Constraints on the vital effect in coccolithophore and dinoflagellate calcite by oxygen isotopic modification of seawater

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 141 (2014): 612-627, doi:10.1016/j.gca.2014.05.002.In this study, we show that there are independent controls of 18O/16O and 13C/12C fractionation in coccolithophore and dinoflagellate calcite due to the contrasting kinetics of each isotope system. We demonstrate that the direction and magnitude of the oxygen isotope fractionation with respect to equilibrium is related to the balance between calcification rate and the replenishment of the internal pool of dissolved inorganic carbon (DIC). As such, in fast growing cells, such as those of Emiliania huxleyi and Gephyrocapsa oceanica (forming the so-called “heavy group”), calcification of the internal carbon pool occurs faster than complete isotopic re-adjustment of the internal DIC pool with H2O molecules. Hence, coccoliths reflect the heavy oxygen isotope signature of the CO2 overprinting the whole DIC pool. Conversely, in large and slow growing cells, such as Coccolithus pelagicus ssp. braarudii, complete re-equilibration is achieved due to limited influx of CO2 leading to coccoliths that are precipitated in conditions close to isotopic equilibrium (“equilibrium group”). Species exhibiting the most negative oxygen isotope composition, such as Calcidiscus leptoporus (“light group”), precipitate coccolith under increased pH in the coccolith vesicle, as previously documented by the “carbonate ion effect”. We suggest that, for the carbon isotope system, any observed deviation from isotopic equilibrium is only “apparent”, as the carbon isotopic composition in coccolith calcite is controlled by a Rayleigh fractionation originating from preferential incorporation of 12C into organic matter. Therefore, species with low PIC/POC ratios as E. huxleyi and G. oceanica are shifted towards positive carbon isotope values as a result of predominant carbon fixation into the organic matter. By contrast, cells with higher PIC/POC as C. braarudii and C. leptoporus maintain, to some extent, the original negative isotopic composition of the CO2. The calcareous dinoflagellate Thoracosphaera heimii exhibits different behaviour for both isotopic systems, in particular with respect to its very negative carbon isotope composition, owing to coeval intra and extracellular biomineralisation in this group. In this study, we also investigate the sensitivity of 18O/16O fractionation to varying ambient oxygen isotope composition of the medium for inorganic, coccolithophore, and dinoflagellate calcite precipitated under controlled laboratory conditions. The varying responses of different taxa to increased oxygen isotope composition of the growth medium may point to a potential bias in sea surface temperature reconstructions that are based on the oxygen isotopic compositions of sedimentary calcite, especially during times of changing seawater oxygen isotopic composition. Overall, this study represent an important step towards establishing a mechanistic understanding of the “vital effect” in coccolith and dinoflagellate calcite, and provides valuable information for interpreting the geochemistry of the calcareous nannofossils in the sedimentary record, at both monospecific and interspecies levels.MH is grateful to the Natural Environment Research Council (NERC) for funding through Postdoctoral Fellowship (NE/H015523/1). TJH is supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Doherty Foundation. REMR was supported through European Research Council (ERC) grant SP2-GA-2008-200915

Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB)

Loops represent an important part of protein structures. The study of loop is critical for two main reasons: First, loops are often involved in protein function, stability and folding. Second, despite improvements in experimental and computational structure prediction methods, modeling the conformation of loops remains problematic. Here, we present a structural classification of loops, ArchDB, a mine of information with application in both mentioned fields: loop structure prediction and function prediction. ArchDB (http://sbi.imim.es/archdb) is a database of classified protein loop motifs. The current database provides four different classification sets tailored for different purposes. ArchDB-40, a loop classification derived from SCOP40, well suited for modeling common loop motifs. Since features relevant to loop structure or function can be more easily determined on well-populated clusters, we have developed ArchDB-95, a loop classification derived from SCOP95. This new classification set shows a ~40% increase in the number of subclasses, and a large 7-fold increase in the number of putative structure/function-related subclasses. We also present ArchDB-EC, a classification of loop motifs from enzymes, and ArchDB-KI, a manually annotated classification of loop motifs from kinases. Information about ligand contacts and PDB sites has been included in all classification sets. Improvements in our classification scheme are described, as well as several new database features, such as the ability to query by conserved annotations, sequence similarity, or uploading 3D coordinates of a protein. The lengths of classified loops range between 0 and 36 residues long. ArchDB offers an exhaustive sampling of loop structures. Functional information about loops and links with related biological databases are also provided. All this information and the possibility to browse/query the database through a web-server outline an useful tool with application in the comparative study of loops, the analysis of loops involved in protein function and to obtain templates for loop modeling

Science teacher as classroom manager in online classes

Exploratory sequential mixed research was conducted to characterize science teachers' experiences as classroom managers in their online classes. There were 15 science teachers from elementary and secondary schools in Cebu, Philippines, participated in the phenomenological study, and 30 teachers responded to the developed tool on their management and its effect on students’ performance. Thematic analysis of the interview results unveiled a series of stages, including a different start of the school year and reintegration of online management skills that eventually led to autonomy in online classes and satisfying academic outcomes. Further exploration of the quantitative aspect of the study revealed that they have very good management, which has led to a good effect on students' performance. The different innovations in classroom management strategies by science teachers led to effective online classes. Training on proactive management and positive feedbacking are recommended

Identification of Novel Feline Paramyxoviruses in Guignas (Leopardus guigna) from Chile

The family of paramyxoviruses has received growing attention as several new species have been identified recently, notably two different clusters in domestic cats, designated as feline morbillivirus (FeMV) and feline paramyxovirus (FPaV). Their phylogenetic origin and whether wild felids also harbor these viruses are currently unknown. Kidney samples from 35 guignas (Leopardus guigna), a wild felid from Chile, were investigated for paramyxoviruses using consensus-RT-PCR. In addition, thirteen serum samples of guignas were screened for the presence of FeMV-specific antibodies by an immunofluorescence assay (IFA). Viral RNA was detected in 31% of the kidney samples. Phylogenetic analyses revealed two well-supported clusters, related to isolates from domestic cats, rodents and bats. No significant histopathology changes were recorded in infected guignas. Serology identified two samples which were positive for FeMV-specific antibodies. Our study highlights the diversity of paramyxovirus infections in felids with special emphasis on guignas from Chile

Safeguarding freshwater life beyond 2020: Recommendations for the new global biodiversity framework from the European experience

Plans are currently being drafted for the next decade of action on biodiversity-both the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD) and Biodiversity Strategy of the European Union (EU). Freshwater biodiversity is disproportionately threatened and underprioritized relative to the marine and terrestrial biota, despite supporting a richness of species and ecosystems with their own intrinsic value and providing multiple essential ecosystem services. Future policies and strategies must have a greater focus on the unique ecology of freshwater life and its multiple threats, and now is a critical time to reflect on how this may be achieved. We identify priority topics including environmental flows, water quality, invasive species, integrated water resources management, strategic conservation planning, and emerging technologies for freshwater ecosystem monitoring. We synthesize these topics with decades of first-hand experience and recent literature into 14 special recommendations for global freshwater biodiversity conservation based on the successes and setbacks of European policy, management, and research. Applying and following these recommendations will inform and enhance the ability of global and European post-2020 biodiversity agreements to halt and reverse the rapid global decline of freshwater biodiversity

Fire and biodiversity in the Anthropocene

The workshop leading to this paper was funded by the Centre Tecnològic Forestal de Catalunya and the ARC Centre of Excellence for Environmental Decisions. L.T.K. was supported by a Victorian Postdoctoral Research Fellowship (Victorian Government), a Centenary Fellowship (University of Melbourne), and an Australian Research Council Linkage Project Grant (LP150100765). A.R. was supported by the Xunta de Galicia (Postdoctoral Fellowship ED481B2016/084-0) and the Foundation for Science and Technology under the FirESmart project (PCIF/MOG/0083/2017). A.L.S. was supported by a Marie Skłodowska-Curie Individual Fellowship (746191) under the European Union Horizon 2020 Programme for Research and Innovation. L.R. was supported by the Australian Government’s National Environmental Science Program through the Threatened Species Recovery Hub. L.B. was partially supported by the Spanish Government through the INMODES (CGL2014-59742-C2-2-R) and the ERANET-SUMFORESTS project FutureBioEcon (PCIN-2017-052). This research was supported in part by the U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station.BACKGROUND Fire has shaped the diversity of life on Earth for millions of years. Variation in fire regimes continues to be a source of biodiversity across the globe, and many plants, animals, and ecosystems depend on particular temporal and spatial patterns of fire. Although people have been using fire to modify environments for millennia, the combined effects of human activities are now changing patterns of fire at a global scale—to the detriment of human society, biodiversity, and ecosystems. These changes pose a global challenge for understanding how to sustain biodiversity in a new era of fire. We synthesize how changes in fire activity are threatening species with extinction across the globe, highlight forward-looking methods for predicting the combined effects of human drivers and fire on biodiversity, and foreshadow emerging actions and strategies that could revolutionize how society manages fire for biodiversity in the Anthropocene. ADVANCES Our synthesis shows that interactions with anthropogenic drivers such as global climate change, land use, and biotic invasions are transforming fire activity and its impacts on biodiversity. More than 4400 terrestrial and freshwater species from a wide range of taxa and habitats face threats associated with modified fire regimes. Many species are threatened by an increase in fire frequency or intensity, but exclusion of fire in ecosystems that need it can also be harmful. The prominent role of human activity in shaping global ecosystems is the hallmark of the Anthropocene and sets the context in which models and actions must be developed. Advances in predictive modeling deliver new opportunities to couple fire and biodiversity data and to link them with forecasts of multiple drivers including drought, invasive plants, and urban growth. Making these connections also provides an opportunity for new actions that could revolutionize how society manages fire. Emerging actions include reintroduction of mammals that reduce fuels, green fire breaks comprising low-flammability plants, strategically letting wildfires burn under the right conditions, managed evolution of populations aided by new genomics tools, and deployment of rapid response teams to protect biodiversity assets. Indigenous fire stewardship and reinstatement of cultural burning in a modern context will enhance biodiversity and human well-being in many regions of the world. At the same time, international efforts to reduce greenhouse gas emissions are crucial to reduce the risk of extreme fire events that contribute to declines in biodiversity. OUTLOOK Conservation of Earth’s biological diversity will be achieved only by recognition of and response to the critical role of fire in shaping ecosystems. Global changes in fire regimes will continue to amplify interactions between anthropogenic drivers and create difficult trade-offs between environmental and social objectives. Scientific input will be crucial for navigating major decisions about novel and changing ecosystems. Strategic collection of data on fire, biodiversity, and socioeconomic variables will be essential for developing models to capture the feedbacks, tipping points, and regime shifts characteristic of the Anthropocene. New partnerships are also needed to meet the challenges ahead. At the local and regional scale, getting more of the “right” type of fire in landscapes that need it requires new alliances and networks to build and apply knowledge. At the national and global scale, biodiversity conservation will benefit from greater integration of fire into national biodiversity strategies and action plans and in the implementation of international agreements and initiatives such as the UN Convention on Biological Diversity. Placing the increasingly important role of people at the forefront of efforts to understand and adapt to changes in fire regimes is central to these endeavors.PostprintPeer reviewe

A Narrative Review of Motor Competence in Children and Adolescents: What We Know and What We Need to Find Out

Lack of physical activity is a global public health problem causing not only morbidity and premature mortality, but it is also a major economic burden worldwide. One of the cornerstones of a physically active lifestyle is Motor Competence (MC). MC is a complex biocultural attribute and therefore, its study requires a multi-sectoral, multi-, inter- and transdisciplinary approach. MC is a growing area of research, especially in children and adolescents due to its positive association with a plethora of health and developmental outcomes. Many questions, however, remain to be answered in this field of research, with regard to: (i) Health and Developmental-related Associations of MC; (ii) Assessment of MC; (iii) Prevalence and Trends of MC; (iv) Correlates and Determinants of MC; (v) MC Interventions, and (vi) Translating MC Research into Practice and Policy. This paper presents a narrative review of the literature, summarizing current knowledge, identifying key research gaps and presenting questions for future investigation on MC in children and adolescents. This is a collaborative effort from the International Motor Competence Network (IMCNetwork) a network of academics and researchers aiming to promote international collaborative research and knowledge translation in the expansive field of MC. The knowledge and deliverables generated by addressing and answering the aforementioned research questions on MC presented in this review have the potential to shape the ways in which researchers and practitioners promote MC and physical activity in children and adolescents across the worl

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database - the quality controlled standard tool for routine identification of human and animal pathogenic fungi

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.This study was supported by an National Health and Medical Research Council of Australia (NH&MRC) grant [#APP1031952] to W Meyer, S Chen, V Robert, and D Ellis; CNPq [350338/2000-0] and FAPERJ [E-26/103.157/2011] grants to RM Zancope-Oliveira; CNPq [308011/2010-4] and FAPESP [2007/08575-1] Fundacao de Amparo Pesquisa do Estado de So Paulo (FAPESP) grants to AL Colombo; PEst-OE/BIA/UI4050/2014 from Fundacao para a Ciencia e Tecnologia (FCT) to C Pais; the Belgian Science Policy Office (Belspo) to BCCM/IHEM; the MEXBOL program of CONACyT-Mexico, [ref. number: 1228961 to ML Taylor and [122481] to C Toriello; the Institut Pasteur and Institut de Veil le Sanitaire to F Dromer and D Garcia-Hermoso; and the grants from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) and the Fundacao de Amparo a Pesquisa do Estado de Goias (FAPEG) to CM de Almeida Soares and JA Parente Rocha. I Arthur would like to thank G Cherian, A Higgins and the staff of the Molecular Diagnostics Laboratory, Division of Microbiology and Infectious Diseases, Path West, QEII Medial Centre. Dromer would like to thank for the technical help of the sequencing facility and specifically that of I, Diancourt, A-S Delannoy-Vieillard, J-M Thiberge (Genotyping of Pathogens and Public Health, Institut Pasteur). RM Zancope-Oliveira would like to thank the Genomic/DNA Sequencing Platform at Fundacao Oswaldo Cruz-PDTIS/FIOCRUZ [RPT01A], Brazil for the sequencing. B Robbertse and CL Schoch acknowledge support from the Intramural Research Program of the NIH, National Library of Medicine. T Sorrell's work is funded by the NH&MRC of Australia; she is a Sydney Medical School Foundation Fellow.info:eu-repo/semantics/publishedVersio

Group A Streptococcus Secreted Esterase Hydrolyzes Platelet-Activating Factor to Impede Neutrophil Recruitment and Facilitate Innate Immune Evasion

The innate immune system is the first line of host defense against invading organisms. Thus, pathogens have developed virulence mechanisms to evade the innate immune system. Here, we report a novel means for inhibition of neutrophil recruitment by Group A Streptococcus (GAS). Deletion of the secreted esterase gene (designated sse) in M1T1 GAS strains with (MGAS5005) and without (MGAS2221) a null covS mutation enhances neutrophil ingress to infection sites in the skin of mice. In trans expression of SsE in MGAS2221 reduces neutrophil recruitment and enhances skin invasion. The sse deletion mutant of MGAS5005 (ΔsseMGAS5005) is more efficiently cleared from skin than the parent strain. SsE hydrolyzes the sn-2 ester bond of platelet-activating factor (PAF), converting biologically active PAF into inactive lyso-PAF. KM and kcat of SsE for hydrolysis of 2-thio-PAF were similar to those of the human plasma PAF acetylhydrolase. Treatment of PAF with SsE abolishes the capacity of PAF to induce activation and chemotaxis of human neutrophils. More importantly, PAF receptor-deficient mice significantly reduce neutrophil infiltration to the site of ΔsseMGAS5005 infection. These findings identify the first secreted PAF acetylhydrolase of bacterial pathogens and support a novel GAS evasion mechanism that reduces phagocyte recruitment to sites of infection by inactivating PAF, providing a new paradigm for bacterial evasion of neutrophil responses

A global agenda for advancing freshwater biodiversity research

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.Peer reviewe