Search

International audience; Advances in single-cell RNA sequencing have allowed for the identification of cellular subtypes on the basis of quantification of the number of transcripts in each cell. However, cells might also differ in the spatial distribution of molecules, including RNAs. Here, we present DypFISH, an approach to quantitatively investigate the subcellular localization of RNA and protein. We introduce a range of analytical techniques to interrogate single-molecule RNA fluorescence in situ hybridization (smFISH) data in combination with protein immunolabeling. DypFISH is suited to study patterns of clustering of molecules, the association of mRNA-protein subcellular localization with microtubule organizing center orientation, and interdependence of mRNA-protein spatial distributions. We showcase how our analytical tools can achieve biological insights by utilizing cell micropatterning to constrain cellular architecture, which leads to reduction in subcellular mRNA distribution variation, allowing for the characterization of their localization patterns. Furthermore, we show that our method can be applied to physiological systems such as skeletal muscle fibers.

Introduced plants become decoupled from their usual pollinators and by relying on resident pollinator species or other reproductive strategies become established in new areas, spread and, eventually, invade. Here, using breeding system experiments, we studied the reproductive biology of the bird-pollinated South American species Nicotiana glauca across native and non-native areas, both inside and outside the range of flower-visiting birds. In the native range, where the species is visited by hummingbirds, open cross-pollinated flowers set as many seeds and almost as many fruits as open pollination controls, suggesting that pollinators make a major contribution to reproductive success. In South Africa, the flowers were pollinated by sunbirds which, although less efficiently, also contributed to N. glauca reproduction, replacing hummingbirds. In contrast, in Mallorca, where nectar feeding birds are absent, fruit production in open cross-pollinated flowers was near zero, and significantly lower than in open pollination controls, suggesting that reproduction is almost entirely by autonomous self-pollination. Hand-pollination experiments showed that the species is self-compatible throughout its range. Pollinator exclusion experiment showed that N. glauca relies on self-pollination only in pollinator poor areas, where plants have a much higher capacity for autonomous self-pollination than elsewhere. A reduction in anther-stigma distance does not seem to account the higher self-pollination capacity in the non-native environment without pollinators. Despite probable evolutionary adaptation, and flexibility in pollinator association and mating system, seed production in the introduced range was somewhat pollen limited, suggesting that the mismatch between N. glauca and its novel pollination environment might retard invasion., Funding for this research was provided by the National Research Council of Argentina (CONICET), the National Ministry of Science and Technology of Argentina, the Department of Science and Technology of South Africa and the Spanish Research Council (CSIC).

15 pages, 2 figures, 4 tables, 1 appendix.-- The data/code that support the findings of this study are available on request from the corresponding author, [E.M.L.]. The data/code are not publicly available because of ongoing research, Although an ecosystem approach to fisheries has been recognized as a means of progressing toward sustainable fishing, successful implementation of this approach has been limited. However, one way in which progress has been made is through the use of suites of indicators. Decision tree frameworks can be used to incorporate trends in ecological, fishing, and environmental indicators into ecosystem assessments. A relatively generic decision tree framework has been developed and successfully applied to multiple ecosystems. This framework incorporates trends in indicators, as well as the impacts of fishing pressure and environmental variability on ecological indicators in order to assess the state of each ecosystem. The inclusion of ecosystem expert knowledge from the outset ensures trends are correctly interpreted and allows analyses to contribute to global comparisons in a robust and meaningful manner. Although ecological and environmental indicators are well developed, those addressing the human dimensions of marine ecosystems are less so. This framework holds the potential to incorporate such indicators in order to fully assess marine ecosystems in a comparative context. Such assessments could help ensure food security from marine resources into the future as well as ensuring the well-being of coastal communities. Here critical review of the potential value of this framework has been conducted, with its usefulness emphasized in the similarities it holds, and in the contribution it could make, to current global methods of ecosystem assessments, This study was funded by the South African Scientific Research Chair Initiative, of the Department of Science and Technology and administered by the National Research Foundation (NRF), through the chair in Marine Ecology and Fisheries. C.L. was supported by the Department for Environment, Food & Rural Affairs of the UK (project MF1228 “Physics to Fisheries”). M.C. was supported by the Spanish Ministry of Economy, Industry and Competitively through the project PELWEB (I+D+I 2018-2020), With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

[Context] PSR B1259–63/LS 2883 is a gamma-ray binary system consisting of a pulsar in an eccentric orbit around a bright Oe stellar-type companion star that features a dense circumstellar disc. The bright broad-band emission observed at phases close to periastron offers a unique opportunity to study particle acceleration and radiation processes in binary systems. Observations at gamma-ray energies constrain these processes through variability and spectral characterisation studies. [Aims] The high- and very-high-energy (HE, VHE) gamma-ray emission from PSR B1259–63/LS 2883 around the times of its periastron passage are characterised, in particular, at the time of the HE gamma-ray flares reported to have occurred in 2011, 2014, and 2017. Short-term and average emission characteristics of PSR B1259–63/LS 2883 are determined. Super-orbital variability is searched for in order to investigate possible cycle-to-cycle VHE flux changes due to different properties of the companion star’s circumstellar disc and/or the conditions under which the HE gamma-ray flares develop. [Methods] Spectra and light curves were derived from observations conducted with the H.E.S.S-II array in 2014 and 2017. Phase-folded light curves are compared with the results obtained in 2004, 2007, and 2011. Fermi-LAT observations from 2010/11, 2014, and 2017 are analysed. [Results] A local double-peak profile with asymmetric peaks in the VHE light curve is measured, with a flux minimum at the time of periastron tp and two peaks coinciding with the times at which the neutron star crosses the companion’s circumstellar disc (~tp ± 16 d). A high VHE gamma-ray flux is also observed at the times of the HE gamma-ray flares (~tp + 30 d) and at phases before the first disc crossing (~tp − 35 d). The spectral energy range now extends to below 200 GeV and up to ~45 TeV. [Conclusions] PSR B1259–63/LS 2883 displays periodic flux variability at VHE gamma-rays without clear signatures of super-orbital modulation in the time span covered by the monitoring of the source with the H.E.S.S. telescopes. This flux variability is most probably caused by the changing environmental conditions, particularly at times close to periastron passage at which the neutron star is thought to cross the circumstellar disc of the companion star twice. In contrast, the photon index remains unchanged within uncertainties for about 200 d around periastron. At HE gamma-rays, PSR B1259–63/LS 2883 has now been detected also before and after periastron, close to the disc crossing times. Repetitive flares with distinct variability patterns are detected in this energy range. Such outbursts are not observed at VHEs, although a relatively high emission level is measured. The spectra obtained in both energy regimes displays a similar slope, although a common physical origin either in terms of a related particle population, emission mechanism, or emitter location is ruled out. The support of the Namibian authorities and of the University of Namibia in facilitating the construction and operation of H.E.S.S. is gratefully acknowledged, as is the support by the German Ministry for Education and Research (BMBF), the Max Planck Society, the German Research Foundation (DFG), the Helmholtz Association, the Alexander von Humboldt Foundation, the French Ministry of Higher Education, Research and Innovation, the Centre National de la Recherche Scientifique (CNRS/IN2P3 and CNRS/INSU), the Commissariat a l’Énergie atomique et aux Énergies alternatives (CEA), the U.K. Science and Technology Facilities Council (STFC), the Knut and Alice Wallenberg Foundation, the National Science Centre, Poland grant no. 2016/22/M/ST9/00382, the South African Department of Science and Technology and National Research Foundation, the University of Namibia, the National Commission on Research, Science & Technology of Namibia (NCRST), the Austrian Federal Ministry of Education, Science and Research and the Austrian Science Fund (FWF), the Australian Research Council (ARC), the Japan Society for the Promotion of Science and by the University of Amsterdam. We appreciate the excellent work of the technical support staff in Berlin, Zeuthen, Heidelberg, Palaiseau, Paris, Saclay, Tübingen and in Namibia in the construction and operation of the equipment. This work benefitted from services provided by the H.E.S.S. Virtual Organisation, supported by the national resource providers of the EGI Federation.

Due to drastic changes in pollinators between native and invaded habitats, we might expect that pollinator-mediated selection on floral traits of alien plants differ from that in their native ranges. Here, through geometric morphometric tools and phenotypic selection analyses, we examined whether adaptation in flower shape and length occurred in Nicotiana glauca as a response to pollinator selection in contrasting pollination environments. We assessed populations of this plant species in the native range (South America), where plants depend on hummingbird pollination, and in two invaded areas, one where sunbirds act as pollinators (South Africa), and another where nectar feeding birds are absent and reproduction is entirely by autonomous self-pollination (Mallorca, Spain). Corolla length and shape varied significantly among pollination environments. Non-native sites were less variable and their range of variation fell within the native range of variation. Flower length in native populations and in a South African population matched the bill length of their respective pollinators. In contrast with the straight floral tubes in the native range, both non-native areas had significantly curved tubes. Curvature may improve the fit with the curved bills of sunbirds in South Africa (versus straight beaks of hummingbirds) and may enhance self-pollination in Mallorca, but this similarity between invaded areas may equally be due to drift and a shared colonization route. We found spatial variation in selection acting on corolla length but not on corolla shape. Overall, selection patterns were not consistent with floral trait variation. Although some results are consistent with both drift and selection, our study suggests that population divergence in flower shape and length is more likely the result of long-term diversifying pollinator-driven selection, which is difficult to detect by studying a single selection event., AAC, ANS, SBV and VP acknowledge the National Research Council of Argentina (CONICET) and the Universidad Nacional de Córdoba (UNC) as researchers. This work was supported by FONCyT (PICT 2015-3089; PICT-2011-0837) to ANS, the Department of Science and Technology of South Africa (438 75946) and the Spanish Ministry of Economy and Competitiveness (CGL2013-44386-P).

Special issue: Environmental change issues.-- 9 pages, 3 figures, 3 tables, Marine biodiversity and ecosystem functioning have changed and are continuing to change in marine ecosystems across the world. These changes are driven by human interactions with the environment and ecosystems, as well as by natural environmental change, both locally (at the ecosystem level) and globally. This paper draws on published research, in particular that using ecosystem indicators to identify, assess and compare changes in biodiversity of exploited marine ecosystems across the globe. We use our results to reflect on the sustainability of our changing exploited marine ecosystems and consider ways forward to incorporate this information in decision making processes, LJS is grateful for funding and the support of the South African Research Chair Initiative (SARChI), funded through the South African Department of Science and Technology (DST) and administered by the South African National Research Foundation (NRF) and hosted by the University of Cape Town. MC was partially funded by the European Union's Horizon research program grant agreement No. 689518 for the MERCES project

We present the optimal reconstruction of the thermal Sunyaev-Zel'dovich (tSZ) effect signal based on the combination of a heterogeneous dataset consisting of Atacama Cosmology Telescope (ACT) and Planck data, with different numbers of channels, angular resolutions, and noise levels. We combine both datasets using two different approaches, a matched multifilter (MMF) technique and an optimized internal linear combination (ILC). We show that when applying the MMF to the combination of ACT and Planck data, the size-flux degeneracy is reduced and the signal-to-noise of clusters detected with their Sunyaev-Zel'dovich (SZ) signal improves by up to a factor of three. In the case of the optimized ILC method, we show that the tSZ map is reconstructed with a resolution of ¿1.5 arcmin. This is more than a factor two improvement compared with the Planck resolution, and with a very good control of noise, meaning that it is limited only by the intrinsic noise of the individual experiments. The combination of ACT and Planck data offers a unique opportunity to improve on the study of the pressure profiles and to study substructure in clusters through their tSZ., The authors acknowledge partial funding from the DIM-ACAV and the Agence Nationale de la Recherche under grant ANR-11-BS56-015. The research leading to these results has received funding from the European Research Council under the H2020 Programme ERC grant agreement no 695561. JMD acknowledges support from project AYA2015-64508-P (MINECO/FEDER, UE) funded by the Ministerio de Economia y Competitividad. DC acknowledges support from the South African Radio Astronomy Observatory, which is a facility of the National Research Foundation, an agency of the Department of Science and Technology

This paper presents a methodological framework for developing scientific mobility indicators based on bibliometric data. We identify nearly 16 million individual authors from publications covered in the Web of Science for the 2008-2015 period. Based on the information provided across individuals' publication records, we propose a general classification for analyzing scientific mobility using institutional affiliation changes. We distinguish between migrants--authors who have ruptures with their country of origin--and travelers--authors who gain additional affiliations while maintaining affiliation with their country of origin. We find that 3.7 percent of researchers who have published at least one paper over the period are mobile. Travelers represent 72.7 percent of all mobile scholars, but migrants have higher scientific impact. We apply this classification at the country level, expanding the classification to incorporate the directionality of scientists' mobility (i.e., incoming and outgoing). We provide a brief analysis to highlight the utility of the proposed taxonomy to study scholarly mobility and discuss the implications for science policy., Comment: Paper accepted for publication in Journal of Informetrics

14 pages, 4 figures, 5 tables, supplementary data https://doi.org/10.1016/j.jmarsys.2017.04.003.-- This study is a contribution to the project ECOTRANS (CTM2011-26333, Ministerio de Economía y Competitividad, Spain), The Mediterranean Sea is an enclosed basin, with narrow connections to the Atlantic Ocean via the Strait of Gibraltar, to the Red Sea via the Suez Canal and to the Black Sea via the Bosphorus Strait. This results in restricted exchange between the water masses, with considerable consequences for both circulation and productivity in the Mediterranean basin. Along with the confined nature of the basin this creates the potential for the impacts of climate change to be even more rapid (Calvo et al., 2012). The Mediterranean Sea exhibits high levels of biodiversity, containing an estimated 7% of the world's marine species and with 67% of these species found in the western basin (Link et al., 2010; Calvo et al., 2012), This project is supported by South African Scientific Research Chair Initiative, which is funded through the South African Department of Science and Technology and administered by the South African National Research Foundation (NRF) (65238). MC was partially funded by the European Commission through the Marie Curie Career Integration Grant Fellowships – PCIG10-GA-2011-303534 - to the BIOWEB project

Reed, Jodie ... et al.-- 12 pages, 4 figures, supplementary data and supplementary material https://doi.org/10.1093/icesjms/fsw150, Trophic level (TL)-based indicators are commonly used to track the ecosystem effects of fishing as the selective removal of organisms from the food web may result in changes to the trophic structure of marine ecosystems. The use of a fixed TL per species in the calculation of TL-based indicators has been questioned, given that species’ TLs vary with ontogeny, as well as over time and space. We conducted a model-based assessment of the performance of fixed TL-based indicators vs. variable TL-based indicators for tracking the effects of fishing pressure. This assessment considered three TL-based indicators (the trophic level of the landed catch (TLc), the marine trophic index (MTI) and the trophic level of the surveyed community (TLsc)), three fishing scenarios that targeted specific model groups (the low TL scenario (LTL), the high TL scenario (HTL) and a scenario encompassing broad-scale exploitation (ALL)) and ten contrasting marine ecosystems with four types of ecosystem modelling approaches that differ in their structure and assumptions. Results showed that, overall, variable TL-based indicators have a greater capacity for detecting the effects of fishing pressure than fixed TL-based indicators. Across TL-based indicators, TLsc displayed the most consistent response to fishing whether fixed or variable species' TLs were used, as well as the highest capacity for detecting fishing effects. This result supports previous studies that promote the use of survey-based indicators over catch-based indicators to explore the impacts of fishing on the structure of marine ecosystems. Across fishing scenarios, the low trophic level fishing scenario (LTL) resulted in the lowest consistency between fixed and variable TL-based indicator responses and the lowest capacity of TL-based indicators for detecting fishing effects. Overall, our results speak to the need for caution when interpreting TL-based indicator trends, and knowledge of the broader context, such as fishing strategies and exploitation history, This study was funded by Euromarine and the EMIBIOS project (FRB Fondation pour la Recherche sur la Biodiversité, Contract no. APP-SCEN-2010-II). JR was funded by the French-South African ICEMASA program and IRD. LS was supported through the South African Research Chair Initiative, funded through the South African Department of Science and Technology (DST) and administered by the South African National Research Foundation (NRF), as well as through additional funding granted by IRD. AG was supported by NOAA’s Integrated Ecosystem Assessment (IEA) programme (http://www.noaa.gov/iea/). GH was funded by IRD-DPF PhD fellowships program of the Institut de Recherche pour le Développement (IRD). JEH was supported by a Beaufort Marine Research Award carried out under the Sea Change Strategy and the Strategy for Science Technology and Innovation (2006–2013), with the support of the Marine Institute, funded under the Marine Research Sub-Programme of the Irish National Development Plan 2007–2013. JJH was supported by the Natural Environment Research Council and Department for Environment, Food and Rural Affairs under the project MERP: Grant no. NE/L003279/1, Marine Ecosystems Research Programme

© 2019 Díaz-Faes et al., ‘Social media metrics’ are bursting into science studies as emerging new measures of impact related to scholarly activities. However, their meaning and scope as scholarly metrics is still far from being grasped. This research seeks to shift focus from the consideration of social media metrics around science as mere indicators confined to the analysis of the use and visibility of publications on social media to their consideration as metrics of interaction and circulation of scientific knowledge across different communities of attention, and particularly as metrics that can also be used to characterize these communities. Although recent research efforts have proposed tentative typologies of social media users, no study has empirically examined the full range of Twitter user’s behavior within Twitter and disclosed the latent dimensions in which activity on Twitter around science can be classified. To do so, we draw on the overall activity of social media users on Twitter interacting with research objects collected from the Altmetic.com database. Data from over 1.3 million unique users, accounting for over 14 million tweets to scientific publications, is analyzed. Based on an exploratory and confirmatory factor analysis, four latent dimensions are identified: ‘Science Engagement’, ‘Social Media Capital’, ‘Social Media Activity’ and ‘Science Focus’. Evidence on the predominant type of users by each of the four dimensions is provided by means of VOSviewer term maps of Twitter profile descriptions. This research breaks new ground for the systematic analysis and characterization of social media users’ activity around science., AADF is currently supported by a Juan de la Cierva-Formación postdoctoral grant (FJCI-2015-23699) from the Spanish Ministry of Economy and Competitiveness and benefited from a visiting stay at the Centre for Science and Technology Studies (CWTS) funded by the 'Call for visit to RISIS Facilities' – Research Infrastructure for Science and Innovation Policy Studies, in February 2018. RC was partially funded by the South African DST-NRF Centre of Excellence in Scientometrics and Science, Technology and Innovation Policy (SciSTIP).

Ticks infest a variety of animal species and transmit pathogens causing disease in both humans and animals worldwide. Tick-host-pathogen interactions have evolved through dynamic processes that accommodated the genetic traits of the hosts, pathogens transmitted and the vector tick species that mediate their development and survival. New approaches for tick control are dependent on defining molecular interactions between hosts, ticks and pathogens to allow for discovery of key molecules that could be tested in vaccines or new generation therapeutics for intervention of tick-pathogen cycles. Currently, tick vaccines constitute an effective and environmentally sound approach for the control of ticks and the transmission of the associated tick-borne diseases. New candidate protective antigens will most likely be identified by focusing on proteins with relevant biological function in the feeding, reproduction, development, immune response, subversion of host immunity of the tick vector and/or molecules vital for pathogen infection and transmission. This review addresses different approaches and strategies used for the discovery of protective antigens, including focusing on relevant tick biological functions and proteins, reverse genetics, vaccinomics and tick protein evolution and interactomics. New and improved tick vaccines will most likely contain multiple antigens to control tick infestations and pathogen infection and transmission., The preparation of this chapter was partially supported by the European Union FP7 ANTIGONE project number 278976. P.K. was supported by the Czech Science Foundation, Grant. No. 13-11043S. CMO is supported by the National Research Foundation of South Africa and the Technology Innovation Agency of South Africa.