Rule-based agents for forecasting algal population dynamics in freshwater lakes discovered by hybrid evolutionary algorithms

In the context of this study two concepts were applied for the development of rule-based agents of algal populations: (1) rule discovery by means of a hybrid evolutionary algorithms (HEA) and rigorous k-fold cross-validation, and (2) rule generalisation by means of merged time-series data of lakes belonging to the same lake category. The rule-based agents developed during this study proved to be both explanatory and predictive. It has been demonstrated that the interpretation of the rules can be brought into the context of empirical and causal knowledge on chlorophyll-a dynamics as well as population dynamics of Microcystis and Oscillatoria under specific water quality conditions. The k-fold cross-validation of the agents based on measured data of each year of similar lakes revealed good forecasting accuracy resulting in r² values ranging between 0.39 and 0.63.     

能源预测预警理论与方法研究进展

能源作为一种稀缺性的战略资源是国民经济增长和社会进步的物质基础,但是随着化石能源耗竭及能源使用造成的环境问题日趋严重,能源安全问题逐渐成为关注的焦点,而能源预测预警也成为能源系统科学领域的新兴学科,其内容包含能源安全理论、基于模型的能源供需预测和基于安全评价指标体系的能源预警等方面内容。通过系统回顾能源安全的理论及其演变的历程,重点综述了自上而下、自下而上和混合建模3种建模思路的能源预测模型,探讨了三类模型的优点和局限性,并根据能源安全预警评价指标浓缩信息的程度,将现有预警评价体系划分单个型指标评价体系和聚合型指标评价体系两大类。通过对以上研究内容的总结分析,明确了当前能源预测预警研究各领域的研究进展,及其在理论和应用方面的优势与不足。在未来研究中,建议从供应链的角度出发,考虑能源系统内部各因素及与外部因素的相互作用,构建基于链式的预警体系,以有效弥补现有研究中的不足。     

Molecular techniques for the early warning of toxic cyanobacteria blooms in freshwater lakes and rivers

The aim of this work was to test the efficacy of molecular techniques for detecting toxigenic cyanobacteria in environmental water samples collected from freshwater lakes, rivers and reservoirs in Portugal. Of 26 environmental samples tested, 21 were found to contain Microcystis using a genus-specific polymerase chain reaction (PCR). Another primer pair was applied to the same DNA template to test for the presence of microcystin synthetase genes. This primer pair resulted in the formation of a PCR product in 15 of the samples containing Microcystis and one sample that did not give a positive result in the Microcystis genus-specific PCR. A restriction assay using the enzyme EcoRV was then applied to show that in most cases, the gene fragment was from toxigenic strains of Microcystis and, in one above-mentioned case, from a microcystin-producing strain of Planktothrix. All environmental samples were examined microscopically to confirm the presence of cyanobacteria species. Samples were also tested for the presence of microcystins using the ELISA plate assay. There was good agreement between the results obtained with molecular techniques and those obtained from microscopy and chemical methods. The PCR techniques applied in this paper were found to be useful, particularly when the concentration of the target organism was very low compared with other organisms. This technique can be used to detect inocula for cyanobacterial populations and therefore provide a useful tool for assessing under which conditions particular species can grow into bloom populations.     

Silicate availability, vertical mixing and grazing control of phytoplankton blooms in mesocosms

Lake Sempach, located in the central part of Switzerland, has a surface area of 14 km², a maximum depth of 87 m and a water residence time of 15 years. Restoration measures to correct historic eutrophication, including artificial mixing and oxygenation of the hypolimnion, were implemented in 1984. By means of the combination of external and internal load reductions, total phosphorus concentrations decreased in the period 1984–2000 from 160 to 42 mg P m^–3. Starting from 1997, hypolimnion oxygenation with pure oxygen was replaced by aeration with fine air bubbles. The reaction of the plankton has been investigated as part of a long-term monitoring program. Taxa numbers, evenness and biodiversity of phytoplankton increased significantly during the last 15 years, concomitant with a marked decline of phosphorus concentration in the lake. Seasonal development of phytoplankton seems to be strongly influenced by the artificial mixing during winter and spring and by changes of the trophic state. Dominance of nitrogen fixing cyanobacteria (Aphanizomenon sp.), causing a severe fish kill in 1984, has been correlated with lower N/P-ratio in the epilimnion. Buoyant algae such as Planktothrix rubescens (syn. Oscillatoria rubescens) increased in abundance due to enlargement of the trophogenic layer and extended mixing depth during winter. The interactions between zoo- and phytoplankton seemed to be depressed as a result of restoration measures. Zooplankton composition changed to more carnivorous and less herbivorous species. Oxygenation of the hypolimnion induced bioturbation of sediments, mainly by oligochaetae worms, and stimulated germination of spores and cysts and hatching of resting eggs.     

大沙河水库冬季浮游植物群落结构与水华分析

于2009年12月、2010年1月和2月对广东省大沙河水库湖泊区距水表层0.5m、5m和10m三个水层的浮游植物进行了定性与定量分析,同时对环境变量进行了测定.采样期间三个月的总降雨量为263mm,水温范围在15.5～19.4℃之间,水体处于混合状态.三次采样中,共检测出浮游植物69种(属),隶属于6个门,浮游植物丰度范围在4.1×10⁶～14.8×10⁶cells·L^-1之间.三个水层的浮游植物优势种类差异不显著(p>0.05),丰度的主要优势种为蓝藻门的卷曲鱼腥藻(Anabaena circinalis)、铜绿微囊藻(Microcystis aeruginosa),这两个种的丰度之和占总丰度的70%以上,在2009年12月和2010年2月的表层出现了轻度鱼腥藻和微囊藻水华.蓝藻自身的浮力调节机制和适应低磷的生活策略是其成为优势种的重要原因,相对稳定的外部条件、水体混合与富营养共同导致的光的可获得性的减少是形成蓝藻水华的关键外部因子.     

Performance of forecasting,warning and detection of malaria epidemics in the highlands of western Kenya

On the 4th July 2002 a leading national newspaper in Kenya, the Daily Nation, ran the headline 'Minister sounds alert on malaria' in an article declaring the onset of epidemics in the highlands of western Kenya. There followed frequent media coverage with quotes from district leaders on the numbers of deaths, and editorials on the failure of the national malaria control strategy. The Ministry of Health made immediate and radical changes to national policy on treatment costs in the highlands by suspending cost-sharing. Development partners and non-governmental organisations also responded with a large increase in the distribution of commodities (approximately 500,000 US dollars) to support preventative strategies across the western highland region. What was conspicuous by its absence was any obvious effort to predict the epidemics in advance of press coverage.     

Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines

Current proteomics experiments can generate vast quantities of data very quickly, but this has not been matched by data analysis capabilities. Although there have been a number of recent reviews covering various aspects of peptide and protein identification methods using MS, comparisons of which methods are either the most appropriate for, or the most effective at, their proposed tasks are not readily available. As the need for high-throughput, automated peptide and protein identification systems increases, the creators of such pipelines need to be able to choose algorithms that are going to perform well both in terms of accuracy and computational efficiency. This article therefore provides a review of the currently available core algorithms for PMF, database searching using MS/MS, sequence tag searches and de novo sequencing. We also assess the relative performances of a number of these algorithms. As there is limited reporting of such information in the literature, we conclude that there is a need for the adoption of a system of standardised reporting on the performance of new peptide and protein identification algorithms, based upon freely available datasets. We go on to present our initial suggestions for the format and content of these datasets.     

Characteristics of the phytoplankton community and bioaccumulation of heavy metals during algal blooms in Xiangjiang River (Hunan,China)

The frequency of algal blooms has increased in the mid and downstream reaches of the Xiangjiang River (Hunan, China), one of the most heavily polluted rivers in China. We identified the bloom-forming species in a bloom that occurred mid-late September 2010. In addition, we determined the extent of metal bioaccumulation in the algae and measured the toxicity of the algae using a mouse bioassay. Water samples were collected at upstream (Yongzhou), midstream (Hengyang), and downstream (Zhuzhou, Xiangtan, and Changsha) sites. The dominant species was Aulacoseira granulata, formerly known as Melosira granulata. The heaviest bloom occurred at Xiangtan and Changsha, where the number of A. granulata peaked at 1.3×10⁵ filaments L⁻¹ and chlorophyll a at 0.04 mg L⁻¹. Concentrations of Al, Fe, and Mn were 4.4×10³, 768.4, and 138.7 mg kg⁻¹ dry weight in the phytoplankton. The bioaccumulation factor was 4.0×10⁵, 7.7×10⁵, and 3.2×10³, respectively. The heavy metal Pb had the greatest tendency to bioaccumulate among the highly toxic heavy metals, with a concentration of 19.2 mg kg⁻¹ dry weight and bioaccumulation factor of 9.6×10³. The mouse bioassay suggested the bloom was toxic. The LD₅₀ was 384 mg kg⁻¹ and all surviving mice lost weight during the first 72 h after exposure. Our results demonstrate that blooms of A. granulata in rivers contaminated with heavy metals pose a threat to freshwater ecosystems and human health. Thus, measures should be taken to control eutrophication and heavy metal pollution in such rivers.     

Daily changes of uptake of inorganic carbon and nitrogen,and their relation to phytoplankton blooms in late spring-early summer in Lake Nakanuma,Japan

Daily changes of inorganic carbon and nitrogen uptake were measured in May in 1986 in Lake Nakanuma, Japan. Uptake of inorganic carbon and ammonium in the light-bottle experiments in the 1 m layers, showed daily changes similar to chlorophyll a changes, though the uptake activities peaked before chlorophyll a peaks (phytoplankton blooms) appeared. Potential growth rates of phytoplankton and observed growth rates were calculated from the uptake rates and chlorophyll a changes. The potential growth rates did not always correspond to the observed growth rates. The potential growth rates did not correlate with the loss rates. The correlation between the observed growth rates and the loss rates was better. These results suggest that though the increase of uptake activities may be necessary for occurrence of phytoplankton blooms, loss processes may affect the occurrence of blooms.     

Thermal denaturation of DNA in situ as studied by acridine orange staining and automated cytofluorometry

Thermal denaturation of nuclear DNA is studied in situ in individual cells or isolated cell nuclei by employing the property of the fluorochrome acridine orange (AO) to differentially stain native and denatured DNA and by using an automated flow-through cytofluorimeter for measurement of cell fluorescence. RNAse-treated cells, or cell nuclei, are heated, stained and measured while in suspension and AO-DNA interaction is studied under equilibrium conditions. Measurements are made rapidly (200 cells/sec); subpopulations of cells from a measured sample can be chosen on the basis of differences in their staining or light-scattering properties and analysed separately. DNA denaturation in situ is rapid; it approaches maximum during the first 5 min of cell heating. Divalent cations stabilize DNA against denaturation. At low pH the transition occurs at lower temperature and the width of the transition curves (‘melting profiles’) is increased. Decrease in ionic strength lowers the DNA melting temperature. This effect is much more pronounced in cells pretreated with acids under conditions known to remove histones. Histones thus appear to stabilize DNA in situ by providing counterions. At least four separate phases can be distinguished in melting profiles of DNA in situ; they are believed to indicate different melting points of DNA in complexes with particular histones. A decrease in cell (nuclear) ability to scatter light coincides with DNA melting in situ, possibly representing altered refractive and/or reflective properties of cell nuclei. Formaldehyde, commonly used to prevent DNA renaturation, is not used in the present method. The heat-induced alterations in nuclear chromatin are adequately stabilized after cell cooling in the absence of this agent. Cells heated at 60–85 °C exhibit increased total fluorescence after AO-staining, which is believed to be due to unmasking of new sites on DNA. This increase is neither correlated with DNA melting, nor with the presence of histones. Possibly, it reflects destruction of DNA superstructure maintained at lower temperatures by DNA associations with other than histone macromolecules (nuclear membrane).     

Inductive reasoning and forecasting of population dynamics of Cylindrospermopsis raciborskii in three sub-tropical reservoirs by evolutionary computation

Seven-day-ahead forecasting models of Cylindrospermopsis raciborskii in three warm-monomictic and mesotrophic reservoirs in south-east Queensland have been developed by means of water quality data from 1999 to 2010 and the hybrid evolutionary algorithm HEA. Resulting models using all measured variables as inputs as well as models using electronically measurable variables only as inputs forecasted accurately timing of overgrowth of C. raciborskii and matched well high and low magnitudes of observed bloom events with 0.45 ≤ r² > 0.61 and 0.4 ≤ r² > 0.57, respectively. The models also revealed relationships and thresholds triggering bloom events that provide valuable information on synergism between water quality conditions and population dynamics of C. raciborskii. Best performing models based on using all measured variables as inputs indicated electrical conductivity (EC) within the range of 206–280 mS m⁻¹ as threshold above which fast growth and high abundances of C. raciborskii have been observed for the three lakes. Best models based on electronically measurable variables for the Lakes Wivenhoe and Somerset indicated a water temperature (WT) range of 25.5–32.7 °C within which fast growth and high abundances of C. raciborskii can be expected. By contrast the model for Lake Samsonvale highlighted a turbidity (TURB) level of 4.8 NTU as indicator for mass developments of C. raciborskii.Experiments with online measured water quality data of the Lake Wivenhoe from 2007 to 2010 resulted in predictive models with 0.61 ≤ r² > 0.65 whereby again similar levels of EC and WT have been discovered as thresholds for outgrowth of C. raciborskii. The highest validity of r² = 0.75 for an in situ data-based model has been achieved after considering time lags for EC by 7 days and dissolved oxygen by 1 day. These time lags have been discovered by a systematic screening of all possible combinations of time lags between 0 and 10 days for all electronically measurable variables. The so-developed model performs seven-day-ahead forecasts and is currently implemented and tested for early warning of C. raciborskii blooms in the Wivenhoe reservoir.     

Unravelling and forecasting algal population dynamics in two lakes different in morphometry and eutrophication by neural and evolutionary computation

Precious ecological information extracted from limnological long-term time series advances the theory on functioning and evolution of freshwater ecosystems. This paper presents results of applications of artificial neural networks (ANN) and evolutionary algorithms (EA) for ordination, clustering, forecasting and rule discovery of complex limnological time-series data of two distinctively different lakes. Ten years of data of the shallow and hypertrophic Lake Kasumigaura (Japan) are utilized in comparison with 13 years of data of the deep and mesotrophic Lake Soyang (Korea). Results demonstrate the potential that: (1) recurrent supervised ANN and EA facilitate 1-week-ahead forecasting of outbreaks of harmful algae or water quality changes, (2) EA discover explanatory rule sets for timing and abundance of harmful outbreaks algal populations, and (3) non-supervised ANN provide clusters to unravel ecological relationships regarding seasons, water quality ranges and long-term environmental changes.     

Conformation of RNA in situ as studied by acridine orange staining and automated cytofluorometry.

Human erythroblasts which are prereticulocyte maturation stages of red blood cells were studied by light microscopic cytochemistry and electron microscopy to provide more information on the ultrastructure of the micronucleoli which are terminal stages of nucleolar changes found during maturation of these cells. As indicated by light microscopy of smeared cells, micronucleoli were virtually the only types of nucleoli present in the last stages of maturing erythroblasts, i.e., polychromatic and orthochromatic (late polychromatic) erythroblasts. Accordingly, they were not portions of the periphery of other nucleoli. Inasmuch as most of the micronucleoli exhibited characteristic segregation of nucleolar fibrillar and granular components they presumably are producing little if any preribosomal RNA, since such segregation generally reflects inhibition of nucleolar RNA synthesis.     

Physical and chemical effects of macrograzers and micrograzers on enclosed,in situ phytoplankton in a Newfoundland lake

Grazing effects were evaluated by comparisons between phytoplankton populations in the lake water and in bicompartmental chambers, deployedin situ in a Newfoundland lake. Micrograzing effects were evaluated separately from both the physical effects of macrograzers and the chemical effects of macrograzer metabolites on phytoplankton assemblages in bicompartmental chambers. Macrograzer metabolites were able to pass through fine gauze between the compartments. Thus, the chemical effects of the macrograzers were observed in one compartment while the physical effects were the dominant treatment in the other. Micrograzer effects were investigated in chambers without added macrograzers.Densities of some of the desmid species were depressed by the physical effects of macrograzers. This is the first ecological study to demonstrate such a grazing effect on desmids. Some individual taxa, such asArthrodesmus triangularis var.rotundatus (Raciborski)comb. nov., andMesotaenium sp. Nägeli (Zygnemaphyceae), were augmented under the chemical effects of macrograzer metabolites. Evidence suggests that the desmids were not micrograzed. Grazing effects on desmids have not previously been studied in waters in which they were abundant.The Chlorophyceae, which were small species in Hogan's pond, and the microflagellates generally maintained their overall population densities in spite of the presence of macrograzers, however, abundances of some individual species within the assemblages changed in the presence of macrograzers. Micrograzers may also affect the species composition and abundance of the individual chlorophycean taxa.With the exceptions ofSynedra sp. Ehrenberg andTabellaria fenestrata var.lacustris Meister the diatoms were unaffected by the grazers. The Chrysophyceae were little affected by micrograzing and physical effects of macrograzers, in contrast to chemical effects of macrograzer metabolites that were evident for individual species.Several of the Cyanobacteria (Cyanophyceae) were augmented in the presence of micrograzers. Evidence indicates that they were not micrograzed. Some individual species, e.g.,Microcystis aeruginosa Kützing, were augmented by both physical and chemical effects of macrograzers.     

Translocation events demonstrated by molecular,in situ hybridization and chromosome pairing analyses in highly asymmetric somatic hybrid plants

Cytological analyses show rearranged chromosomes in some highly asymmetric nuclear hybrids obtained after fusion of mesophyll protoplasts ofNicotiana plumbaginifolia (wild type) with γ-irradiated (100 krad), kanamycin-resistant mesophyll protoplasts ofPetunia hybrida. Molecular, cytogenetic andin situ hybridization analyses performed on the asymmetric somatic hybrid P₁, previously identified as having a clearly metacentric chromosome besides a nearly completeNicotiana chromosome complement, are reported. Meiotic analysis andin situ hybridization experiments using ribosomal DNA as a probe showed that this metacentric chromosome represents a translocation of a chromosome fragment onto chromosome 9 ofN. plumbaginifolia. Southern hybridization with an rDNA probe showed that onlyNicotiana-specific rDNA was present.In situ hybridization experiments, using total genomic DNA ofP. hybrida as a probe, demonstrated that the translocated fragment representedPetunia DNA.     

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster

Reversible protein phosphorylation ranks among the most important post-translational modifications, and elucidation of phosphorylation sites is essential to understand the regulation of key cellular processes such as signal transduction. Enrichment of phosphorylated peptides is a prerequisite for successful analysis due to their low stoichiometry, heterogeneity, and low abundance. Enrichment is often performed manually, which is inherently labor-intensive and a major hindrance in large-scale analyses. Automation of the enrichment method would vastly improve reproducibility and thereby facilitate 'high-throughput' phosphoproteomics research. Here, we describe a robust and automated online TiO 2-based two-dimensional chromatographic approach to selectively enrich phosphorylated peptides from digests of complete cellular lysates. We demonstrate method enhancement for both adsorption and desorption of phosphorylated peptides resulting in lower limits of detection. Phosphorylated peptides from a mere 500 attomole tryptic digest of a protein mixture were easily detected. With the combination of strong cation exchange chromatography with the online TiO 2 enrichment, 2152 phosphopeptides were enriched from 250 microg of protein originating for the cell lysate of Drosophila melanogaster S2 cells. This is a 4-fold improvement when compared to an enrichment strategy based solely on strong cation exchange/LC-MS. Phosphopeptide enrichment methods are intrinsically biased against relatively basic phosphopeptides. Analysis of the p I distributions of the enriched/detected phosphopeptides showed that the p I profile resembles that of a total Drosophila protein digest, revealing that the current described online procedure does not discriminate against either more acidic or basic phosphopeptides. However, careful comparison of our new and existing phosphopeptide enrichment techniques also reveal that, like many enrichment techniques, we are still far from comprehensive phosphoproteomics analyses, and we describe several factors that still require to be addressed. Still, as the online approach allows the complementary measurements of phosphopeptides and their nonphosphorylated counterparts in subsequent analyses, this method is well-suited for automated quantitative phosphoproteomics.