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The eyes of Tullimonstrum reveal a vertebrate affinity

Nature - Wed, 04/13/2016 - 00:00

The eyes of Tullimonstrum reveal a vertebrate affinity

Nature 532, 7600 (2016). doi:10.1038/nature17647

Authors: Thomas Clements, Andrei Dolocan, Peter Martin, Mark A. Purnell, Jakob Vinther & Sarah E. Gabbott

Tullimonstrum gregarium is an iconic soft-bodied fossil from the Carboniferous Mazon Creek Lagerstätte (Illinois, USA). Despite a large number of specimens and distinct anatomy, various analyses over the past five decades have failed to determine the phylogenetic affinities of the ‘Tully monster’, and although it has been allied to such disparate phyla as the Mollusca, Annelida or Chordata, it remains enigmatic. The nature and phylogenetic affinities of Tullimonstrum have defied confident systematic placement because none of its preserved anatomy provides unequivocal evidence of homology, without which comparative analysis fails. Here we show that the eyes of Tullimonstrum possess ultrastructural details indicating homology with vertebrate eyes. Anatomical analysis using scanning electron microscopy reveals that the eyes of Tullimonstrum preserve a retina defined by a thick sheet comprising distinct layers of spheroidal and cylindrical melanosomes. Time-of-flight secondary ion mass spectrometry and multivariate statistics provide further evidence that these microbodies are melanosomes. A range of animals have melanin in their eyes, but the possession of melanosomes of two distinct morphologies arranged in layers, forming retinal pigment epithelium, is a synapomorphy of vertebrates. Our analysis indicates that in addition to evidence of colour patterning, ecology and thermoregulation, fossil melanosomes can also carry a phylogenetic signal. Identification in Tullimonstrum of spheroidal and cylindrical melanosomes forming the remains of retinal pigment epithelium indicates that it is a vertebrate; considering its body parts in this new light suggests it was an anatomically unusual member of total group Vertebrata.

Categories: Literature

Microbiome: Eating for trillions

Nature - Wed, 04/13/2016 - 00:00

Microbiome: Eating for trillions

Nature 532, 7599 (2016). doi:10.1038/nature17887

Authors: Derrick M. Chu & Kjersti M. Aagaard

Three studies investigate the bacteria in the guts of malnourished children and find that, when this microbiota is transferred into mice, supplements of certain microbes or sugars from human breast milk can restore normal growth.

Categories: Literature

Distinct bone marrow blood vessels differentially regulate haematopoiesis

Nature - Wed, 04/13/2016 - 00:00

Distinct bone marrow blood vessels differentially regulate haematopoiesis

Nature 532, 7599 (2016). doi:10.1038/nature17624

Authors: Tomer Itkin, Shiri Gur-Cohen, Joel A. Spencer, Amir Schajnovitz, Saravana K. Ramasamy, Anjali P. Kusumbe, Guy Ledergor, Yookyung Jung, Idan Milo, Michael G. Poulos, Alexander Kalinkovich, Aya Ludin, Orit Kollet, Guy Shakhar, Jason M. Butler, Shahin Rafii, Ralf H. Adams, David T. Scadden, Charles P. Lin & Tsvee Lapidot

Bone marrow endothelial cells (BMECs) form a network of blood vessels that regulate both leukocyte trafficking and haematopoietic stem and progenitor cell (HSPC) maintenance. However, it is not clear how BMECs balance these dual roles, and whether these events occur at the same vascular site.

Categories: Literature

Detection of a Cooper-pair density wave in Bi2Sr2CaCu2O8+x

Nature - Wed, 04/13/2016 - 00:00

Detection of a Cooper-pair density wave in Bi2Sr2CaCu2O8+x

Nature 532, 7599 (2016). doi:10.1038/nature17411

Authors: M. H. Hamidian, S. D. Edkins, Sang Hyun Joo, A. Kostin, H. Eisaki, S. Uchida, M. J. Lawler, E.-A. Kim, A. P. Mackenzie, K. Fujita, Jinho Lee & J. C. Séamus Davis

The quantum condensate of Cooper pairs forming a superconductor was originally conceived as being translationally invariant. In theory, however, pairs can exist with finite momentum Q, thus generating a state with a spatially modulated Cooper-pair density. Such a state has been created in ultracold 6Li gas but never observed directly in any superconductor. It is now widely hypothesized that the pseudogap phase of the copper oxide superconductors contains such a ‘pair density wave’ state. Here we report the use of nanometre-resolution scanned Josephson tunnelling microscopy to image Cooper pair tunnelling from a d-wave superconducting microscope tip to the condensate of the superconductor Bi2Sr2CaCu2O8+x. We demonstrate condensate visualization capabilities directly by using the Cooper-pair density variations surrounding zinc impurity atoms and at the Bi2Sr2CaCu2O8+x crystal supermodulation. Then, by using Fourier analysis of scanned Josephson tunnelling images, we discover the direct signature of a Cooper-pair density modulation at wavevectors QP ≈ (0.25, 0)2π/a0 and (0, 0.25)2π/a0 in Bi2Sr2CaCu2O8+x. The amplitude of these modulations is about five per cent of the background condensate density and their form factor exhibits primarily s or s′ symmetry. This phenomenology is consistent with Ginzburg–Landau theory when a charge density wave with d-symmetry form factor and wavevector QC = QP coexists with a d-symmetry superconductor; it is also predicted by several contemporary microscopic theories for the pseudogap phase.

Categories: Literature

Daily magnesium fluxes regulate cellular timekeeping and energy balance

Nature - Wed, 04/13/2016 - 00:00

Daily magnesium fluxes regulate cellular timekeeping and energy balance

Nature 532, 7599 (2016). doi:10.1038/nature17407

Authors: Kevin A. Feeney, Louise L. Hansen, Marrit Putker, Consuelo Olivares-Yañez, Jason Day, Lorna J. Eades, Luis F. Larrondo, Nathaniel P. Hoyle, John S. O’Neill & Gerben van Ooijen

Circadian clocks are fundamental to the biology of most eukaryotes, coordinating behaviour and physiology to resonate with the environmental cycle of day and night through complex networks of clock-controlled genes. A fundamental knowledge gap exists, however, between circadian gene expression cycles and the biochemical mechanisms that ultimately facilitate circadian regulation of cell biology. Here we report circadian rhythms in the intracellular concentration of magnesium ions, [Mg2+]i, which act as a cell-autonomous timekeeping component to determine key clock properties both in a human cell line and in a unicellular alga that diverged from each other more than 1 billion years ago. Given the essential role of Mg2+ as a cofactor for ATP, a functional consequence of [Mg2+]i oscillations is dynamic regulation of cellular energy expenditure over the daily cycle. Mechanistically, we find that these rhythms provide bilateral feedback linking rhythmic metabolism to clock-controlled gene expression. The global regulation of nucleotide triphosphate turnover by intracellular Mg2+ availability has potential to impact upon many of the cell’s more than 600 MgATP-dependent enzymes and every cellular system where MgNTP hydrolysis becomes rate limiting. Indeed, we find that circadian control of translation by mTOR is regulated through [Mg2+]i oscillations. It will now be important to identify which additional biological processes are subject to this form of regulation in tissues of multicellular organisms such as plants and humans, in the context of health and disease.

Categories: Literature

Age-dependent modulation of vascular niches for haematopoietic stem cells

Nature - Wed, 04/13/2016 - 00:00

Age-dependent modulation of vascular niches for haematopoietic stem cells

Nature 532, 7599 (2016). doi:10.1038/nature17638

Authors: Anjali P. Kusumbe, Saravana K. Ramasamy, Tomer Itkin, Maarja Andaloussi Mäe, Urs H. Langen, Christer Betsholtz, Tsvee Lapidot & Ralf H. Adams

Blood vessels define local microenvironments in the skeletal system, play crucial roles in osteogenesis and provide niches for haematopoietic stem cells. The properties of niche-forming vessels and their changes in the ageing organism remain incompletely understood. Here we show that Notch signalling in endothelial cells leads to the expansion of haematopoietic stem cell niches in bone, which involves increases in CD31-positive capillaries and platelet-derived growth factor receptor-β (PDGFRβ)-positive perivascular cells, arteriole formation and elevated levels of cellular stem cell factor. Although endothelial hypoxia-inducible factor signalling promotes some of these changes, it fails to enhance vascular niche function because of a lack of arterialization and expansion of PDGFRβ-positive cells. In ageing mice, niche-forming vessels in the skeletal system are strongly reduced but can be restored by activation of endothelial Notch signalling. These findings indicate that vascular niches for haematopoietic stem cells are part of complex, age-dependent microenvironments involving multiple cell populations and vessel subtypes.

Categories: Literature

The diversity-generating benefits of a prokaryotic adaptive immune system

Nature - Wed, 04/13/2016 - 00:00

The diversity-generating benefits of a prokaryotic adaptive immune system

Nature 532, 7599 (2016). doi:10.1038/nature17436

Authors: Stineke van Houte, Alice K. E. Ekroth, Jenny M. Broniewski, Hélène Chabas, Ben Ashby, Joseph Bondy-Denomy, Sylvain Gandon, Mike Boots, Steve Paterson, Angus Buckling & Edze R. Westra

Prokaryotic CRISPR-Cas adaptive immune systems insert spacers derived from viruses and other parasitic DNA elements into CRISPR loci to provide sequence-specific immunity. This frequently results in high within-population spacer diversity, but it is unclear if and why this is important. Here we show that, as a result of this spacer diversity, viruses can no longer evolve to overcome CRISPR-Cas by point mutation, which results in rapid virus extinction. This effect arises from synergy between spacer diversity and the high specificity of infection, which greatly increases overall population resistance. We propose that the resulting short-lived nature of CRISPR-dependent bacteria–virus coevolution has provided strong selection for the evolution of sophisticated virus-encoded anti-CRISPR mechanisms.

Categories: Literature

USP14 deubiquitinates proteasome-bound substrates that are ubiquitinated at multiple sites

Nature - Wed, 04/13/2016 - 00:00

USP14 deubiquitinates proteasome-bound substrates that are ubiquitinated at multiple sites

Nature 532, 7599 (2016). doi:10.1038/nature17433

Authors: Byung-Hoon Lee, Ying Lu, Miguel A. Prado, Yuan Shi, Geng Tian, Shuangwu Sun, Suzanne Elsasser, Steven P. Gygi, Randall W. King & Daniel Finley

USP14 is a major regulator of the proteasome and one of three proteasome-associated deubiquitinating enzymes. Its effects on protein turnover are substrate-specific, for unknown reasons. We report that USP14 shows a marked preference for ubiquitin–cyclin B conjugates that carry more than one ubiquitin modification or chain. This specificity is conserved from yeast to humans and is independent of chain linkage type. USP14 has been thought to cleave single ubiquitin groups from the distal tip of a chain, but we find that it removes chains from cyclin B en bloc, proceeding until a single chain remains. The suppression of degradation by USP14’s catalytic activity reflects its capacity to act on a millisecond time scale, before the proteasome can initiate degradation of the substrate. In addition, single-molecule studies showed that the dwell time of ubiquitin conjugates at the proteasome was reduced by USP14-dependent deubiquitination. In summary, the specificity of the proteasome can be regulated by rapid ubiquitin chain removal, which resolves substrates based on a novel aspect of ubiquitin conjugate architecture.

Categories: Literature

Origins of the obesity pandemic can be analysed

Nature - Wed, 04/13/2016 - 00:00

Origins of the obesity pandemic can be analysed

Nature 532, 7598 (2016). http://www.nature.com/doifinder/10.1038/532149a

Author: John Frank

Statistical and biological methods are available to probe why the prevalence of obesity has risen more in some countries than in others, says John Frank.

Categories: Literature

Geology: Fluid flow in landslides

Nature - Wed, 04/13/2016 - 00:00

Geology: Fluid flow in landslides

Nature 532, 7598 (2016). doi:10.1038/532150a

Vibrations that ripple through rocks as they tumble downhill explain why some landslides travel farther than expected. The finding could help towns to better prepare for landslide hazards.In 'long runout' landslides, falling rocks can move tens to hundreds of kilometres on flat land —

Categories: Literature

Genetics: Disease mutations but no disease

Nature - Wed, 04/13/2016 - 00:00

Genetics: Disease mutations but no disease

Nature 532, 7598 (2016). doi:10.1038/532150b

An analysis of genetic data from more than half a million people has uncovered 13 individuals who have disease-causing mutations but are healthy.Mendelian diseases such as cystic fibrosis begin in childhood, can be caused by a single mutation and lack effective treatments. Rong Chen

Categories: Literature

Ecology: Catfish face migration barriers

Nature - Wed, 04/13/2016 - 00:00

Ecology: Catfish face migration barriers

Nature 532, 7598 (2016). doi:10.1038/532150c

Amazonian catfish make the longest known freshwater migrations, covering thousands of kilometres, but their epic voyages are threatened by new dams.Brachyplatystoma catfish can measure up to three metres in length, and are top predators. To study their migrations, Fabrice Duponchelle of the Institute

Categories: Literature

Astronomy: Black-hole disk launches jet

Nature - Wed, 04/13/2016 - 00:00

Astronomy: Black-hole disk launches jet

Nature 532, 7598 (2016). doi:10.1038/532150d

Scientists have caught one of the best glimpses yet of a jet of plasma streaming from the black hole at the heart of a distant galaxy.Intense magnetic fields around black holes are thought to launch these beams, which travel nearly at the speed of

Categories: Literature

Anthropology: War uncommon in prehistoric Japan

Nature - Wed, 04/13/2016 - 00:00

Anthropology: War uncommon in prehistoric Japan

Nature 532, 7598 (2016). doi:10.1038/532150e

Hunter-gatherers living in Japan thousands of years ago were not particularly violent, adding weight to a contentious idea that violence and warfare were not the norm in early history.Hisashi Nakao at Yamaguchi University in Japan and his colleagues analysed published data on the skeletal

Categories: Literature

Microbiology: Salmonella live on thanks to toxin

Nature - Wed, 04/13/2016 - 00:00

Microbiology: Salmonella live on thanks to toxin

Nature 532, 7598 (2016). doi:10.1038/532151a

A toxin protein secreted by typhoid-causing bacteria seems to keep infected hosts alive, allowing the bacteria to persist in the body.Salmonella enterica Typhi (S. Typhi), which causes typhoid fever in humans but not in mice, produces a DNA-damaging protein. To study

Categories: Literature

Astrochemistry: Sugars made in simulated space

Nature - Wed, 04/13/2016 - 00:00

Astrochemistry: Sugars made in simulated space

Nature 532, 7598 (2016). doi:10.1038/532151b

A key sugar found in DNA has been created in the laboratory under conditions similar to those around comets.Ribose forms the backbone of DNA and RNA, but its ancient origin remains a mystery. Cornelia Meinert and Uwe Meierhenrich of the University of Nice Sophia

Categories: Literature

Heart disease: Molecule melts away cholesterol

Nature - Wed, 04/13/2016 - 00:00

Heart disease: Molecule melts away cholesterol

Nature 532, 7598 (2016). doi:10.1038/532151c

The next weapon against heart disease could be a compound that is currently used to make drugs more soluble.In atherosclerosis, plaques containing crystallized cholesterol clog up blood vessels. Eicke Latz of the University Hospital in Bonn, Germany, and his colleagues tested a compound called

Categories: Literature

Biochemistry: Bioplastic made from glucose

Nature - Wed, 04/13/2016 - 00:00

Biochemistry: Bioplastic made from glucose

Nature 532, 7598 (2016). doi:10.1038/532151d

Researchers have combined three biochemical pathways to produce a biodegradable plastic from glucose in the laboratory.Some industrial chemicals are made by microorganisms in bioreactors, but reengineering the organisms' metabolic pathways to boost yields is challenging, so researchers are keen to find cell-free production methods.

Categories: Literature

Neuroimmunology: Protein linked to immune privilege

Nature - Wed, 04/13/2016 - 00:00

Neuroimmunology: Protein linked to immune privilege

Nature 532, 7598 (2016). doi:10.1038/532151e

A protein found in neurons helps to limit inflammation in the central nervous system (CNS), contributing to the system's specialized immune environment.The CNS can stave off excessive inflammation. This 'immune privilege' has been attributed to the blood–brain barrier that restricts the entry of certain

Categories: Literature

The week in science: 8–14 April 2016

Nature - Wed, 04/13/2016 - 00:00

The week in science: 8–14 April 2016

Nature 532, 7598 (2016). http://www.nature.com/doifinder/10.1038/532152a

Human embryos made HIV-resistant; reusable rocket lands on ship; Pfizer calls off merger with Allergan.

Categories: Literature

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