Freight logistics services for rural economies : User needs and future challenges

Peer reviewedPublisher PD

Planet Hunters. VI: An Independent Characterization of KOI-351 and Several Long Period Planet Candidates from the Kepler Archival Data

We report the discovery of 14 new transiting planet candidates in the Kepler field from the Planet Hunters citizen science program. None of these candidates overlapped with Kepler Objects of Interest (KOIs) at the time of submission. We report the discovery of one more addition to the six planet candidate system around KOI-351, making it the only seven planet candidate system from Kepler. Additionally, KOI-351 bears some resemblance to our own solar system, with the inner five planets ranging from Earth to mini-Neptune radii and the outer planets being gas giants; however, this system is very compact, with all seven planet candidates orbiting $\lesssim 1$ AU from their host star. A Hill stability test and an orbital integration of the system shows that the system is stable. Furthermore, we significantly add to the population of long period transiting planets; periods range from 124-904 days, eight of them more than one Earth year long. Seven of these 14 candidates reside in their host star's habitable zone.Comment: 27 pages, 6 figures, 5 tables, Accepted to AJ (in press) (updated title from original astro-ph submission

Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain.

BACKGROUND: Chlamydia trachomatis is the most common cause of sexually transmitted infections globally and the leading cause of preventable blindness in the developing world. There are two biovariants of C. trachomatis: 'trachoma', causing ocular and genital tract infections, and the invasive 'lymphogranuloma venereum' strains. Recently, a new variant of the genital tract C. trachomatis emerged in Sweden. This variant escaped routine diagnostic tests because it carries a plasmid with a deletion. Failure to detect this strain has meant it has spread rapidly across the country provoking a worldwide alert. In addition to being a key diagnostic target, the plasmid has been linked to chlamydial virulence. Analysis of chlamydial plasmids and their cognate chromosomes was undertaken to provide insights into the evolutionary relationship between chromosome and plasmid. This is essential knowledge if the plasmid is to be continued to be relied on as a key diagnostic marker, and for an understanding of the evolution of Chlamydia trachomatis. RESULTS: The genomes of two new C. trachomatis strains were sequenced, together with plasmids from six C. trachomatis isolates, including the new variant strain from Sweden. The plasmid from the new Swedish variant has a 377 bp deletion in the first predicted coding sequence, abolishing the site used for PCR detection, resulting in negative diagnosis. In addition, the variant plasmid has a 44 bp duplication downstream of the deletion. The region containing the second predicted coding sequence is the most highly conserved region of the plasmids investigated. Phylogenetic analysis of the plasmids and chromosomes are fully congruent. Moreover this analysis also shows that ocular and genital strains diverged from a common C. trachomatis progenitor. CONCLUSION: The evolutionary pathways of the chlamydial genome and plasmid imply that inheritance of the plasmid is tightly linked with its cognate chromosome. These data suggest that the plasmid is not a highly mobile genetic element and does not transfer readily between isolates. Comparative analysis of the plasmid sequences has revealed the most conserved regions that should be used to design future plasmid based nucleic acid amplification tests, to avoid diagnostic failures

Protrudin functions from the endoplasmic reticulum to support axon regeneration in the adult CNS

Funder: Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation); doi: https://doi.org/10.13039/100000865Funder: Christopher and Dana Reeve Foundation (Christopher & Dana Reeve Foundation); doi: https://doi.org/10.13039/100001305Funder: International Foundation for Research in Paraplegia (Internationale Stiftung für Forschung in Paraplegie); doi: https://doi.org/10.13039/501100001708Funder: Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.); doi: https://doi.org/10.13039/100000009Funder: Christopher and Dana Reeve Foundation (Christopher & Dana Reeve Foundation)Abstract: Adult mammalian central nervous system axons have intrinsically poor regenerative capacity, so axonal injury has permanent consequences. One approach to enhancing regeneration is to increase the axonal supply of growth molecules and organelles. We achieved this by expressing the adaptor molecule Protrudin which is normally found at low levels in non-regenerative neurons. Elevated Protrudin expression enabled robust central nervous system regeneration both in vitro in primary cortical neurons and in vivo in the injured adult optic nerve. Protrudin overexpression facilitated the accumulation of endoplasmic reticulum, integrins and Rab11 endosomes in the distal axon, whilst removing Protrudin’s endoplasmic reticulum localization, kinesin-binding or phosphoinositide-binding properties abrogated the regenerative effects. These results demonstrate that Protrudin promotes regeneration by functioning as a scaffold to link axonal organelles, motors and membranes, establishing important roles for these cellular components in mediating regeneration in the adult central nervous system

The mouse Gene Expression Database (GXD): 2021 update.

The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded GXD to include RNA-Seq data. Uniformly processed RNA-Seq data are imported from the EBI Expression Atlas and then integrated with the other types of expression data in GXD, and with the genetic, functional, phenotypic and disease-related information in Mouse Genome Informatics (MGI). This integration has made the RNA-Seq data accessible via GXD\u27s enhanced searching and filtering capabilities. Further, we have embedded the Morpheus heat map utility into the GXD user interface to provide additional tools for display and analysis of RNA-Seq data, including heat map visualization, sorting, filtering, hierarchical clustering, nearest neighbors analysis and visual enrichment

Bringing together approaches to reporting on within species genetic diversity

1. Genetic diversity is one of the three main levels of biodiversity recognised in the Convention on Biological Diversity (CBD). Fundamental for species adaptation to environmental change, genetic diversity is nonetheless under-reported within global and national indicators. When it is reported, the focus is often narrow and confined to domesticated or other commercial species. 2. Several approaches have recently been developed to address this shortfall in reporting on genetic diversity of wild species. While multiplicity of approaches is helpful in any development process, it can also lead to confusion among policy makers and heighten a perception that conservation genetics is too abstract to be of use to organisations and governments. 3. As the developers of five of the different approaches, we have come together to explain how various approaches relate to each other and propose a scorecard, as a unifying reporting mechanism for genetic diversity. 4. Policy implications. We believe the proposed combined approach captures the strengths of its components and is practical for all nations and subnational governments. It is scalable and can be used to evaluate species conservation projects as well as genetic conservation projects.ISSN:0021-8901ISSN:1365-266

Ecological implications of a flower size/number trade-off in tropical forest trees

Peer reviewedPublisher PD

Nighttime chemical transformation in biomass burning plumes : A box model analysis initialized with aircraft observations

Biomass burning (BB) is a large source of reactive compounds in the atmosphere. While the daytime photochemistry of BB emissions has been studied in some detail, there has been little focus on nighttime reactions despite the potential for substantial oxidative and heterogeneous chemistry. Here, we present the first analysis of nighttime aircraft intercepts of agricultural BB plumes using observations from the NOAA WP-3D aircraft during the 2013 Southeast Nexus (SENEX) campaign. We use these observations in conjunction with detailed chemical box modeling to investigate the formation and fate of oxidants (NO3, N2O5, O3, and OH) and BB volatile organic compounds (BBVOCs), using emissions representative of agricultural burns (rice straw) and western wildfires (ponderosa pine). Field observations suggest NO3 production was approximately 1 ppbv hr–1, while NO3 and N2O5 were at or below 3 pptv, indicating rapid NO3/N2O5 reactivity. Model analysis shows that >99% of NO3/N2O5 loss is due to BBVOC + NO3 reactions rather than aerosol uptake of N2O5. Nighttime BBVOC oxidation for rice straw and ponderosa pine fires is dominated by NO3 (72, 53%, respectively) but O3 oxidation is significant (25, 43%), leading to roughly 55% overnight depletion of the most reactive BBVOCs and NO2

The mouse Gene Expression Database (GXD): 2019 update.

The mouse Gene Expression Database (GXD) is an extensive, well-curated community resource freely available at www.informatics.jax.org/expression.shtml. Covering all developmental stages, GXD includes data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments in wild-type and mutant mice. GXD\u27s gene expression information is integrated with the other data in Mouse Genome Informatics and interconnected with other databases, placing these data in the larger biological and biomedical context. Since the last report, the ability of GXD to provide insights into the molecular mechanisms of development and disease has been greatly enhanced by the addition of new data and by the implementation of new web features. These include: improvements to the Differential Gene Expression Data Search, facilitating searches for genes that have been shown to be exclusively expressed in a specified structure and/or developmental stage; an enhanced anatomy browser that now provides access to expression data and phenotype data for a given anatomical structure; direct access to the wild-type gene expression data for the tissues affected in a specific mutant; and a comparison matrix that juxtaposes tissues where a gene is normally expressed against tissues, where mutations in that gene cause abnormalities

Forecasting the ambient solar wind with numerical models. II. An adaptive prediction system for specifying solar wind speed near the Sun

The ambient solar wind flows and fields influence the complex propagation dynamics of coronal mass ejections in the interplanetary medium and play an essential role in shaping Earth's space weather environment. A critical scientific goal in the space weather research and prediction community is to develop, implement, and optimize numerical models for specifying the large-scale properties of solar wind conditions at the inner boundary of the heliospheric model domain. Here we present an adaptive prediction system that fuses information from in situ measurements of the solar wind into numerical models to better match the global solar wind model solutions near the Sun with prevailing physical conditions in the vicinity of Earth. In this way, we attempt to advance the predictive capabilities of well-established solar wind models for specifying solar wind speed, including the Wang–Sheeley–Arge model. In particular, we use the Heliospheric Upwind eXtrapolation (HUX) model for mapping the solar wind solutions from the near-Sun environment to the vicinity of Earth. In addition, we present the newly developed Tunable HUX (THUX) model, which solves the viscous form of the underlying Burgers equation. We perform a statistical analysis of the resulting solar wind predictions for the period 2006–2015. The proposed prediction scheme improves all the investigated coronal/heliospheric model combinations and produces better estimates of the solar wind state at Earth than our reference baseline model. We discuss why this is the case and conclude that our findings have important implications for future practice in applied space weather research and prediction