Cyanobacterial blooms are an increasing threat to water quality and global water security caused by the nutrient enrichment of freshwaters. There is also a broad consensus that blooms are increasing ...with global warming, but the impacts of other concomitant environmental changes, such as an increase in extreme rainfall events, may affect this response. One of the potential effects of high rainfall events on phytoplankton communities is greater loss of biomass through hydraulic flushing. Here we used a shallow lake mesocosm experiment to test the combined effects of: warming (ambient vs. +4°C increase), high rainfall (flushing) events (no events vs. seasonal events) and nutrient loading (eutrophic vs. hypertrophic) on total phytoplankton chlorophyll‐a and cyanobacterial abundance and composition. Our hypotheses were that: (a) total phytoplankton and cyanobacterial abundance would be higher in heated mesocosms; (b) the stimulatory effects of warming on cyanobacterial abundance would be enhanced in higher nutrient mesocosms, resulting in a synergistic interaction; (c) the recovery of biomass from flushing induced losses would be quicker in heated and nutrient‐enriched treatments, and during the growing season. The results supported the first and, in part, the third hypotheses: total phytoplankton and cyanobacterial abundance increased in heated mesocosms with an increase in common bloom‐forming taxa—Microcystis spp. and Dolichospermum spp. Recovery from flushing was slowest in the winter, but unaffected by warming or higher nutrient loading. Contrary to the second hypothesis, an antagonistic interaction between warming and nutrient enrichment was detected for both cyanobacteria and chlorophyll‐a demonstrating that ecological surprises can occur, dependent on the environmental context. While this study highlights the clear need to mitigate against global warming, oversimplification of global change effects on cyanobacteria should be avoided; stressor gradients and seasonal effects should be considered as important factors shaping the response.
Cyanobacteria are expected to benefit from a warmer climate, especially in nutrient‐rich waters. However, other important climate change factors—more extreme rainfall events—could affect this response (e.g. loss through flushing). This mesocosm study tested the combined effects of warming, extreme rainfall events and nutrient loading on cyanobacterial abundance. Warming increased the abundance of bloom‐forming taxa, but in combination with very high nutrient loading resulted in a negative, not positive, interaction. The impact of extreme rainfall events was only apparent in the winter. Stressor gradients and season should be considered as important factors shaping the response to global change.
Monitoring and understanding the physical, chemical and biological status of global inland waters are immensely important to scientists and policy makers alike. Whereas conventional monitoring ...approaches tend to be limited in terms of spatial coverage and temporal frequency, remote sensing has the potential to provide an invaluable complementary source of data at local to global scales. Furthermore, as sensors, methodologies, data availability and the network of researchers and engaged stakeholders in this field develop, increasingly widespread use of remote sensing for operational monitoring of inland waters can be envisaged. This special issue on Remote Sensing of Inland Waters comprises 16 articles on freshwater ecosystems around the world ranging from lakes and reservoirs to river systems using optical data from a range of in situ instruments as well as airborne and satellite platforms. The papers variably focus on the retrieval of in-water optical and biogeochemical parameters as well as information on the biophysical properties of shoreline and benthic vegetation. Methodological advances include refined approaches to adjacency correction, inversion-based retrieval models and in situ inherent optical property measurements in highly turbid waters. Remote sensing data are used to evaluate models and theories of environmental drivers of change in a number of different aquatic ecosystems. The range of contributions to the special issue highlights not only the sophistication of methods and the diversity of applications currently being developed, but also the growing international community active in this field. In this introductory paper we briefly highlight the progress that the community has made over recent decades as well as the challenges that remain. It is argued that the operational use of remote sensing for inland water monitoring is a realistic ambition if we can continue to build on these recent achievements.
•Challenges, progress and issues motivating the special issue are outlined.•Special issue contributions are summarized.•Highlights from state-of-the-art in science, community coordination, future outlook
Biomedical research and clinical practice are struggling to cope with the growing complexity that the progress of health care involves. The most challenging diseases, those with the largest ...socioeconomic impact (cardiovascular conditions; musculoskeletal conditions; cancer; metabolic, immunity, and neurodegenerative conditions), are all characterized by a complex genotype-phenotype interaction and by a "systemic" nature that poses a challenge to the traditional reductionist approach. In 2005 a small group of researchers discussed how the vision of computational physiology promoted by the Physiome Project could be translated into clinical practice and formally proposed the term Virtual Physiological Human. Our knowledge about these diseases is fragmentary, as it is associated with molecular and cellular processes on the one hand and with tissue and organ phenotype changes (related to clinical symptoms of disease conditions) on the other. The problem could be solved if we could capture all these fragments of knowledge into predictive models and then compose them into hypermodels that help us tame the complexity that such systemic behavior involves. In 2005 this was simply not possible-the necessary methods and technologies were not available. Now, 10 years later, it seems the right time to reflect on the original vision, the results achieved so far, and what remains to be done.
The Earth's surface waters are a fundamental resource and encompass a broad range of ecosystems that are core to global biogeochemical cycling and food and energy production. Despite this, the ...Earth's surface waters are impacted by multiple natural and anthropogenic pressures and drivers of environmental change. The complex interaction between physical, chemical and biological processes in surface waters poses significant challenges for in situ monitoring and assessment and often limits our ability to adequately capture the dynamics of aquatic systems and our understanding of their status, functioning and response to pressures. Here we explore the opportunities that Earth observation (EO) has to offer to basin-scale monitoring of water quality over the surface water continuum comprising inland, transition and coastal water bodies, with a particular focus on the Danube and Black Sea region. This review summarises the technological advances in EO and the opportunities that the next generation satellites offer for water quality monitoring. We provide an overview of algorithms for the retrieval of water quality parameters and demonstrate how such models have been used for the assessment and monitoring of inland, transitional, coastal and shelf–sea systems. Further, we argue that very few studies have investigated the connectivity between these systems especially in large river–sea systems such as the Danube–Black Sea. Subsequently, we describe current capability in operational processing of archive and near real-time satellite data. We conclude that while the operational use of satellites for the assessment and monitoring of surface waters is still developing for inland and coastal waters and more work is required on the development and validation of remote sensing algorithms for these optically complex waters, the potential that these data streams offer for developing an improved, potentially paradigm-shifting understanding of physical and biogeochemical processes across large scale river–sea systems including the Danube–Black Sea is considerable.
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•River-delta–sea systems require integrated approaches to ecological assessment.•Lack of systematic transboundary monitoring across the Danube catchment•Remote sensing has shown promise for large-scale assessment but limited application.•New satellites have potential for synergistic multi-scale operational observation.•Need for further algorithm development and validation for optically complex waters
Computational biologists have been developing standards and formats for nearly two decades, with the aim of easing the description and exchange of experimental data, mathematical models, simulation ...experiments, etc. One of those efforts is CellML (cellml.org), an XML-based markup language for the encoding of mathematical models. Early CellML-based environments include COR and OpenCell. However, both of those tools have limitations and were eventually replaced with OpenCOR (opencor.ws). OpenCOR is an open source modeling environment that is supported on Windows, Linux and OS X. It relies on a modular approach, which means that all of its features come in the form of plugins. Those plugins can be used to organize, edit, simulate and analyze models encoded in the CellML format. We start with an introduction to CellML and two of its early adopters, which limitations eventually led to the development of OpenCOR. We then go onto describing the general philosophy behind OpenCOR, as well as describing its openness and its development process. Next, we illustrate various aspects of OpenCOR, such as its user interface and some of the plugins that come bundled with it (e.g., its editing and simulation plugins). Finally, we discuss some of the advantages and limitations of OpenCOR before drawing some concluding remarks.
This study assesses the ability of a new active fluorometer, the LabSTAF, to diagnostically assess the physiology of freshwater cyanobacteria in a reservoir exhibiting annual blooms. Specifically, we ...analyse the correlation of relative cyanobacteria abundance with photosynthetic parameters derived from fluorescence light curves (FLCs) obtained using several combinations of excitation wavebands, photosystem II (PSII) excitation spectra and the emission ratio of 730 over 685 nm (Fo(730/685)) using excitation protocols with varying degrees of sensitivity to cyanobacteria and algae. FLCs using blue excitation (B) and green−orange−red (GOR) excitation wavebands capture physiology parameters of algae and cyanobacteria, respectively. The green−orange (GO) protocol, expected to have the best diagnostic properties for cyanobacteria, did not guarantee PSII saturation. PSII excitation spectra showed distinct response from cyanobacteria and algae, depending on spectral optimisation of the light dose. Fo(730/685), obtained using a combination of GOR excitation wavebands, Fo(GOR, 730/685), showed a significant correlation with the relative abundance of cyanobacteria (linear regression, p-value < 0.01, adjusted R2 = 0.42). We recommend using, in parallel, Fo(GOR, 730/685), PSII excitation spectra (appropriately optimised for cyanobacteria versus algae), and physiological parameters derived from the FLCs obtained with GOR and B protocols to assess the physiology of cyanobacteria and to ultimately predict their growth. Higher intensity LEDs (G and O) should be considered to reach PSII saturation to further increase diagnostic sensitivity to the cyanobacteria component of the community.
Klebsiella pneumoniae is a major cause of opportunistic healthcare-associated infections, which are increasingly complicated by the presence of extended-spectrum beta-lactamases (ESBLs) and ...carbapenem resistance. We conducted a year-long prospective surveillance study of K. pneumoniae clinical isolates in hospital patients. Whole-genome sequence (WGS) data reveals a diverse pathogen population, including other species within the K. pneumoniae species complex (18%). Several infections were caused by K. variicola/K. pneumoniae hybrids, one of which shows evidence of nosocomial transmission. A wide range of antimicrobial resistance (AMR) phenotypes are observed, and diverse genetic mechanisms identified (mainly plasmid-borne genes). ESBLs are correlated with presence of other acquired AMR genes (median n = 10). Bacterial genomic features associated with nosocomial onset are ESBLs (OR 2.34, p = 0.015) and rhamnose-positive capsules (OR 3.12, p < 0.001). Virulence plasmid-encoded features (aerobactin, hypermucoidy) are observed at low-prevalence (<3%), mostly in community-onset cases. WGS-confirmed nosocomial transmission is implicated in just 10% of cases, but strongly associated with ESBLs (OR 21, p < 1 × 10
). We estimate 28% risk of onward nosocomial transmission for ESBL-positive strains vs 1.7% for ESBL-negative strains. These data indicate that K. pneumoniae infections in hospitalised patients are due largely to opportunistic infections with diverse strains, with an additional burden from nosocomially-transmitted AMR strains and community-acquired hypervirulent strains.
Patients' own gut microbiota were the major source of Klebsiella pneumoniae, but extended-spectrum β-lactamase strains were acquired in the referring hospital. This highlights the potential for ...rectal screening, and the importance of the wider hospital network, for local risk management.
Abstract
Background
Klebsiella pneumoniae is a leading cause of extended-spectrum β-lactamase (ESBL)-producing hospital-associated infections, for which elderly patients are at increased risk.
Methods
We conducted a 1-year prospective cohort study, in which a third of patients admitted to 2 geriatric wards in a specialized hospital were recruited and screened for carriage of K. pneumoniae by microbiological culture. Clinical isolates were monitored via the hospital laboratory. Colonizing and clinical isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing.
Results
K. pneumoniae throat carriage prevalence was 4.1%, rectal carriage 10.8%, and ESBL carriage 1.7%, and the incidence of K. pneumoniae infection was 1.2%. The isolates were diverse, and most patients were colonized or infected with a unique phylogenetic lineage, with no evidence of transmission in the wards. ESBL strains carried blaCTX-M-15 and belonged to clones associated with hospital-acquired ESBL infections in other countries (sequence type ST 29, ST323, and ST340). One also carried the carbapenemase blaIMP-26. Genomic and epidemiological data provided evidence that ESBL strains were acquired in the referring hospital. Nanopore sequencing also identified strain-to-strain transmission of a blaCTX-M-15 FIBK/FIIK plasmid in the referring hospital.
Conclusions
The data suggest the major source of K. pneumoniae was the patient's own gut microbiome, but ESBL strains were acquired in the referring hospital. This highlights the importance of the wider hospital network to understanding K. pneumoniae risk and infection prevention. Rectal screening for ESBL organisms on admission to geriatric wards could help inform patient management and infection control in such facilities.
The 10-year archive of MEdium Resolution Imaging Spectrometer (MERIS) data is an invaluable resource for studies on lake system dynamics at regional and global scales. MERIS data are no longer ...actively acquired but their capacity for global scale monitoring of lakes from satellites will soon be re-established through the forthcoming Sentinel-3 Ocean and Land Colour Instrument (OLCI). The development and validation of in-water algorithms for the accurate retrieval of biogeochemical parameters is thus of key importance if the potential of MERIS and OLCI data is to be fully exploited for lake monitoring. This study presents the first extensive validation of algorithms for chlorophyll-a (chl-a) retrieval by MERIS in the highly turbid and productive waters of Lake Balaton, Hungary. Six algorithms for chl-a retrieval from MERIS over optically complex Case 2 waters, including band-difference and neural network architectures, were compared using the MERIS archive for 2007–2012. The algorithms were locally-tuned and validated using in situ chl-a data (n=289) spanning the five year processed image time series and from all four lake basins. In general, both band-difference algorithms tested (Fluorescence Line Height (FLH) and Maximum Chlorophyll Index (MCI)) performed well, whereas the neural network processors were generally found to much less accurately retrieve in situ chl-a concentrations. The Level 1b FLH algorithm performed best overall in terms of chl-a retrieval (R2=0.87; RMSE=4.19mgm−3; relative RMSE=30.75%) and particularly at chl-a concentrations of ≥10mgm−3 (R2=0.85; RMSE=4.81mgm−3; relative RMSE=20.77%). However, under mesotrophic conditions (i.e., chl-a<10mgm−3) FLH was outperformed by the locally-tuned FUB/WeW processor (relative FLH RMSE<10mgm−3=57.57% versus relative FUB/WeW RMSE<10mgm−3=46.96%). An ensemble selection of in-water algorithms is demonstrated to improve chl-a retrievals.
•6 chlorophyll-a (chl-a) retrieval algorithms are validated for a large turbid lake.•Extensive in situ matchup dataset allowed insight into temporal and spatial nuances.•Fluorescence Line Height (FLH) most accurately retrieved chl-a overall.•Neural network-based processors were generally inaccurate, even when locally-tuned.•FUB/WeW processor outperformed FLH under mesotrophic conditions.
The CellML Model Repository Lloyd, Catherine M.; Lawson, James R.; Hunter, Peter J. ...
Bioinformatics,
09/2008, Letnik:
24, Številka:
18
Journal Article
Recenzirano
Odprti dostop
The CellML Model Repository provides free access to over 330 biological models. The vast majority of these models are derived from published, peer-reviewed papers. Model curation is an important and ...ongoing process to ensure the CellML model is able to accurately reproduce the published results. As the CellML community grows, and more people add their models to the repository, model annotation will become increasingly important to facilitate data searches and information retrieval. Availability: The CellML Model Repository is publicly accessible at http://www.cellml.org/models Contact: c.lloyd@auckland.ac.nz
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