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Volume 507 Number 7491 |
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nature |
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The
science that matters. Every week. | |
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Learn how to identify and mitigate error in
NGS projects. This article discusses the sources
of experimental error in NGS and presents a simple
analysis for characterizing and abating error. The
author, Kimberly Robasky, formerly a student of
George Church, is currently a Bioinformatics
Director at EA|Quintiles.
Read More...
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Jump
to the content that matters to you |
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Reflection from the strong
gravity regime in a lensed quasar at redshift
z=0.658
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Measurements
of the spin of a supermassive black hole more
than 6 billion light years away - the most
distant black hole for which a spin has been
measured - offer new clues as to how these
objects grow. The reflection-dominated spectrum
of a 'lensed' quasar at z=0.658, together
with archival X-ray data, show that it is
rotating rapidly and that much of its radiation
comes from a compact region close to the black
hole. The data suggest that the black hole has
grown by coherent accretion rather than in a
chaotic manner. |
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Hydrous mantle transition
zone indicated by ringwoodite included within
diamond
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It
is not clear just how much water there is within
the solid Earth, or where it is to be found.
Graham Pearson and co-authors present evidence
from a diamond inclusion from Juína, Brazil, for
the first known terrestrial occurrence of
ringwoodite - a high-pressure form of olivine
mineral first identified in meteorites and
thought to be a major constituent of the Earth's
mantle transition zone. The water-rich nature of
this inclusion provides direct evidence that, at
least locally, the transition zone is hydrous,
to about one weight per cent. |
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Derived immune and ancestral
pigmentation alleles in a 7,000-year-old
Mesolithic European
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The
emergence of agriculture may have caused many of
the changes in human physiology evident in the
fossil record. Which changes it is hard to say
in the absence of a baseline - a record of human
physiology just before the advent of farming. We
may now have that in the form of genome of a
Mesolithic hunter-gatherer from Spain. The genes
of this male, alive around 7,000 years ago, had
more in common with ancient genomes from Siberia
than with other Europeans, suggesting a wide
genetic continuity across Eurasia. He was
probably lactose intolerant and digested starchy
food less effectively than did Neolithic
farmers, supporting the idea that these changes
came in with agriculture. And he had the unusual
combination of dark skin and blue eyes,
suggesting that in the Mesolithic, the
transition to a lighter 'modern European' skin
tone was incomplete and that eye-colour changes
came first. |
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In
this week's
podcast: This week, how a thirteenth century
cosmologist predicted the Big Bang, the ocean of
water hidden deep in the Earth's mantle, and
what the wolves of Yellowstone tell us about
ecosystems. |
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Don’t
hide the decline ▶ |
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US
scientists should not be placated by the ‘flat budget’
myth. Funds are decreasing, and the situation will get
worse. |
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An
elegant chaos ▶ |
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Universal
theories are few and far between in ecology, but that is
what makes it fascinating. |
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Share
alike ▶ |
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Research
communities need to agree on standard etiquette for
data-sharing. |
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7
days: 7–13 March 2014 ▶ |
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The
week in science: Infant HIV cure; Craig Venter launches
genomics company; and asteroid caught falling
apart. |
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History: A medieval multiverse ▶ |
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Ideas
in a thirteenth-century treatise on the nature of matter
still resonate today, say Tom C. B. McLeish and
colleagues. |
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In
retrospect: Sylva ▶ |
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Gabriel
Hemery celebrates the 350th anniversary of John Evelyn's
treatise on the science and practice of forestry. |
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The New York Stem Cell Foundation is
accepting proposals for high-risk, high-reward
projects exploring the therapeutic potential of
stem cells. The awards provide $1.5M USD over 5
years.
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Haematopoietic stem cells require a highly
regulated protein synthesis rate ▶ |
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Robert
A. J. Signer, Jeffrey A. Magee, Adrian Salic et
al. |
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Haematopoietic
stem cells (HSCs) have a lower rate of protein synthesis
in vivo than most other haematopoietic cells, and both
increases and decreases in the rate of protein synthesis
impair HSC function, demonstrating that HSC
maintenance—and hence, cellular homeostasis—requires the
rate of protein synthesis to be highly regulated. |
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Coupling
of angiogenesis and osteogenesis by a specific vessel
subtype in bone ▶ |
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Anjali
P. Kusumbe, Saravana K. Ramasamy, Ralf H. Adams |
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Bone
homeostasis and repair declines with ageing and the
mechanisms regulating the relationship between bone
growth and blood vessel formation have remained unknown;
this mouse study identifies the endothelial cells that
promote the formation of new bone, a small microvessel
subtype that can be identified by high CD31 and high
Emcn expression. |
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Unexpected link between an antibiotic,
pannexin channels and apoptosis ▶ |
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Ivan
K. H. Poon, Yu-Hsin Chiu, Allison J. Armstrong et
al. |
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The
pannexin 1 channel on the plasma membrane of apoptotic
cells mediates the release of find-me molecular signals
to attract phagocytic cells for clearance of the
apoptotic cells; here the quinolone antibiotic
trovafloxacin is identified as a direct inhibitor of
pannexin 1, which results in dysregulated fragmentation
of apoptotic cells and may partly explain quinolone
toxicity. |
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Inhibition of miR-25 improves
cardiac contractility in the failing heart ▶ |
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Christine
Wahlquist, Dongtak Jeong, Agustin Rojas-Muñoz et
al. |
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Reduced
activity of the calcium-transporting ATPase SERCA2a is a
hallmark of heart failure; here, microRNAs that
downregulate SERCA2a function are identified, and
antagonism of one, miR-25, is shown to halt heart
failure in mice. |
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Structure of a type IV secretion
system ▶ |
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Harry
H. Low, Francesca Gubellini, Angel Rivera-Calzada et
al. |
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The
three-dimensional structure of the type IV secretion
system encoded by the Escherichia coli R388
conjugative plasmid. |
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A new
fossil species supports an early origin for toothed
whale echolocation ▶ |
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Jonathan
H. Geisler, Matthew W. Colbert, James L. Carew |
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Phylogenetic
analysis of a new species of fossil toothed whale,
Cotylocara macei, from the Oligocene epoch places
it in a basal clade of odontocetes, and its features
suggest that rudimentary echolocation evolved in the
early Oligocene and was followed by convergent evolution
in their skulls. |
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Obesity-associated variants within
FTO form long-range functional connections with
IRX3 ▶ |
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Scott
Smemo, Juan J. Tena, Kyoung-Han Kim et
al. |
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Obesity-associated
noncoding sequences within FTO are functionally
connected with IRX3, and long-range enhancers in
this region recapitulate aspects of IRX3
expression, suggesting that the obesity-associated
interval is part of IRX3 regulation;
Irx3-deficient mice have lower body weight and
are resistant to diet-induced obesity, suggesting IRX3
as a novel determinant of body mass and
composition. |
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Herbivores and nutrients control grassland
plant diversity via light limitation ▶ |
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Elizabeth
T. Borer, Eric W. Seabloom, Daniel S. Gruner et
al. |
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Experimental
data collected from 40 grasslands on 6 continents show
that nutrients and herbivores can serve as counteracting
forces to control local plant diversity; nutrient
addition reduces local diversity through light
limitation, and herbivory rescues diversity at sites
where it alleviates light limitation. |
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Alveolar
progenitor and stem cells in lung development, renewal
and cancer ▶ |
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Tushar
J. Desai, Douglas G. Brownfield, Mark A. Krasnow |
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Lung
alveoli are lined by two types of alveolar epithelial
cells, squamous alveolar type (AT) 1 cells that mediate
gas exchange and cuboidal AT2 cells that secrete
surfactant to prevent alveolar collapse during
breathing; here alveolar markers, genetic lineage
tracing and clonal analysis are used in mice to identify
alveolar progenitor and stem cells in vivo, and
to map their locations and potential during lung
development, maintenance and cancer. |
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C9orf72 nucleotide repeat
structures initiate molecular cascades of
disease ▶ |
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Aaron
R. Haeusler, Christopher J. Donnelly, Goran Periz et
al. |
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Structurally
polymorphic C9orf72 hexanucleotide repeats cause
an impairment in transcriptional processivity and lead
to accumulation of truncated repeat-containing
transcripts that bind to specific ribonucleoproteins,
such as nucleolin, in a conformation-dependent manner
resulting in nucleolar stress and C9orf72-linked
pathology in amyotrophic lateral sclerosis and
frontotemporal dementia. |
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Proof of
principle for epitope-focused vaccine design ▶ |
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Bruno
E. Correia, John T. Bates, Rebecca J. Loomis et
al. |
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Computational
protein design methods are used to generate new
candidates for a human respiratory syncytial virus (RSV)
vaccine; artificial protein scaffolds that mimic the
structure of a RSV epitope are shown to induce
RSV-specific neutralizing antibodies in macaques. |
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Derived
immune and ancestral pigmentation alleles in a
7,000-year-old Mesolithic European ▶ |
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Iñigo
Olalde, Morten E. Allentoft, Federico Sánchez-Quinto
et al. |
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A
complete pre-agricultural European human genome from a
∼7,000-year-old Mesolithic skeleton suggests the
existence of a common genomic signature across western
and central Eurasia from the Upper Paleolithic to the
Mesolithic, and ancestral alleles in several skin
pigmentation genes suggest that the light skin of modern
Europeans was not yet ubiquitous in Mesolithic
times. |
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doublesex is a mimicry
supergene ▶ |
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K.
Kunte, W. Zhang, A. Tenger-Trolander et
al. |
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The
phenomenon of sex-limited mimicry is phylogenetically
widespread in the swallowtail butterfly genus
Papilio — now, a single gene, doublesex,
is shown to control supergene mimicry, a finding that is
in contrast to the long-held view that supergenes are
likely to be controlled by a tightly linked cluster of
loci. |
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Dynamic
sensory cues shape song structure in Drosophila
▶ |
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Philip
Coen, Jan Clemens, Andrew J. Weinstein et
al. |
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Drosophila
male courtship songs were thought to have a fixed
structure with song repetition variations introduced
unintentionally because of neural noise; this
behavioural assay and computational modelling study
instead reveals that males use fast changes in sensory
information to actively pattern individual song
sequences. |
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An
excitatory paraventricular nucleus to AgRP neuron
circuit that drives hunger ▶ |
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Michael
J. Krashes, Bhavik P. Shah, Joseph C. Madara et
al. |
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The
AgRP-expressing neurons in the arcuate nucleus drive
food-seeking behaviours during caloric restriction; a
mouse study of monosynaptic retrograde rabies spread and
optogenetic circuit mapping reveals that these neurons
are activated by input from hypothalamic paraventricular
nucleus cells and their activation or inhibition can
modulate feeding behaviour. |
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L-Myc
expression by dendritic cells is required for optimal
T-cell priming ▶ |
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Wumesh
KC, Ansuman T. Satpathy, Aaron S. Rapaport et
al. |
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L-Myc,
a paralogue of the proto-oncogene c-Myc, is shown to
regulate dendritic cell homeostasis and functionality;
unlike c-Myc, L-Myc is not repressed by interferons and
its expression allows for optimal dendritic cell
proliferation and T-cell priming in the presence of
inflammation. |
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A
cascade of DNA-binding proteins for sexual commitment
and development in Plasmodium ▶ |
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Abhinav
Sinha, Katie R. Hughes, Katarzyna K. Modrzynska et
al. |
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Malaria
parasites must produce gametocytes for transmission to
the mosquito vector, although the molecular mechanisms
underlying commitment to gametocyte production remain
unclear; here this process is found to be controlled by
PbAP2-G, a member of the ApiAP2 family of DNA-binding
proteins, in the rodent-infecting Plasmodium
berghei parasite. |
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DNA-guided DNA interference by a
prokaryotic Argonaute ▶ |
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Daan
C. Swarts, Matthijs M. Jore, Edze R. Westra et
al. |
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Here,
Argonaute from the prokaryote Thermus
thermophilus is shown to use small DNA guides to
interfere directly with invading foreign DNA, rather
than being involved in RNA-guided RNA interference, as
observed in eukaryotes. |
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The
Structural Genomics Consortium (SGC),
Natureconferences, and the São Paulo
Research Foundation are pleased to
present:
Chemical Probe-based Open
Science: Uncovering New Human and Plant
Biology
April 28-29, 2014
Faculdade
de Ciências Médicas, State University of Campinas
(UNICAMP), Brazil
Click
here for more
information or to register for this conference
today! |
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Inhibition of miR-25 improves
cardiac contractility in the failing heart ▶ |
|
| |
Christine
Wahlquist, Dongtak Jeong, Agustin Rojas-Muñoz et
al. |
|
| |
Reduced
activity of the calcium-transporting ATPase SERCA2a is a
hallmark of heart failure; here, microRNAs that
downregulate SERCA2a function are identified, and
antagonism of one, miR-25, is shown to halt heart
failure in mice. |
|
| | |
|
| |
|
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| |
| |
| |
Obesity-associated variants within
FTO form long-range functional connections with
IRX3 ▶ |
|
| |
Scott
Smemo, Juan J. Tena, Kyoung-Han Kim et
al. |
|
| |
Obesity-associated
noncoding sequences within FTO are functionally
connected with IRX3, and long-range enhancers in
this region recapitulate aspects of IRX3
expression, suggesting that the obesity-associated
interval is part of IRX3 regulation;
Irx3-deficient mice have lower body weight and
are resistant to diet-induced obesity, suggesting IRX3
as a novel determinant of body mass and
composition. |
|
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C9orf72 nucleotide repeat
structures initiate molecular cascades of
disease ▶ |
|
| |
Aaron
R. Haeusler, Christopher J. Donnelly, Goran Periz et
al. |
|
| |
Structurally
polymorphic C9orf72 hexanucleotide repeats cause
an impairment in transcriptional processivity and lead
to accumulation of truncated repeat-containing
transcripts that bind to specific ribonucleoproteins,
such as nucleolin, in a conformation-dependent manner
resulting in nucleolar stress and C9orf72-linked
pathology in amyotrophic lateral sclerosis and
frontotemporal dementia. |
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Efficient rotational cooling of
Coulomb-crystallized molecular ions by a helium buffer
gas ▶ |
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A.
K. Hansen, O. O. Versolato, Ł. Kłosowski et
al. |
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In
combination with sympathetic cooling of translational
degrees of freedom (leading to Coulomb crystallization),
cooling of the rotational degrees of freedom of
magnesium hydride ions using a helium buffer gas leads
to temperatures in a tunable range from 60 kelvin down
to about 7 kelvin for a single ion, the lowest such
temperature so far recorded. |
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Interrogating selectivity in catalysis
using molecular vibrations ▶ |
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Anat
Milo, Elizabeth N. Bess, Matthew S. Sigman |
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A
set of parameters based on the response of a molecule’s
properties to infrared vibrations can be used to model
and predict selectivity trends for molecular reactions
with interlinked steric and electronic effects at
positions of interest |
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Conformation-induced remote
meta-C–H activation of amines ▶ |
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Ri-Yuan
Tang, Gang Li, Jin-Quan Yu |
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In
anilines and benzylic amines, a recyclable chemical
template can direct the olefination and acetoxylation of
meta-C–H bonds as far as 11 bonds away from a
functional group; in particular, it is able to direct
the meta-selective C–H functionalization of
bicyclic heterocycles via a highly strained,
tricyclic-cyclophane-like palladated
intermediate. |
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Brief
Communications Arising |
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FREE POSTER: Dyslipidaemia and its
treatment
Disorders of plasma lipid and lipoprotein
metabolism can cause atherosclerotic
cardiovascular disease. This poster displays the
main lipid-metabolism pathways in the body, the
points at which monogenetic protein mutations lead
to dyslipidaemia, and the mechanisms of action of
both established and novel lipid-modifying
drugs.
This poster was produced with support
from:
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Geoscience: Fracking fundamentals ▶ |
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Scientists
in the United States who are looking to ride the
gas-exploration boom can find a variety of options for
employment, from chemical research to environmental
monitoring. |
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Skewed
rankings ▶ |
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Female
researchers avoid collaborating with lower-ranked female
colleagues, finds study. |
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Costs of
childcare ▶ |
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Breaks
due to childcare are associated with lower wages for
female physicians, says study. |
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naturejobs.com Science jobs of the
week |
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No
matter what your career stage, student, postdoc or senior
scientist, you will find articles on naturejobs.com to
help guide you in your science career. Keep up-to-date with
the latest sector trends, vote in our reader
poll and sign-up to receive the monthly Naturejobs newsletter. |
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• natureevents Directory featured
events |
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natureevents directory featured
events |
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Natureevents
Directory is the premier resource for scientists looking
for the latest scientific conferences, courses, meetings and
symposia. Featured across Nature Publishing Group journals and
centrally at natureevents.com it is an essential
reference guide to scientific events worldwide. |
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