A Sensitive and Versatile Multiplex PCR System for the Rapid Detection of Enterotoxigenic (ETEC), Enterohaemorrhagic (EHEC) and Enteropathogenic (EPEC) Strains of Escherichia coli

Although Escherichia coli is widely distributed in the marine environment, only a small percentage are pathogenic to humans. Nonetheless, the widespread occurrence of waterborne infections of E. coli origin in humans has become one of the major health problems worldwide. To date, several types of enterovirulent E. coli have been recognized as the aetiologic agents of various gastrointestinal infections in humans. The most commonly encountered are those belonging to the enterotoxigenic (ETEC), enteroinvasive (EIEC), enterohaemorrhagic (EHEC) and enteropathogenic (EPEC) subtypes. In order to better determine the health risks that are associated with exposure to some of these specific subtypes, we have developed a very sensitive multiplex PCR system for the rapid detection and typing of ETEC, EHEC and possibly EPEC strains of E. coli in the aquatic environment. The target genes chosen for this investigation included: the PHO-A housekeeping gene (present in all E. coli); the LT1, LT2 and ST1 genes of ETEC; the VT1 and VT2 verotoxin, and EAE virulence genes of EHEC and EPEC, respectively. Six pairs of oligonucleotide primers were designed to simultaneously amplify internal fragments of these genes by multiplex PCR to generate PCR products that could be analysed and confirmed with relative ease by gel electrophoresis and HincII enzyme digestion. The results showed that the six sets of PCR primers were highly specific for their target genes and produced specific amplimers of the expected size from several control strains of E. coli – ATCC 35401 (LT1+/ST1+); SA53 (LT2+/VT2+); and O157 (VT1+/VT2+/EAE+). The detection sensitivity of the multiplex PCR system for the six target genes in an E. coli cell mixture was optimized and enhanced by preincubating serially diluted cells in Luria-Bertani broth for 6 h prior to PCR analysis. The results obtained indicated a detection sensitivity of 10° CFU (of each strain) per 100 μl reaction. Multiplex PCR analysis of seawater samples collected from four sewage-polluted sites in Hong Kong indicated the presence in all four samples of E. coli bacteria that were positive for LT1, ST1, VT1 and EAE virulence genes. Overall, the data indicated that the multiplex PCR system described in this study is a potentially very useful and powerful method for routine monitoring and risk assessment of water quality.     

Multiple Discriminant Analysis of Marine Sediment Data

A multivariate statistical approach was used in the analysis of inter-relationships among marine benthic infaunal structure, physical and chemical characteristics of sediment samples and toxicity data derived from laboratory tests at 16 locations in shallow, inshore waters of Hong Kong. The method involved classification (cluster analysis using the Bray–Curtis similarity index) and ordination (multi-dimensional scaling) of infaunal patterns and the use of multiple discriminant analysis to relate groupings of the locations to the selected environmental and toxicity data. Analysis of the combined sediment physical, biological, chemical and toxicity dataset by stepwise multiple discriminant analysis allowed identification of those variables most sensitive for discriminating location groups. The use of multiple discriminant analysis in sediment quality characterization was evaluated against the Sediment Quality Triad approach and other statistical techniques.     

Numerical Investigation of the Somali Jet Interaction with the Western Ghat Mountains

—Several major features of the interaction of the Somali jet with the Western Ghat Mountains have been observed. These include a pressure ridge, strong vertical motions, and occurrences of highly reflective cloud and heavy rainfall rates along the west coast of India. A triple nested regional weather prediction model has been used to investigate the dynamic interaction between the Somali jet and the Western Ghat Mountains. Two numerical experiments were conducted; one with the topography of western India and the other without. In the experiment without topography, the Western Ghat Mountains were removed from the innermost domain. The results for the innermost domain in the two experiments were analyzed and compared. The results from the simulation with topography captured several of the observed features of the Somali jet interaction with the Western Ghat Mountains. The simulation without topography failed to reveal these features. The results suggest that the blocking effect of the Western Ghats plays an important role in the prediction of the rainfall over the west coast of India.     

Pattern Characteristics of Foreshock Sequences

—Earthquake clusterings in both space and time have various forms, in particular, two typical examples are the foreshock sequences and earthquake swarms. Based on the analysis of 8 foreshock sequences in mainland China during 1966–1996, this study concentrates on the pattern characteristics of foreshock sequences. The following pattern characteristics of foreshock sequences have been found (1) the epicenters of foreshock sequences were densely concentrated in space; (2) the focal mechanisms of foreshocks were similar to that of the main shock. Such consistency of focal mechanisms with main shocks did not exist in aftershock series as well as in several earthquake swarms; (3) we found no case in mainland China during the past thirty years that a main shock is preceded by an earthquake clustering with inconsistent focal mechanisms. Finally, we found 5% of the main shocks in mainland China are preceded by foreshock sequences.     

Spatiotemporal characteristics of precipitation and extreme events on the Loess Plateau of China between 1957 and 2009

Spatiotemporal trends in precipitation may influence vegetation restoration, and extreme precipitation events profoundly affect soil erosion processes on the Loess Plateau. Daily data collected at 89 meteorological stations in the area between 1957 and 2009 were used to analyze the spatiotemporal trends of precipitation on the Loess Plateau and the return periods of different types of precipitation events classified in the study. Nonparametric methods were employed for temporal analysis, and the Kriging interpolation method was employed for spatial analysis. The results indicate a small decrease in precipitation over the Loess Plateau in last 53 years (although a Mann–Kendall test did not show this decrease to be significant), a southward shift in precipitation isohyets, a slightly delayed rainy season, and prolonged return periods, especially for rainstorm and heavy rainstorm events. Regional responses to global climate change have varied greatly. A slightly increasing trend in precipitation in annual and sub‐annual series, with no obvious shift of isohyets, and an evident decreasing trend in extreme precipitation events were detected in the northwest. In the southeast, correspondingly, a more seriously decreasing trend occurred, with clear shifts of isohyets and a slightly decreasing trend in extreme precipitation events. The result suggests that a negative trend in annual precipitation may have led to decreased soil erosion but an increase in sediment yield during several extreme events. These changes in the precipitation over the Loess Plateau should be noted, and countermeasures should be taken to reduce their adverse impacts on the sustainable development of the region. Copyright © 2013 John Wiley & Sons, Ltd.     

Hydrologic responses to land cover change: the case of Jedeb mesoscale catchment,Abay/Upper Blue Nile basin,Ethiopia

The objective of this study was to quantify the impacts of land use/land cover (LULC) change on the hydrology of the Jedeb, an agricultural dominated mesoscale catchment, in the Abay/Upper Blue Nile basin, Ethiopia. Two methods have been used. First, the trends of certain daily flow variability parameters were evaluated to detect statistical significance of the change of the hydrologic response. Second, a conceptual monthly hydrological model was used to detect changes in the model parameters over different periods to infer LULC change. The results from the statistical analysis of the daily flows between 1973 and 2010 reveal a significant change in the response of the catchment. Peak flow is enhanced, i.e. response appears to be flashier. There is a significant increase in the rise and fall rates of the flow hydrograph, as well as the number of low‐flow pulses below a threshold level. The discharge pulses show a declining duration with time. The model result depicts a change in model parameters over different periods, which could be attributed to an LULC change. The model parameters representing soil moisture conditions indicated a gradual decreasing trend, implying limited storage capacity likely attributed to increasing agricultural farming practices in the catchment. This resulted in more surface runoff and less infiltration into the soil layers. The results of the monthly flow duration curve analysis indicated large changes of the flow regime. The high flow has increased by 45% between the 1990s and 2000s, whereas the reduction in low flows was larger: a 15% decrease between 1970s and 1980s, 39% between 1980s and 1990s and up to 71% between 1990s and 2000s. These results, could guide informed catchment management practices to reduce surface runoff and augment soil moisture level in the Jedeb catchment. Copyright © 2013 John Wiley & Sons, Ltd.     

A new approach to rapid,desktop-level,environmental flow assessments for rivers in South Africa

Abstract

An approach is presented for desktop-level environmental flow requirement (EFR) determination that is aligned with the Habitat Flow–Stressor Response (HFSR) method which evolved in South Africa over recent years. The HFSR method integrates hydrological, hydraulic and ecological habitat data, involves ecological and hydraulic specialists and is data-intensive and time-consuming. The revised desktop method integrates hydrological information with estimates of channel hydraulic cross-sectional characteristics to generate habitat-type frequencies under changing flow conditions. This information is used with the expected natural habitat requirements to determine acceptable habitat availability under different levels of ecological protection, which is then used with the hydraulic data to define flow regime characteristics that meet the ecological objectives. The paper describes the model components, discusses the assumptions, data requirements and limitations and presents some example results. The revised desktop approach uses approaches that are aligned with the more complex methods and generates results that are similar.

Editor D. Koutsoyiannis; Guest editor M. Acreman

Citation Hughes, D.A., Desai, A.Y., Birkhead, A.L., and Louw, D., 2014. A new approach to rapid, desktop-level, environmental flow assessments for rivers in South Africa. Hydrological Sciences Journal, 59 (3–4), 673–687.     

Observation of the seasonal evolution of the Yellow Sea Cold Water Mass in 1996–1998

We use the hydrographic data obtained during the joint survey of the Yellow Sea by the First Institute of Oceanography, China and the Korea Ocean Research and Development Institute, Korea, to quantify the spatial structures and temporal evolution of the southern Yellow Sea Cold Water Mass (YSCWM). It is indicated that the southern YSCWM is a water mass that develops in summer and decays in fall. In winter, due to the intrusion of the Yellow Sea Warm Current (YSWC), the central area (approximately between 34°N and 35°N, 122°E and 124°E) of the Yellow Sea is mainly occupied by relatively high temperature water (T>10 °C). By contrast, from early summer to fall, under the seasonal thermocline, the central area of Yellow Sea is occupied by cold water (T<10 °C). In summer, the southern YSCWM has two cold cores. One is formed locally southeast of Shandong Peninsula, and the other one has a tongue-like feature occupying the area approximately between 34°N and 37°N, 123°E and 126°E. The bottom layer temperature anomalies from February to July in the cold tongue region, along with the trajectories of the bottom floaters, suggest that the cold water mass in the northeast region has a displacement from the north to the central area of the Yellow Sea during the summer.     

Flow based oversampling technique for multiscale finite element methods

Oversampling techniques are often used in porous media simulations to achieve high accuracy in multiscale simulations. These methods reduce the effect of artificial boundary conditions that are imposed in computing local quantities, such as upscaled permeabilities or basis functions. In the problems without scale separation and strong non-local effects, the oversampling region is taken to be the entire domain. The basis functions are computed using single-phase flow solutions which are further used in dynamic two-phase simulations. The standard oversampling approaches employ generic global boundary conditions which are not associated with actual flow boundary conditions. In this paper, we propose a flow based oversampling method where the actual two-phase flow boundary conditions are used in constructing oversampling auxiliary functions. Our numerical results show that the flow based oversampling approach is several times more accurate than the standard oversampling method. We provide partial theoretical explanation for these numerical observations.     

Application of implicit sub-time stepping to simulate flow and transport in fractured porous media

In general, the accuracy of numerical simulations is determined by spatial and temporal discretization levels. In fractured porous media, the time step size is a key factor in controlling the solution accuracy for a given spatial discretization. If the time step size is restricted by the relatively rapid responses in the fracture domain to maintain an acceptable level of accuracy in the entire simulation domain, the matrix tends to be temporally over-discretized. Implicit sub-time stepping applies smaller sub-time steps only to the sub-domain where the accuracy requirements are less tolerant and is most suitable for problems where the response is high in only a small portion of the domain, such as within and near the fractures in fractured porous media. It is demonstrated with illustrative examples that implicit sub-time stepping can significantly improve the simulation efficiency with minimal loss in accuracy when simulating flow and transport in fractured porous media. The methodology is successfully applied to density-dependent flow and transport simulations in a Canadian Shield environment, where the flow and transport is dominated by discrete, highly conductive fracture zones.