    Experts question claims that malaria and osteonecrosis contributed to Pharaoh's decline.

    • Declan Butler

  • Column |

    To sustain innovation, pharmaceutical companies will have to change the way they do research, says Derek Lowe. But does anyone know what changes to make?

    • Derek Lowe

  • News |

    Asia defies patent-filing downturn as global economy slips.

    • David Cyranoski

  • Letter |

    Although new amino acids with desirable properties can be devised, only a few have been successfully introduced into proteins by the cellular machinery. Even then, only one type of unnatural amino acid can be added to a given protein. Here, a new system has been designed that could allow the incorporation of up to 200 novel amino acids. The system involves an orthogonal ribosome that uses quadruplet — rather than triplet — codons, as well as orthogonal tRNA synthetase–tRNA pairs.

    • Heinz Neumann
    • , Kaihang Wang
    •  & Jason W. Chin

  • Letter |

    De novo emergence of phenotypically defined haematopoietic stem cells (Sca1+, c kit+, CD41+) directly from ventral aortic haemogenic endothelial cells is shown in mice. Although the study did not visualize live embryos, it instead developed a dissection procedure to visualize the deeply located aorta.

    • Jean-Charles Boisset
    • , Wiggert van Cappellen
    •  & Catherine Robin

  • Letter |

    One of two papers showing the generation of haematopoietic stem cells (HSCs) from the ventral wall of the dorsal aorta in live zebrafish embryos. Here, using imaging of live zebrafish, HSCs are shown to emerge directly from the aorta floor. This process does not involve cell division but movement of single endothelial cells out of the aorta ventral wall into the sub aortic space, where they transform into haematopoietic cells.

    • Karima Kissa
    •  & Philippe Herbomel

  • Letter |

    One of two papers showing the generation of haematopoietic stem cells (HSCs) from the ventral wall of the dorsal aorta in live zebrafish embryos. Here, combined fluorescent reporter transgenes, confocal time-lapse microscopy and flow cytometry identify and isolate the stepwise intermediates as aortic haemogenic endothelium transitions to nascent HSCs. HSCs generated from this haemogenic endothelium are the lineal founders of virtually all of the adult haematopoietic system.

    • Julien Y. Bertrand
    • , Neil C. Chi
    •  & David Traver

  • Letter |

    Semaphorins and their receptors, plexins, relay guidance information to neurons during development and regulate actin dynamics through an unknown mechanism. Recently, proteins of the Mical family of enzymes have been found to associate with plexins; here, Mical is reported to directly link semaphorins and their plexin receptors to the precise control of actin filament dynamics.

    • Ruei-Jiun Hung
    • , Umar Yazdani
    •  & Jonathan R. Terman

  • Article
    | Open Access

    The first genome sequence of an ancient human is reported. It comes from an approximately 4,000-year-old permafrost-preserved hair from a male from the first known culture to settle in Greenland. Functional single-nucleotide polymorphism (SNP) assessment is used to assign possible phenotypic characteristics and high-confidence SNPs are compared to those of contemporary populations to find those most closely related to the individual.

    • Morten Rasmussen
    • , Yingrui Li
    •  & Eske Willerslev

  • Article |

    Pancreatic β-cells release insulin, which controls energy homeostasis in vertebrates, and its lack causes diabetes mellitus. The transcription factor neurogenin 3 (Neurog3) initiates differentiation of β-cells and other islet cell types from pancreatic endoderm; here, the transcription factor Rfx6 is shown to direct islet cell differentiation downstream of Neurog3 in mice and humans. This may be useful in efforts to generate β-cells for patients with diabetes.

    • Stuart B. Smith
    • , Hui-Qi Qu
    •  & Michael S. German

  • Article |

    Benzodiazepines, such as valium, are used both in clinics and for recreational purposes, but lead to addiction in some individuals. Addictive drugs increase the levels of dopamine and trigger synaptic adaptations in the mesolimbic reward system, but the neural basis for the addictive nature of benzodiazepines remains elusive. Here, they are shown to increase firing of dopamine neurons in the ventral tegmental area through GABAA receptor activation in nearby interneurons.

    • Kelly R. Tan
    • , Matthew Brown
    •  & Christian Lüscher

  • Article |

    The genome of the wild grass Brachypodium distachyon (Brachypodium), a member of the Pooideae subfamily, is sequenced. The Pooideae are one of three subfamilies of grasses that provide the bulk of human nutrition and may become major sources of renewable energy. Availability of the genome sequence should help establish Brachypodium as a model for developing new energy and food crops.

    • John P. Vogel
    • , David F. Garvin
    •  & Ivan Baxter

  • News & Views |

    Defects in mitochondria are implicated in Parkinson's disease. Study of a quality-control pathway involving the proteins PINK1 and Parkin provides further clues about the mechanism involved.

    • Asa Abeliovich

  • News & Views |

    DNA is particularly well preserved in hair — enabling the genome of a human to be sequenced, and his ancestry and appearance to be determined, from 4,000-year-old remains.

    • David M. Lambert
    •  & Leon Huynen

  • News & Views |

    Chronic drug use can lead to addiction, which is initiated by specific brain circuits. The mystery of how one class of drugs, the benzodiazepines, affects activity in this circuitry has finally been solved.

    • Arthur C. Riegel
    •  & Peter W. Kalivas

  • News & Views |

    Experiments with simple chordate animals show how decay may make the resulting fossils seem less evolved. The consequence is to distort evidence of the evolution of the earliest vertebrates and their precursors.

    • Derek E. G. Briggs

  • News |

    An expensive recovery plan to save the ivory-billed woodpecker from extinction may come decades too late.

    • Rex Dalton

  • News Feature |

    Eske Willerslev combines Arctic escapades with meticulous lab work in his quest to pull ancient DNA from the ice. Rex Dalton talks to the adventurer about extracting the first ancient human genome.

    • Rex Dalton

  • Letter |

    The evolutionary interrelationships of arthropods has long been a matter of dispute. A new phylogeny applies an arsenal of techniques to more than 41,000 base pairs of DNA from 75 arthropod species. The results support the idea that insects are land–living crustaceans, that crustaceans comprise a diverse assemblage of at last three distinct arthropod types, and that myriapods (millipedes and centipedes) comprise the closest relatives of this great 'pancrustacean' group.

    • Jerome C. Regier
    • , Jeffrey W. Shultz
    •  & Clifford W. Cunningham

  • Muse |

    The finding that religion scarcely influences moral intuition undermines the idea that a godless society will be immoral, says Philip Ball. Whether it 'explains' religion is another matter.

    • Philip Ball

  • Letter |

    Ca2+ channels and calmodulin (CaM) are two prominent hubs of biological signalling networks, affecting functions such as cardiac excitability and gene transcription. The prevailing view has been that the ultrastrong affinity of channels for the Ca2+-free form of calmodulin (apoCaM) ensures their saturation with CaM and yields a form of concentration independence between Ca2+ channels and CaM. Here, however, significant exceptions to this autonomy are shown to exist.

    • Xiaodong Liu
    • , Philemon S. Yang
    •  & David T. Yue

  • Letter |

    The transcription factor Tbx3 is shown to significantly improve the quality of induced pluripotent stem (iPS) cells. Tbx3 binding sites in embryonic stem cells are present in genes involved in pluripotency and reprogramming factors. Furthermore, there are intrinsic qualitative differences in iPS cells generated by different methods in terms of their pluripotency, thus highlighting the need to rigorously characterize iPS cells beyond in vitro studies.

    • Jianyong Han
    • , Ping Yuan
    •  & Bing Lim

  • Article |

    To survive and evade host responses, malaria parasites export several hundred proteins into the host cell on infection. A feature of these proteins is a conserved, pentameric motif that is cleaved by an unknown protease before export. This is one of two independent studies revealing the identity of the protease as plasmepsin V, an aspartic acid protease located in the endoplasmic reticulum. This enzyme is essential for parasite viability and is an attractive candidate for drug development.

    • Ilaria Russo
    • , Shalon Babbitt
    •  & Daniel E. Goldberg

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