The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

International audienceCurrent sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans

The role of browsers in maintaining the openness of savanna grazing lawns

In savannas, ruminant herbivores can have divergent impacts on tree recruitment and subsequent woody cover. Whereas heavy grazing by cattle results in woody thickening, intensive grazing by wildlife instead tends to be associated with lower woody cover. To disentangle why woody cover is low in areas heavily grazed by wildlife, we investigated (a) whether grazing lawns attract indigenous mammalian browsers, and if a preference for short-grass habitat decreases with browser body mass as predator susceptibility decreases; and (b) whether browser attraction to grazing lawns translates into the suppression of woody plants, including seedlings and saplings, thus maintaining the openness of heavily grazed short-grass areas. In Kruger National Park, South Africa, we contrasted browser abundance (using dung counts) on grazing lawns and on low-herbivory sites characterised by tall grass. Additionally, a herbivore exclosure experiment was set up to investigate the combined impact of browser removal and grass height habitat type on seedling survival and sapling growth of a dominant woody plant species. Finally, in Hluhluwe-iMfolozi Park (HiP), we examined the long-term (10 years) impact of browser removal on the growth rates of a range of woody species, monitored across ten sites along a gradient of herbivory ranging from grazing lawn to tall grass. Steenbok and impala selected short- over tall grass as preferred browsing sites, while elephant preferred tall grass. Browser abundance on short grass decreased with browser body mass, indicating that predator avoidance might be a key factor driving mesoherbivores to utilise grazing lawns. Seedling survival was lowest on grazing lawns when browsers were present, with mortality occurring in two out of every three seedlings. Similarly, sapling growth was lowest on grazing lawns, although browser removal had no significant effect. Evidence for increased browser impact on grazing lawns was clearest from our long-term herbivore exclosure experiment in HiP, which demonstrated that browsers strongly modify the growth rates of woody plants in short-grass habitats. Synthesis. These results provide support for the hypothesis that browsers, particularly browsing mesoherbivores and mixed feeders, are attracted to short-grass habitats, and that they help maintain grazing lawn openness by suppressing seedling survival and woody plant growth where grass is kept short by grazers.SUPPORTING INFORMATION: Table S1. Proportion short grass calculated as the mean proportion of grass height below 10 cm, recorded at ten sites in HiP (Hluhluwe and iMfolozi Game Reserves). The mean number of grazer dung piles per year (species: buffalo, blue wildebeest, impala, warthog, white rhino and zebra) are shown for each site. Values in brackets represent standard errors.Figure S1. The effect of grass height and exclosure status (fenced vs. unfenced) on tree height gain (mean ± SE). Browsing impact on tree height gain was higher in areas with short grass i.e. browsers utilised trees in short-grass ecosystems more than in tall-grass ecosystems. Results of linear regression analyses are displayed for the unfenced treatment of two dominant woody plant species: a) D. cinerea (R2 = 0.38, p = 0.05) and b) A. nilotica (R2 = 0.44, p = 0.11), and for two woody plant functional types: c) fine-leaved (R2 = 0.33, p = 0.09) and d) broad-leaved (R2 = 0.60, p = 0.02), across 10 sites in Hluhluwe-iMfolozi Park for the period 2000-2009.DATA AVAILABILITY STATEMENT: Data are available from the Dryad Digital Repository https://doi-org.uplib.idm.oclc.org/10.5061/dryad.76hdr7st3 (Voysey et al., 2020).The USAID/NAS program ‘Partnerships for Enhanced Engagement in Research' (sub-grant 2000004946, Cycle 3) and the South African National Research Foundation, Department of Science and Technology, Innovation and Priority Research Masters Scholarship.http://www.wileyonlinelibrary.com/journal/jechj2022Plant Production and Soil Scienc

Small‐scale fires interact with herbivore feedbacks to create persistent grazing lawn environments

Abstract Fire‐herbivory feedbacks strongly influence the formation of grazing lawns in savanna ecosystems. Preliminary findings suggest that small‐scale (&lt;25 ha) fires can engineer grazing lawns by concentrating herbivores on the post‐burn green flush; however, the persistence of such grazing lawns over the longer term and without repeated fire is unknown. We used high‐resolution Light Detection and Ranging (LiDAR) to investigate the long‐term effects of fire manipulation on short grass structure (height, cover, volume and spatial continuity) and grazing lawn establishment in Kruger National Park, South Africa. We analysed the effects of fire exclusion and experimental burns applied over a 7‐year period (2013–2019) followed by a 1‐year cessation of burning at varying spatial scales during the early and late dry seasons. Fires contributed a fourfold increase in short grass cover, regardless of fire season or size. The distribution of grass height differed significantly between fire‐induced grazing lawns and recently unburnt parts of the landscape where controlled fires were excluded over the experimental period. The volume (corresponding to bulk density) of short grass on the landscape responded strongly to fires, with grass volume &lt;20 cm in height increasing with both early and late dry season fires. Early dry season fires caused larger and more homogeneous short grass patches. Furthermore, early dry season fires were more influential in increasing the cover of the shortest grass height class (1–5 cm). Synthesis and applications. Our results demonstrate that fire‐induced grazing lawns can persist over the longer term, even when fires are no longer applied, leading to the creation of vertical and horizontal heterogeneity in the grass layer. Small‐scale fires, therefore, represent a feasible management approach to expanding grazing lawn extent, potentially benefiting grazer coexistence and diversity. </jats:p

Quasi-simultaneous Radio/X-Ray Observations of the Candidate Transitional Millisecond Pulsar 3FGL J1544.6-1125 during its Low-luminosity Accretion-disk State

3FGL J1544.6-1125 is a candidate transitional millisecond pulsar (tMSP). Similar to the well-established tMSPs - PSR J1023+0038, IGR J18245-2452, and XSS J12270-4859 - 3FGL J1544.6-1125 shows γ-ray emission and discrete X-ray "low"and "high"modes during its low-luminosity accretion-disk state. Coordinated radio/X-ray observations of PSR J1023+0038 in its current low-luminosity accretion-disk state showed rapidly variable radio continuum emission - possibly originating from a compact, self-absorbed jet, the "propellering"of accretion material, and/or pulsar moding. 3FGL J1544.6-1125 is currently the only other (candidate) tMSP system in this state, and can be studied to see whether tMSPs are typically radio-loud compared to other neutron star binaries. In this work, we present a quasi-simultaneous Very Large Array and Swift radio/X-ray campaign on 3FGL J1544.6-1125. We detect 10 GHz radio emission varying in flux density from 47.7 ± 6.0 μJy down to ≲15 μJy (3σ upper limit) at four epochs spanning three weeks. At the brightest epoch, the radio luminosity is L 5 GHz = (2.17 ± 0.17) × 1027 erg s-1 for a quasi-simultaneous X-ray luminosity L 2-10 keV = (4.32 ± 0.23) × 1033 erg s-1 (for an assumed distance of 3.8 kpc). These luminosities are close to those of PSR J1023+0038, and the results strengthen the case that 3FGL J1544.6-1125 is a tMSP showing similar phenomenology to PSR J1023+0038.A.J. and J.W.T.H. acknowledge funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement nr. 337062 (DRAGNET). A.J. also acknowledges support from the NuSTAR mission. A.P. acknowledges support from an NWO Vidi Fellowship. J.C.A.M.-J. is the recipient of an Australian Research Council Future Fellowship (FT 140101082). S.B. was supported in part by NASA Swift Guest Investigator Cycle 12 program grant NNX16AN79G awarded through Columbia University

Etiology of Pediatric Bacterial Meningitis Pre- and Post-PCV13 Introduction Among Children Under 5 Years Old in Lomé, Togo.

BACKGROUND: Pediatric bacterial meningitis (PBM) causes severe morbidity and mortality within Togo. Thus, as a member of the World Health Organization coordinated Invasive Bacterial Vaccine Preventable Diseases network, Togo conducts surveillance targeting Streptococcus pneumoniae (pneumococcus), Neisseria meningitidis (meningococcus), and Haemophilus influenzae, at a sentinel hospital within the capital city, Lomé, in the southernmost Maritime region. METHODS: Cerebrospinal fluid was collected from children <5 years with suspected PBM admitted to the Sylvanus Olympio Teaching Hospital. Phenotypic detection of pneumococcus, meningococcus, and H. influenzae was confirmed through microbiological techniques. Samples were shipped to the Regional Reference Laboratory to corroborate results by species-specific polymerase chain reaction. RESULTS: Overall, 3644 suspected PBM cases were reported, and 98 cases (2.7%: 98/3644) were confirmed bacterial meningitis. Pneumococcus was responsible for most infections (67.3%: 66/98), followed by H. influenzae (23.5%: 23/98) and meningococcus (9.2%: 9/98). The number of pneumococcal meningitis cases decreased by 88.1% (52/59) postvaccine introduction with 59 cases from July 2010 to June 2014 and 7 cases from July 2014 to June 2016. However, 5 cases caused by nonvaccine serotypes were observed. Fewer PBM cases caused by vaccine serotypes were observed in infants <1 year compared to children 2-5 years. CONCLUSIONS: Routine surveillance showed that PCV13 vaccination is effective in preventing pneumococcal meningitis among children <5 years of age in the Maritime region. This complements the MenAfriVac vaccination against meningococcal serogroup A to prevent meningitis outbreaks in the northern region of Togo. Continued surveillance is vital for estimating the prevalence of PBM, determining vaccine impact, and anticipating epidemics in Togo

Declines in Pediatric Bacterial Meningitis in the Republic of Benin Following Introduction of Pneumococcal Conjugate Vaccine: Epidemiological and Etiological Findings, 2011-2016.

BACKGROUND: Pediatric bacterial meningitis (PBM) remains an important cause of disease in children in Africa. We describe findings from sentinel site bacterial meningitis surveillance in children <5 years of age in the Republic of Benin, 2011-2016. METHODS: Cerebrospinal fluid (CSF) was collected from children admitted to Parakou, Natitingou, and Tanguieta sentinel hospitals with suspected meningitis. Identification of Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Neisseria meningitidis (meningococcus) was performed by rapid diagnostic tests, microbiological culture, and/or polymerase chain reaction; where possible, serotyping/grouping was performed. RESULTS: A total of 10 919 suspected cases of meningitis were admitted to the sentinel hospitals. Most patients were 0-11 months old (4863 [44.5%]) and there were 542 (5.0%) in-hospital deaths. Overall, 4168 CSF samples were screened for pathogens and a total of 194 (4.7%) PBM cases were confirmed, predominantly caused by pneumococcus (98 [50.5%]). Following pneumococcal conjugate vaccine (PCV) introduction in 2011, annual suspected meningitis cases and deaths (case fatality rate) progressively declined from 2534 to 1359 and from 164 (6.5%) to 14 (1.0%) in 2012 and 2016, respectively (P < .001). Additionally, there was a gradual decline in the proportion of meningitis cases caused by pneumococcus, from 77.3% (17/22) in 2011 to 32.4% (11/34) in 2016 (odds ratio, 7.11 [95% confidence interval, 2.08-24.30]). Haemophilus influenzae meningitis fluctuated over the surveillance period and was the predominant pathogen (16/34 [47.1%]) by 2016. CONCLUSIONS: The observed decrease in pneumococcal meningitis after PCV introduction may be indicative of changing patterns of PBM etiology in Benin. Maintaining vigilant and effective surveillance is critical for understanding these changes and their wider public health implications

IL-24 Inhibits lung cancer cell migration and invasion by disrupting the SDF-1/CXCR4 signaling axis

© 2015 Panneerselvam et al. Background The stromal cell derived factor (SDF)-1/chemokine receptor (CXCR)-4 signaling pathway plays a key role in lung cancer metastasis and is molecular target for therapy. In the present study we investigated whether interleukin (IL)-24 can inhibit the SDF-1/CXCR4 axis and suppress lung cancer cell migration and invasion in vitro. Further, the efficacy of IL-24 in combination with CXCR4 antagonists was investigated. Methods Human H1299, A549, H460 and HCC827 lung cancer cell lines were used in the present study. The H1299 lung cancer cell line was stably transfected with doxycycline-inducible plasmid expression vector carrying the human IL-24 cDNA and used in the present study to determine the inhibitory effects of IL-24 on SDF-1/CXCR4 axis. H1299 and A549 cell lines w ere used in transient transfection studies. The inhibitory effects of IL-24 on SDF1/CXCR4 and its downstream targets were analyzed by quantitative RT-PCR, western blot, luciferase reporter assay, flow cytometry and immunocytochemistry. Functional studies included cell migration and invasion assays. Principal Findings Endogenous CXCR4 protein expression levels varied among the four human lung cancer cell lines. Doxycycline-induced IL-24 expression in the H1299-IL24 cell line resulted in reduced CXCR4 mRNA and protein expression. IL-24 post-transcriptionally regulated CXCR4 mRNA expression by decreasing the half-life of CXCR4 mRNA ( > 40%). Functional studies showed IL-24 inhibited tumor cell migration and invasion concomitant with reduction in CXCR4 and its downstream targets (pAKTS 473 , pmTORS 2448 , pPRAS40 T246 and HIF-1α). Additionally, IL-24 inhibited tumor cell migration both in the presence and absence of the CXCR4 agonist, SDF-1. Finally, IL-24 when combined with CXCR4 inhibitors (AMD3100, SJA5) or with CXCR4 siRNA demonstrated enhanced inhibitory activity on tumor cell migration. Conclusions IL-24 disrupts the SDF-1/CXCR4 signaling pathway and inhibits lung tumor cell migration and invasion. Additionally, IL-24, when combined with CXCR4 inhibitors exhibited enhanced anti-metastatic activity and is an attractive therapeutic strategy for lung metastasi

Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction.

Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of Streptococcus pneumoniae which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 S. pneumoniae isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test P value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (n=6) in the post-PCV introduction period compared to 21.9 % (n=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (n=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (n=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact