Automated Secchi disk depth measurement based on artificial intelligence object recognition.

Water transparency affects the degree of sunlight penetration in water, which is important to many water quality processes. It can be visually measured by lowering a Secchi disk (SD) into water and recording its disappearance depth - the Secchi disk depth (SDD). High frequency SDD measurement is manpower intensive, precluding better understanding of the daily and diurnal variation of water transparency. For the first time, an artificial intelligence based object detection algorithm was employed for the automatic detection of SD from images, mimicking SDD measurement by human eyes. The trained model was validated on a large number of images (about 2000 for a single day in daytime) obtained from a remote-controlled imaging system in a fish farm in a Hong Kong embayment, demonstrating high detection accuracy of 93 %. The work opens up opportunities in the nowcast and forecast of short-term water quality changes (e.g. algal blooms) in coastal waters.

Remote sensing of coastal algal blooms using unmanned aerial vehicles (UAVs).

The explosive growth of phytoplankton under favorable conditions in subtropical coastal waters can lead to water discolouration and massive fish kills. Traditional water quality monitoring relies on manual field sampling and laboratory analysis of chlorophyll-a (Chl-a) concentration, which is resources intensive and time consuming. The cloudy weather of Hong Kong also precludes using satellite images for algal blooms monitoring. This study for the first time demonstrates the use of an Unmanned Aerial Vehicle (UAVs) to quantitatively map surface water Chl-a distribution in coastal waters from a low altitude. An estimation model for Chl-a concentration from visible images taken by a digital camera on a UAV has been developed and validated against one-year field data. The cost-effective and robust technology is able to map the spatial and temporal variations of Chl-a concentration during an algal bloom. The proposed method offers a useful complement to traditional field monitoring for fisheries management.

Tracking major endocrine disruptors in coastal waters using an integrative approach coupling field-based study and hydrodynamic modeling.

Many of the world's large coastal cities discharge partially treated wastewater effluents containing various endocrine disrupting chemicals (EDCs) to coastal environments. Nonylphenols (NP) and bisphenol A (BPA) were found to be the most abundant EDCs in sewage effluents in Hong Kong. The environmental fate and ecological risk of these two EDCs remains largely unknown, particular for coastal systems with complex hydrodynamic flows. Based on a validated three-dimensional (3D) multiple-scale hydrodynamic model, a field-based study was conducted to track the two EDCs from potential sources to the only marine reserve in Hong Kong. The two compounds were detected in all seawater, suspended particle, and sediment samples, with higher aqueous concentrations in wet season than in dry season. High concentrations in sediments suggest sediment is a sink, posing an ecological risk to the benthos. The fate and transport of the two EDCs was predicted using a 3D near-field Lagrangian jet model seamlessly coupled with a 3D shallow water circulation model. The results suggested the NP and BPA in the marine reserve cannot be solely attributed to the nearby submarine sewage outfall, but likely concurrently contributed by other sources. This study calls for more effective measures of reducing the use and release of these EDCs, and research to investigate their impacts on the marine benthos.

Real-time forecasting of Hong Kong beach water quality by 3D deterministic model.

Bacterial level (e.g. Escherichia coli) is generally adopted as the key indicator of beach water quality due to its high correlation with swimming associated illnesses. A 3D deterministic hydrodynamic model is developed to provide daily water quality forecasting for eight marine beaches in Tsuen Wan, which are only about 8 km from the Harbour Area Treatment Scheme (HATS) outfall discharging 1.4 million m(3)/d of partially-treated sewage. The fate and transport of the HATS effluent and its impact on the E. coli level at nearby beaches are studied. The model features the seamless coupling of near field jet mixing and the far field transport and dispersion of wastewater discharge from submarine outfalls, and a spatial-temporal dependent E. coli decay rate formulation specifically developed for sub-tropical Hong Kong waters. The model prediction of beach water quality has been extensively validated against field data both before and after disinfection of the HATS effluent. Compared with daily beach E. coli data during August-November 2011, the model achieves an overall accuracy of 81-91% in forecasting compliance/exceedance of beach water quality standard. The 3D deterministic model has been most valuable in the interpretation of the complex variation of beach water quality which depends on tidal level, solar radiation and other hydro-meteorological factors. The model can also be used in optimization of disinfection dosage and in emergency response situations.

Validation of an extracted tooth model of endodontic irrigation.

An extracted tooth model of endodontic irrigation, incorporating reproducible inoculation and irrigation procedures, was tested against Enterococcus faecalis using a variety of different irrigants in a Latin square methodology. ANOVA revealed no significant variations between the twelve teeth or experiments undertaken on different occasions; however, variation between irrigants was significant.

Recognition and manipulation of branched DNA by the RusA Holliday junction resolvase of Escherichia coli.

Homologous recombination is a fundamental cellular process that shapes and reshapes the genomes of all organisms and promotes repair of damaged DNA. A key step in this process is the resolution of Holliday junctions formed by homologous DNA pairing and strand exchange. In Escherichia coli , a Holliday junction is processed into recombinant products by the concerted activities of the RuvA and RuvB proteins, which together drive branch migration, and RuvC endonuclease, which resolves the structure. In the absence of RuvABC, recombination can be promoted by increasing the expression of the RusA endonuclease, a Holliday junction resolvase encoded by a cryptic prophage gene. Here, we describe the DNA binding properties of RusA. We found that RusA was highly selective for branched molecules and formed complexes with these structures even in the presence of a large excess of linear duplex DNA. However, it does bind weakly to linear duplex DNA. Under conditions where there was no detectable binding to duplex DNA, RusA formed a highly structured complex with a synthetic Holliday junction that was remarkably stable and insensitive to divalent metal ions. The duplex arms were found to adopt a specific alignment within this complex that approximated to a tetrahedral conformation of the junction.

Sequence specificity and biochemical characterization of the RusA Holliday junction resolvase of Escherichia coli.

The RusA protein of Escherichia coli is an endonuclease that resolves Holliday intermediates in recombination and DNA repair. Analysis of its subunit structure revealed that the native protein is a dimer. Its resolution activity was investigated using synthetic X-junctions with homologous cores. Resolution occurs by dual strand incision predominantly 5' of CC dinucleotides located symmetrically. A junction lacking homology is not resolved. The efficiency of resolution is related inversely to the number of base pairs in the homologous core, which suggests that branch migration is rate-limiting. Inhibition of resolution at high ratios of protein to DNA suggests that binding of RusA may immobilize the junction point at non-cleavable sites. Resolution is stimulated by alkaline pH and by Mn2+. The protein is unstable in the absence of substrate DNA and loses approximately 80% of its activity within 1 min under standard reaction conditions. DNA binding stabilizes the activity. Junction resolution is inhibited in the presence of RuvA. This observation probably explains why RusA is unable to promote efficient recombination and DNA repair in ruvA+ strains unless it is expressed at a high level.

Interactions between RuvA and RuvC at Holliday junctions: inhibition of junction cleavage and formation of a RuvA-RuvC-DNA complex.

The RuvAB and RuvC enzymes of Escherichia coli define a molecular pathway for the resolution of Holliday intermediates in recombination and DNA repair. They bind specifically to Holliday junctions, and catalyse their branch migration and cleavage, respectively. In a RuvA(B)-junction complex, the Holliday structure is held in an open (square planar) configuration on the concave surface of a 4-fold symmetrical tetramer of RuvA, whereas in a RuvC-junction complex it is folded in an alternative arrangement as part of the cleavage reaction. Genetic studies have shown that the activity of RuvC in vivo depends on RuvAB, which suggests that the two enzymes act in concert, with junction cleavage by RuvC following from branch migration by RuvAB. We have investigated how RuvC can take over a junction from RuvAB to cleave the DNA. We show that RuvA inhibits junction cleavage by RuvC, probably by sandwiching the junction between two tetramers. The extent of inhibition depends on the reaction kinetics of RuvA binding relative to RuvC binding and cleavage. The presence of RuvB and the concentration of Mg2+ both have a significant effect on cleavage in the presence of RuvA. However, a novel protein-DNA complex can be formed when junction DNA is incubated with both RuvA and RuvC. Its mobility is consistent with a RuvC dimer binding to a junction held in an open configuration on the surface of a RuvA tetramer. We suggest that this arrangement provides RuvC with the means to scan the junction during the RuvAB-mediated branch migration reaction for DNA sequences that it can cleave. We further suggest that recognition of the target may provide a trigger for dissociating RuvA, allowing the junction to be folded and cleaved by RuvC.

Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions.

The formation and subsequent resolution of Holliday junctions are critical stages in recombination. We describe a new Escherichia coli endonuclease that resolves Holliday intermediates by junction cleavage. The 14 kDa Rus protein binds DNA containing a synthetic four-way junction (X-DNA) and introduces symmetrical cuts in two strands to give nicked duplex products. Rus also processes Holliday intermediates made by RecA into products that are characteristic of junction resolution. The cleavage activity on X-DNA is remarkably similar to that of RuvC. Both proteins preferentially cut the same two strands at the same location. Increased expression of Rus suppresses the DNA repair and recombination defects of ruvA, ruvB and ruvC mutants. We conclude that all ruv strains are defective in junction cleavage, and discuss pathways for Holliday junction resolution by RuvAB, RuvC, RecG and Rus.