RESEARCH NEWS & VIEWS
2014 EDITORS’ CHOICE Extracts from selected News & Views articles published this year. POPULATION HEALTH
IMMATURITY IN THE GUT MICROBIAL COMMUNITY Physical measurements, such as weight for height, scored relative to a reference population are indispensable tools in the assessment and treatment of undernutrition. But Subramanian et al. have charted a different path — one in which the milestones are microbial — for young children living in the Mirpur urban slum of Dhaka, Bangladesh. By surveying the bacterial communities in faecal samples from 50 well-nourished subjects, the authors defined two indicators of gut-microbiota maturation: relative microbiota maturity and a microbiota-for-age Z-score. Compared with healthy children, malnourished children showed significant microbiota immaturity. In the 2–3 months following treatment, the children’s microbiota-maturation scores improved; however, after this period, much of this catch-up maturation was lost. The approach presented by the authors could be used to develop standards across the globe, and then to monitor gut colonization during early childhood, as an early-warning system for microbiotas that are falling ‘off track’. Nature 510, 417–421 (2014).
ACCELERATOR PHYSICS
SURF’S UP AT SLAC
Mike Downer & Rafal Zgadzaj (Nature 515, 40–41; 2014) In November 2012, Guinness World Records reported that 120 surfers in Australia rode the same wave simultaneously for more than 5 seconds. “The trick was to get them all to do the same thing at the same time,” said group leader Wes Smith. “It was an operation of militarylike precision and we finally got there.” Now Litos and colleagues, in work at the SLAC National Accelerator Laboratory, have ‘got there’, too, by surfing half a billion 20-billion-electronvolt electrons on a steep charge-density wave about the size of a marine phytoplankton, travelling through ionized gas (plasma). The wave was driven by a companion electron bunch as it raced at nearly the speed of light through a 30-centimetre-long chamber filled with plasma. Although this inaugural experiment lost about 90% of its ‘surfers’ along the way, the surviving electrons gained 1.6 billion electronvolts in energy with unparalleled uniformity, maintaining roughly 1% energy spread throughout their wild ride, while sucking away an unprecedented fraction (up to 30%) of the wave’s energy. The result might herald a new generation of compact ‘plasma afterburners’ that could boost the energy of conventional particle accelerators and potentially reduce the skyrocketing cost of high-energy physics machinery. Nature 515, 92–95 (2014).
SYLVIE DEMOUCHY
Elizabeth K. Costello & David A. Relman (Nature 510, 344–345; 2014)
EARTH SCIENCE
MISSING LINK IN MANTLE DYNAMICS Greg Hirth (Nature 507, 42–43; 2014) The viscosity of Earth’s upper mantle controls a wide range of processes, from the attenuation of seismic waves and the rate of surface deformation after earthquakes to the slow, global-scale flow that is associated with mantle convection and the dynamics of tectonic plates. This viscosity is logically interpreted as being dominated by the physical properties of olivine, the most abundant mineral in Earth’s upper mantle, as well as in those of the other terrestrial planets (Mars, Venus and Mercury) and the Moon. Cordier et al. report how new techniques to analyse the microstructure of grain boundaries in olivine (pictured) allowed them to discover crystal defects called disclinations in this mineral. This observation is probably a first for geological materials, and has ramifications for our understanding of the processes that control mantle dynamics. Nature 507, 51–56 (2014).
EVOLUTIONARY DEVELOPMENTAL BIOLOGY
USE IT OR LOSE IT
Bau-lin Huang & Susan Mackem (Nature 511, 34–35; 2014) Adaptive digit loss enables specialized functions such as running or flight, and has repeatedly evolved in parallel. But the developmental mechanisms underlying deviation from the five-digit ground state are unclear, partly owing to the hurdles involved in analysing embryos from animals that are not typically studied in the laboratory. Cooper et al. find that, in three-toed jerboas, expanded apoptotic regions encompass the digit I and V precursors, and that camels and horses also use such celldeath mechanisms to reduce digit number. But the cell-death machinery is unaltered in some ungulates. Instead, Cooper et al. and Lopez-Rios et al. implicate reduced Ptch1 gene expression as the primary basis for digit loss in cows and pigs, although the extent of digit reduction differs. Further dissecting the diverse mechanisms converging on similar structures will require characterization of the tissue-specific regulation for each candidate gene. Nature 511, 41–45, 46–51 (2014).
3 4 0 | NAT U R E | VO L 5 1 6 | 1 8 / 2 5 D E C E M B E R 2 0 1 4
© 2014 Macmillan Publishers Limited. All rights reserved
NEWS & VIEWS RESEARCH
365 DAYS: SOLVIN ZANKL/VISUALS UNLIMITED/SPL
the year in science
a turning point in the design of programmes for counteracting climate change in Africa.
NEUROSCIENCE
ORDERED RANDOMNESS IN FLY LOVE SONGS
Biogeosciences 11, 381–407 (2014).
Bence P. Ölveczky (Nature 507, 177–178; 2014) Well-crafted love songs can be the ticket to reproductive success, whether you are a member of the Beatles or one of the many animals that woo their mates by singing. Most animals vary their mating-song patterns, but how the brain generates such variability remains a mystery. To address this, Coen et al. focus on the song of the male fruit fly. Just as the Beatles made a career of mixing ‘love’, ‘you’, ‘me’, ‘she’ and ‘baby’ in different ways, so male flies switch between ‘sine’ and ‘pulse’ songs. The authors find that the male’s visual experience of the female’s movements shapes his song through neural circuits that control locomotion. In fact, the best predictor of song structure is not the female’s movements, but the singer’s own. The picture that emerges is one in which the male executes a tightly integrated song-and-dance number, inspired by his partner’s movements. This study demonstrates that detailed analysis can distil seemingly complex and unpredictable behavioural patterns into simple rules and sensorimotor transformations. Nature 507, 233–237 (2014).
BIOGEOSCIENCE
AFRICA’S GREENHOUSE-GAS BUDGET IS IN THE RED Cheikh Mbow (Nature 508, 192–193; 2014)
JAKE LYELL/ALAMY
One of the biggest challenges in curbing climate change is to obtain robust estimates of greenhouse-gas emissions and sequestration. Writing in Biogeosciences, Valentini et al. have risen to this challenge by providing a full greenhouse-gas assessment for Africa. Until now, scientific opinion has held that Africa could help to reduce emissions or sequester carbon if deforestation of large areas could be avoided, or if tree and forest cover could be increased through sustainable practices, for example agroforestry (pictured) and plantation management. The authors concur that Africa is a small carbon sink on an annual timescale. But, more surprisingly, they find that it may be a net source of radiative forcing — reradiation of heat back towards Earth’s surface by greenhouse-gas molecules — when the greenhouse gases methane and nitrous oxide are included in the annual budgeting. This paper could instigate
SOLAR SYSTEM
STRANDED IN NO-MAN’S-LAND Megan E. Schwamb (Nature 507, 435–436; 2014) A decade after its discovery, Sedna still remains one of the strangest objects in the Solar System. This remote icy body has a highly eccentric orbit that extends to about 1,000 astronomical units and has a perihelion of 76 au. Its orbit is well beyond the reach of Neptune, which is located at 30 au, and is a long way from the edge of the Solar System, where the Oort cloud, the reservoir of long-orbital-period comets, resides at about 10,000 au. Although other potential candidates have been found, Sedna had remained the solitary confirmed member of a proposed inner Oort cloud beyond 70 au. Trujillo and Sheppard report the discovery of an object, called 2012 VP113, which joins Sedna as the second confirmed member of the inner Oort cloud. The finding solidifies the existence of a population of icy bodies probably ranging in size from a few to a thousand kilometres. Nature 507, 471–474 (2014).
FORUM: Synthetic biology ENGINEERING EXPLORED (Nature 509, 166–167; 2014)
The aim of synthetic biology is to predictably bioengineer organisms that perform beneficial functions. This involves modifying and reassembling biological components. Two views are presented here on the best way to engineer these components so that they reliably generate organisms with desired traits.
RATIONALIZING NATURE Pamela A. Silver & Jeffrey C. Way The gene was originally defined as the basic biological unit. But manipulation of DNA has revealed tantalizing levels of modularity that extend to many other cellular regulatory elements. The dream of the rational designer is to understand these modular parts in sufficient detail to be able to assemble them logically, much as an engineer would build a machine for a certain purpose. There are already success stories — for example, assembly of simple genetic circuits that rely on the existence of two stable states in a system.
EVOLVING WITH PURPOSE Frances H. Arnold & Joseph T. Meyerowitz Synthetic biologists cannot yet create an enzyme or a biosynthetic pathway that compares favourably with nature’s engineering outputs. The reason is simple: in biology, details matter a lot, and we don’t understand the details. Rational design will not move forward until our understanding of the details of biology has improved dramatically. Luckily, we do not have to wait. Evolution is a time-tested tool for engineering the details, and we can use it in the lab to circumvent our profound ignorance of how sequence encodes function. ■ 1 8 / 2 5 D E C E M B E R 2 0 1 4 | VO L 5 1 6 | NAT U R E | 3 4 1
© 2014 Macmillan Publishers Limited. All rights reserved
2014 EDITORS’ CHOICE Extracts from selected News & Views articles published this year. POPULATION HEALTH
IMMATURITY IN THE GUT MICROBIAL COMMUNITY Physical measurements, such as weight for height, scored relative to a reference population are indispensable tools in the assessment and treatment of undernutrition. But Subramanian et al. have charted a different path — one in which the milestones are microbial — for young children living in the Mirpur urban slum of Dhaka, Bangladesh. By surveying the bacterial communities in faecal samples from 50 well-nourished subjects, the authors defined two indicators of gut-microbiota maturation: relative microbiota maturity and a microbiota-for-age Z-score. Compared with healthy children, malnourished children showed significant microbiota immaturity. In the 2–3 months following treatment, the children’s microbiota-maturation scores improved; however, after this period, much of this catch-up maturation was lost. The approach presented by the authors could be used to develop standards across the globe, and then to monitor gut colonization during early childhood, as an early-warning system for microbiotas that are falling ‘off track’. Nature 510, 417–421 (2014).
ACCELERATOR PHYSICS
SURF’S UP AT SLAC
Mike Downer & Rafal Zgadzaj (Nature 515, 40–41; 2014) In November 2012, Guinness World Records reported that 120 surfers in Australia rode the same wave simultaneously for more than 5 seconds. “The trick was to get them all to do the same thing at the same time,” said group leader Wes Smith. “It was an operation of militarylike precision and we finally got there.” Now Litos and colleagues, in work at the SLAC National Accelerator Laboratory, have ‘got there’, too, by surfing half a billion 20-billion-electronvolt electrons on a steep charge-density wave about the size of a marine phytoplankton, travelling through ionized gas (plasma). The wave was driven by a companion electron bunch as it raced at nearly the speed of light through a 30-centimetre-long chamber filled with plasma. Although this inaugural experiment lost about 90% of its ‘surfers’ along the way, the surviving electrons gained 1.6 billion electronvolts in energy with unparalleled uniformity, maintaining roughly 1% energy spread throughout their wild ride, while sucking away an unprecedented fraction (up to 30%) of the wave’s energy. The result might herald a new generation of compact ‘plasma afterburners’ that could boost the energy of conventional particle accelerators and potentially reduce the skyrocketing cost of high-energy physics machinery. Nature 515, 92–95 (2014).
SYLVIE DEMOUCHY
Elizabeth K. Costello & David A. Relman (Nature 510, 344–345; 2014)
EARTH SCIENCE
MISSING LINK IN MANTLE DYNAMICS Greg Hirth (Nature 507, 42–43; 2014) The viscosity of Earth’s upper mantle controls a wide range of processes, from the attenuation of seismic waves and the rate of surface deformation after earthquakes to the slow, global-scale flow that is associated with mantle convection and the dynamics of tectonic plates. This viscosity is logically interpreted as being dominated by the physical properties of olivine, the most abundant mineral in Earth’s upper mantle, as well as in those of the other terrestrial planets (Mars, Venus and Mercury) and the Moon. Cordier et al. report how new techniques to analyse the microstructure of grain boundaries in olivine (pictured) allowed them to discover crystal defects called disclinations in this mineral. This observation is probably a first for geological materials, and has ramifications for our understanding of the processes that control mantle dynamics. Nature 507, 51–56 (2014).
EVOLUTIONARY DEVELOPMENTAL BIOLOGY
USE IT OR LOSE IT
Bau-lin Huang & Susan Mackem (Nature 511, 34–35; 2014) Adaptive digit loss enables specialized functions such as running or flight, and has repeatedly evolved in parallel. But the developmental mechanisms underlying deviation from the five-digit ground state are unclear, partly owing to the hurdles involved in analysing embryos from animals that are not typically studied in the laboratory. Cooper et al. find that, in three-toed jerboas, expanded apoptotic regions encompass the digit I and V precursors, and that camels and horses also use such celldeath mechanisms to reduce digit number. But the cell-death machinery is unaltered in some ungulates. Instead, Cooper et al. and Lopez-Rios et al. implicate reduced Ptch1 gene expression as the primary basis for digit loss in cows and pigs, although the extent of digit reduction differs. Further dissecting the diverse mechanisms converging on similar structures will require characterization of the tissue-specific regulation for each candidate gene. Nature 511, 41–45, 46–51 (2014).
3 4 0 | NAT U R E | VO L 5 1 6 | 1 8 / 2 5 D E C E M B E R 2 0 1 4
© 2014 Macmillan Publishers Limited. All rights reserved
NEWS & VIEWS RESEARCH
365 DAYS: SOLVIN ZANKL/VISUALS UNLIMITED/SPL
the year in science
a turning point in the design of programmes for counteracting climate change in Africa.
NEUROSCIENCE
ORDERED RANDOMNESS IN FLY LOVE SONGS
Biogeosciences 11, 381–407 (2014).
Bence P. Ölveczky (Nature 507, 177–178; 2014) Well-crafted love songs can be the ticket to reproductive success, whether you are a member of the Beatles or one of the many animals that woo their mates by singing. Most animals vary their mating-song patterns, but how the brain generates such variability remains a mystery. To address this, Coen et al. focus on the song of the male fruit fly. Just as the Beatles made a career of mixing ‘love’, ‘you’, ‘me’, ‘she’ and ‘baby’ in different ways, so male flies switch between ‘sine’ and ‘pulse’ songs. The authors find that the male’s visual experience of the female’s movements shapes his song through neural circuits that control locomotion. In fact, the best predictor of song structure is not the female’s movements, but the singer’s own. The picture that emerges is one in which the male executes a tightly integrated song-and-dance number, inspired by his partner’s movements. This study demonstrates that detailed analysis can distil seemingly complex and unpredictable behavioural patterns into simple rules and sensorimotor transformations. Nature 507, 233–237 (2014).
BIOGEOSCIENCE
AFRICA’S GREENHOUSE-GAS BUDGET IS IN THE RED Cheikh Mbow (Nature 508, 192–193; 2014)
JAKE LYELL/ALAMY
One of the biggest challenges in curbing climate change is to obtain robust estimates of greenhouse-gas emissions and sequestration. Writing in Biogeosciences, Valentini et al. have risen to this challenge by providing a full greenhouse-gas assessment for Africa. Until now, scientific opinion has held that Africa could help to reduce emissions or sequester carbon if deforestation of large areas could be avoided, or if tree and forest cover could be increased through sustainable practices, for example agroforestry (pictured) and plantation management. The authors concur that Africa is a small carbon sink on an annual timescale. But, more surprisingly, they find that it may be a net source of radiative forcing — reradiation of heat back towards Earth’s surface by greenhouse-gas molecules — when the greenhouse gases methane and nitrous oxide are included in the annual budgeting. This paper could instigate
SOLAR SYSTEM
STRANDED IN NO-MAN’S-LAND Megan E. Schwamb (Nature 507, 435–436; 2014) A decade after its discovery, Sedna still remains one of the strangest objects in the Solar System. This remote icy body has a highly eccentric orbit that extends to about 1,000 astronomical units and has a perihelion of 76 au. Its orbit is well beyond the reach of Neptune, which is located at 30 au, and is a long way from the edge of the Solar System, where the Oort cloud, the reservoir of long-orbital-period comets, resides at about 10,000 au. Although other potential candidates have been found, Sedna had remained the solitary confirmed member of a proposed inner Oort cloud beyond 70 au. Trujillo and Sheppard report the discovery of an object, called 2012 VP113, which joins Sedna as the second confirmed member of the inner Oort cloud. The finding solidifies the existence of a population of icy bodies probably ranging in size from a few to a thousand kilometres. Nature 507, 471–474 (2014).
FORUM: Synthetic biology ENGINEERING EXPLORED (Nature 509, 166–167; 2014)
The aim of synthetic biology is to predictably bioengineer organisms that perform beneficial functions. This involves modifying and reassembling biological components. Two views are presented here on the best way to engineer these components so that they reliably generate organisms with desired traits.
RATIONALIZING NATURE Pamela A. Silver & Jeffrey C. Way The gene was originally defined as the basic biological unit. But manipulation of DNA has revealed tantalizing levels of modularity that extend to many other cellular regulatory elements. The dream of the rational designer is to understand these modular parts in sufficient detail to be able to assemble them logically, much as an engineer would build a machine for a certain purpose. There are already success stories — for example, assembly of simple genetic circuits that rely on the existence of two stable states in a system.
EVOLVING WITH PURPOSE Frances H. Arnold & Joseph T. Meyerowitz Synthetic biologists cannot yet create an enzyme or a biosynthetic pathway that compares favourably with nature’s engineering outputs. The reason is simple: in biology, details matter a lot, and we don’t understand the details. Rational design will not move forward until our understanding of the details of biology has improved dramatically. Luckily, we do not have to wait. Evolution is a time-tested tool for engineering the details, and we can use it in the lab to circumvent our profound ignorance of how sequence encodes function. ■ 1 8 / 2 5 D E C E M B E R 2 0 1 4 | VO L 5 1 6 | NAT U R E | 3 4 1
© 2014 Macmillan Publishers Limited. All rights reserved
