Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation ...challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation.
Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N
size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production.
Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.
Progress in atomic, optical and quantum science has led to rapid improvements in atomic clocks. At the same time, atomic clock research has helped to advance the frontiers of science, affecting both ...fundamental and applied research. The ability to control quantum states of individual atoms and photons is central to quantum information science and precision measurement, and optical clocks based on single ions have achieved the lowest systematic uncertainty of any frequency standard. Although many-atom lattice clocks have shown advantages in measurement precision over trapped-ion clocks, their accuracy has remained 16 times worse. Here we demonstrate a many-atom system that achieves an accuracy of 6.4 × 10(-18), which is not only better than a single-ion-based clock, but also reduces the required measurement time by two orders of magnitude. By systematically evaluating all known sources of uncertainty, including in situ monitoring of the blackbody radiation environment, we improve the accuracy of optical lattice clocks by a factor of 22. This single clock has simultaneously achieved the best known performance in the key characteristics necessary for consideration as a primary standard-stability and accuracy. More stable and accurate atomic clocks will benefit a wide range of fields, such as the realization and distribution of SI units, the search for time variation of fundamental constants, clock-based geodesy and other precision tests of the fundamental laws of nature. This work also connects to the development of quantum sensors and many-body quantum state engineering (such as spin squeezing) to advance measurement precision beyond the standard quantum limit.
Introduction and Objective
The risks and benefits of medication use in pregnancy are typically established through post-marketing observational studies. As there is currently no standardised or ...systematic approach to the post-marketing assessment of medication safety in pregnancy, data generated through pregnancy pharmacovigilance (PregPV) research can be heterogenous and difficult to interpret. The aim of this article is to describe the development of a reference framework of core data elements (CDEs) for collection in primary source PregPV studies that can be used to standardise data collection procedures and, thereby, improve data harmonisation and evidence synthesis capabilities.
Methods
This CDE reference framework was developed within the Innovative Medicines Initiative (IMI) ConcePTION project by experts in pharmacovigilance, pharmacoepidemiology, medical statistics, risk–benefit communication, clinical teratology, reproductive toxicology, genetics, obstetrics, paediatrics, and child psychology. The framework was produced through a scoping review of data collection systems used by established PregPV datasets, followed by extensive discussion and debate around the value, definition, and derivation of each data item identified from these systems.
Results
The finalised listing of CDEs comprises 98 individual data elements, arranged into 14 tables of related fields. These data elements are openly available on the European Network of Teratology Information Services (ENTIS) website (
http://www.entis-org.eu/cde
).
Discussion
With this set of recommendations, we aim to standardise PregPV primary source data collection processes to improve the speed at which high-quality evidence-based statements can be provided about the safety of medication use in pregnancy.
Envisioning Sociology is a landmark work, the first major study of the founding of sociology in Britain and the enormous contributions made by the intellectual circle led by Victor Branford and ...Patrick Geddes. Authors John Scott and Ray Bromley chronicle the biographical connections and personal partnerships of the circle's key participants, their international connections, their organization-building work, and the business activities that underpinned their efforts. Branford and Geddes fashioned an ambitious and wide-ranging interdisciplinary vision, drawing on geography, anthropology, economics, and urban planning, in addition to sociology. This vision was an integral part of a project of social reconstruction, a "third way" eschewing both liberalism and communism in favor of cooperation, redistribution, and federalism. Envisioning Sociology uncovers a previously hidden history of the social sciences, giving readers a fascinating glimpse into early twentieth-century social science and political economy, while demonstrating the contemporary relevance of the ideas of these underrated figures. Although Branford and Geddes failed to establish the grand sociology they envisioned, their ideas helped develop the theory and practice of community development, participatory democracy, bioregionalism, historic preservation, and neighborhood upgrading.
The degradation of aniline by bacterial consortia was investigated under aerobic, fermentative, nitrate-reducing and sulphate-reducing conditions and a variety of salt concentrations (0.2, 4 and 7% ...NaCl w/v) and pH values (5 and 7). A variety of degradation conditions were studied to provide information and recommendations for large-scale biological treatment of aniline-containing wastewater. Under aerobic conditions, degradation of aniline (2 mM) was achieved under all combinations of salinity and pH tested. The rate of bacterial growth decreased with increasing salinity. The bacterial consortium of each batch culture generally maintained its ability to degrade aniline when salt concentrations and pHs were changed although often the lag-phase prior to growth was extended. Microbial populations in fixed film continuous reactors were also able to resist changes in NaCl concentration. Increasing aniline concentration (0.25–1 g l
−1) under 0.2% NaCl (pH 5 and 7) conditions, resulted in aniline removal without affecting growth rates. At the lower pH, cell yield was not adversely affected by an increase in aniline concentration. However, at neutral pH, cell yield decreased with increasing aniline concentration. Cultures capable of degrading aniline under fermentative, nitrate-reducing and sulphate-reducing conditions were not obtained.
Graphene growth by low-pressure chemical vapor deposition on low cost copper foils shows great promise for large scale applications. It is known that the local crystallography of the foil influences ...the graphene growth rate. Here we find an epitaxial relationship between graphene and copper foil. Interfacial restructuring between graphene and copper drives the formation of （nl0） facets on what is otherwise a mostly Cu（100） surface, and the facets in turn influence the graphene orientations from the onset of growth. Angle resolved photoemission shows that the electronic structure of the graphene is decoupled from the copper indicating a weak interaction between them. Despite this, two preferred orientations of graphene are found, ±8° from the Cu010 direction, creating a non-uniform distribution of graphene grain boundary misorientation angles. Comparison with the model system of graphene growth on single crystal Cu（110） indicates that this orientational alignment is due to mismatch epitaxy. Despite the differences in symmetry the orientation of the graphene is defined by that of the copper. We expect these observations to not only have importance for controlling and understanding the growth process for graphene on copper, but also to have wider implications for the growth of two-dimensional materials on low cost metal substrates.
The El Niño–Southern Oscillation (ENSO) has been suggested
as a strong forcing in the methane cycle and as a driver of recent trends in
global atmospheric methane mole fractions CH4. Such a ...sensitivity
of the global CH4 budget to climate events would have important
repercussions for climate change mitigation strategies and the accuracy of
projections for future greenhouse forcing. Here, we test the impact of ENSO
on atmospheric CH4 in a correlation analysis. We use local and
global records of CH4, as well as stable carbon isotopic records
of atmospheric CH4 (δ13CH4), which are
particularly sensitive to the combined ENSO effects on CH4
production from wetlands and biomass burning. We use a variety of nominal,
smoothed, and detrended time series including growth rate records. We find
that at most 36 % of the variability in CH4 and
δ13CH4 is attributable to ENSO, but only for detrended
records in the southern tropics. Trend-bearing records from the southern
tropics, as well as all studied hemispheric and global records, show a minor
impact of ENSO, i.e. < 24 % of variability explained. Additional
analyses using hydrogen cyanide (HCN) records show a detectable ENSO
influence on biomass burning (up to 51 %–55 %), suggesting that it
is wetland CH4 production that responds less to ENSO than
previously suggested. Dynamics of the removal by hydroxyl likely counteract
the variation in emissions, but the expected isotope signal is not evident.
It is possible that other processes obscure the ENSO signal, which itself
indicates a minor influence of the latter on global CH4 emissions.
Trends like the recent rise in atmospheric CH4 can therefore not
be attributed to ENSO. This leaves anthropogenic methane sources as the
likely driver, which must be mitigated to reduce anthropogenic climate
change.
A growing body of evidence suggests that protein-protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and ...N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the ffluc reporters and epitope tags. Our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta.
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