| | Microbiomes: Curating communities from plants
Large-scale cultivation and genome sequencing of the bacteria that inhabit the leaves and roots of Arabidopsis plants have paved the way for probing how microbial communities assemble and function.
| Biodiversity: Recovery as nitrogen declines
Pollution from atmospheric nitrogen deposition is a major threat to biodiversity. The 160-year-old Park Grass experiment has uniquely documented this threat and demonstrated how nitrogen reductions lead to recovery.
| HIV: Cure by killing
Two bi-specific protein constructs have been designed that direct the body's T cells to kill HIV-infected cells. The feat provides a step on the path to removing the latent virus reservoir that persists in patients on antiretroviral therapy.
| Planetary science: How the Solar System didn't form
Standard planet-formation models have been unable to reconstruct the distributions of the Solar System's small, rocky planets and asteroids in the same simulation. A new analysis suggests that it cannot be done.
| ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis
A new deep proteomic analysis method is used to identify proteins that interact with wild-type cystic fibrosis transmembrane conductance regulator (CFTR) and its mutant version that is the major cause of cystic fibrosis.
| Growth and splitting of neural sequences in songbird vocal development
Neural sequences recorded from the vocal premotor area HVC in juvenile birds learning song 'syllables' show 'prototype' syllables forming early, with multiple new highly divergent neural sequences emerging from this precursor syllable as learning progresses.
| Signal integration by Ca2+ regulates intestinal stem-cell activity
Drosophila intestinal stem cells (ISCs) respond to changes in diet, particularly L-glutamate levels, by modulating Ca2+ signalling to adapt their proliferation rate; furthermore, Ca2+ is shown to be central to the response of ISCs to a wide range of dietary and stress stimuli.
| Functional overlap of the Arabidopsis leaf and root microbiota
The microbiota of the rhizosphere (roots) and phyllosphere (leaves) of healthy plants consist of taxonomically structured bacterial communities; here the majority of species representing the main bacterial phyla from these two organs were isolated and genomes of about 400 representative bacteria were sequenced; the resources of cultured bacteria, corresponding genomes and a gnotobiotic plant system enabled an examination of the taxonomic overlap and functional specialization between the rhizosphere and phyllosphere bacterial microbiota.
| Complete nitrification by Nitrospira bacteria
Until now, the oxidation steps necessary for complete nitrification have always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by van Kessel et al., Daims et al. report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as "comammox" (for complete ammonia oxidation).
| Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells
The first formal evidence of the shared and independent ability of basal cells and luminal pro-genitors isolated from normal human mammary tissue and transduced with a single oncogene to initiate tumorigeneses when introduced into mice.
| A large-scale dynamo and magnetoturbulence in rapidly rotating core-collapse supernovae
Global, three-dimensional simulations of rapidly rotating massive stars show that turbulence driven by magnetohydrodynamic instability is a promising mechanism for the formation of pulsars and magnetars, the latter potentially powering hyperenergetic and superluminous supernovae.
| Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
Growing evidence from metagenome-wide association studies link multiple common disorders to microbial dysbiosis but effects of drug treatment are often not accounted for; here, the authors re-analyse two previous metagenomic studies of type 2 diabetes mellitus patients together with a novel cohort to determine the effects of the widely prescribed antidiabetic drug metformin and highlight the need to distinguish the effects of a disease from the effects of treatment on the gut microbiota.
| Dense magnetized plasma associated with a fast radio burst
Fast radio burst FRB 110523, discovered in archival data, reveals Faraday rotation and scattering that suggests dense magnetized plasma near the source; this means that to infer the source of the burst, models should involve young stellar populations such as magnetars.
| Replication stress activates DNA repair synthesis in mitosis
Common fragile sites (CFSs) are difficult-to-replicate regions of eukaryotic genomes that are sensitive to replication stress and that require resolution by the MUS81–EME1 endonuclease to re-initiate POLD3-dependent DNA synthesis in early mitosis; this study defines the specific pathway of events causing the CFS fragility phenotype.
| Grassland biodiversity bounces back from long-term nitrogen addition
Data from the long-running Park Grass Experiment is used to show that grassland biodiversity is recovering since UK atmospheric nitrogen levels started to decline 25 years ago in all but the most acidic soils.
| Complete nitrification by a single microorganism
Until now, the oxidation steps necessary for complete nitrification had always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by Daims et al., van Kessel et al. report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as 'comammox' (for complete ammonia oxidation).
| Corrigendum: Domains of genome-wide gene expression dysregulation in Down's syndrome
| Corrigendum: A SUMOylation-defective MITF germline mutation predisposes to melanoma and renal carcinoma
| Corrigendum: Identification of the pollen self-incompatibility determinant in Papaver rhoeas
| | Soil biodiversity and human health
Soil biodiversity sustains human health and its loss can be mitigated by sustainable management.
Diana H. Wall, Uffe N. Nielsen, Johan Six | Managing nitrogen for sustainable development
Careful management of nitrogen fertilizer usage is required to ensure world food security while limiting environmental degradation; an analysis of historical nitrogen use efficiency reveals socio-economic factors and technological innovations that have influenced a range of past national trends and that suggest ways to improve global food production and environmental stewardship by 2050.
Xin Zhang, Eric A. Davidson, Denise L. Mauzerall et al. | The contentious nature of soil organic matter
Instead of containing stable and chemically unique 'humic substances', as has been widely accepted, soil organic matter is a mixture of progressively decomposing organic compounds; this has broad implications for soil science and its applications.
Johannes Lehmann, Markus Kleber | | Measuring entanglement entropy in a quantum many-body system
Entanglement, which describes non-local correlations between quantum objects, is very difficult to measure, especially in systems of itinerant particles; here spatial entanglement is measured for ultracold bosonic atoms in optical lattices.
Rajibul Islam, Ruichao Ma, Philipp M. Preiss et al. | Thermal biases and vulnerability to warming in the world's marine fauna
How marine communities will respond to climate change depends on the thermal sensitivities of existing communities; existing reef communities do not show a perfect fit between current temperatures and the thermal niches of the species within them and this thermal bias is a major contributor to projected local species loss.
Rick D. Stuart-Smith, Graham J. Edgar, Neville S. Barrett et al. | Brain tumour cells interconnect to a functional and resistant network
Brain tumours are difficult to treat because of their propensity to infiltrate brain tissue; here long processes, or tumour microtubes, extended by astrocytomas are shown to promote brain infiltration and to create an interconnected network that enables multicellular communication and that protects the tumours from radiotherapy-induced cell death, suggesting that disruption of the network could be a new therapeutic approach.
Matthias Osswald, Erik Jung, Felix Sahm et al. | Overflow metabolism in Escherichia coli results from efficient proteome allocation
Using experimental proteomics and modelling in E. coli, the amount of protein needed to run respiration (per ATP produced) is shown to be twice as much as that needed to run fermentation; results demonstrate that overflow metabolism (known as the Warburg effect in cancer cells) is a necessary outcome of optimal bacterial growth, governed by a global resource allocation program, and that the methodology is directly applicable to synthetic biology and cancer research.
Markus Basan, Sheng Hui, Hiroyuki Okano et al. | | Reversal of phenotypes in MECP2 duplication mice using genetic rescue or antisense oligonucleotides
Genetic correction of MeCP2 levels largely reversed the behavioural, molecular and physiological deficits associated with MECP2 duplication syndrome in a transgenic mouse model; similarly, reduction of MeCP2 levels using an antisense oligonucleotide strategy resulted in phenotypic rescue in adult transgenic mice, and dose-dependently corrected MeCP2 levels in cells from patients with MECP2 duplication.
Yehezkel Sztainberg, Hong-mei Chen, John W. Swann et al. | Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
A DNase sequencing method termed scDNase-seq detects DNase I hypersensitive sites genome-wide in single cells and pools of cells dissected from cancer biopsies.
Wenfei Jin, Qingsong Tang, Mimi Wan et al. | Therapeutic antibodies reveal Notch control of transdifferentiation in the adult lung
Inhibitory antibodies to two specific human and mouse Notch ligands, Jagged1 and Jagged2, are generated and shown to have beneficial effects in a goblet cell metaplasia asthma model; systemic Jagged1 inhibition transdifferentiates secretory cells into ciliated cells in the mouse, demonstrating that Jagged1 from ciliated cells normally holds back secretory cells to adopt the ciliated fate.
Daniel Lafkas, Amy Shelton, Cecilia Chiu et al. | Warm–hot baryons comprise 5–10 per cent of filaments in the cosmic web
In the local Universe, the census of all observed baryons falls short of the estimated number by a factor of two, and simulations have indicated that the missing baryons reside throughout the filaments of the cosmic web; X-ray observations of filamentary structures associated with the galaxy cluster Abell 2744 now find that 5 to 10 per cent of the filament mass is in the form of baryonic gas.
Dominique Eckert, Mathilde Jauzac, HuanYuan Shan et al. | Relativistic baryonic jets from an ultraluminous supersoft X-ray source
Persistent low-velocity baryonic jets have been detected from a supersoft X-ray source; the low velocity suggests that these jets have not been launched from a white dwarf, and the persistence speaks against the origin being a canonical black hole or neutron star, indicating that a different type of source must be implicated.
Ji-Feng Liu, Yu Bai, Song Wang et al. | Ab initio alpha–alpha scattering
An ab initio calculation of alpha–alpha scattering is described for which the number of computational operations scales approximately quadratically with particle number and which uses lattice Monte Carlo simulations and lattice effective field theory, combined with the adiabatic projection method to reduce the eight-body system to a two-cluster system.
Serdar Elhatisari, Dean Lee, Gautam Rupak et al. | Potential sea-level rise from Antarctic ice-sheet instability constrained by observations
Recent work has suggested that sections of the West Antarctic ice sheet are already rapidly retreating, raising concerns about increased sea-level rise; now, an ice-sheet model is used to simulate the mass loss from the entire Antarctic ice sheet to 2200, suggesting that it could contribute up to 30 cm of sea-level rise by 2100 and 72 cm by 2200, but is unlikely to contribute more.
Catherine Ritz, Tamsin L. Edwards, Gaël Durand et al. | Death from drought in tropical forests is triggered by hydraulics not carbon starvation
It has been suggested that carbon starvation, owing to reduced availability of non-structural carbohydrates (NSCs), is an important contributor to tree mortality during drought in tropical rainforests; however, data from the world's longest-running experimental drought study presented here show no evidence of carbon starvation, and instead the researchers conclude that impaired water hydraulic processes (involving the transport of water from soil to leaf) have a more important role in triggering tree death from long-term drought.
L. Rowland, A. C. L. da Costa, D. R. Galbraith et al. | A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance
Regulatory T cells need to express a diverse T-cell-receptor repertoire to control pathogenic self-reactive T cells; here it is shown that repertoire diversification depends on the intronic Foxp3 enhancer CNS3 acting at the regulatory T-cell-precursor stage to induce T-cell-receptor responsiveness to low-strength signals.
Yongqiang Feng, Joris van der Veeken, Mikhail Shugay et al. | Depletion of fat-resident Treg cells prevents age-associated insulin resistance
Fat-resident regulatory T cells (fTreg cells) accumulate in adipose tissue of mice as a function of age, but not obesity; mice without fTreg cells are protected against age-associated insulin resistance, but remain susceptible to obesity-associated insulin resistance and metabolic disease, indicating different aetiologies of age-associated versus obesity-associated insulin resistance.
Sagar P. Bapat, Jae Myoung Suh, Sungsoon Fang et al. | Transcriptional regulators form diverse groups with context-dependent regulatory functions
A large-scale enhancer complementation assay assessing the activating or repressing contributions of over 800 Drosophila transcription factors and cofactors to combinatorial enhancer control reveals a more complex picture than expected, with many factors having diverse regulatory functions that depend on the enhancer context.
Gerald Stampfel, Tomáš Kazmar, Olga Frank et al. | | | | |
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