Developing biosensors as monitoring tools to assess the performance of biochar amended contaminated soil

The application of biochar as a soil amendment is an emerging technique for low-cost remediation of contaminated soil. The high porosity and large surface area of biochar make it suitable for adsorption of contaminants such as heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs). Adsorption reduces the bio-availability of contaminants to soil microorganisms thus potentially increasing soil function and productivity. Many different biochars are available which differ in key properties such as contaminant adsorption and stability. To assess biochar performance as a soil amendment we will develop bacterial biosensors to measure contaminant bioavailability and toxicity at a cellular level. Biosensors are a complementary tool to chemical analysis. Please click on the file below for full content of the abstract

Adsorption isotherm determination and heavy metal removal by acid-washed softwood biochar

Heavy metal concentrations above critical range in soils may pose environmental and economic problems by hindering plant growth and limiting land usage. Biochar used as soil amendment is a low-cost, natural remediation technique, which has the capability to immobilize and reduce metals (exchangeable, oxide-bound, and organic matter-bound) bioavailable for plant uptake. Its large surface area provides high capacity for binding metals through sorption reactions. Please click on the file below for full content of the abstract

Simulations of spectral lines from an eccentric precessing accretion disc

Two dimensional SPH simulations of a precessing accretion disc in a q=0.1 binary system (such as XTE J1118+480) reveal complex and continuously varying shape, kinematics, and dissipation. The stream-disc impact region and disc spiral density waves are prominent sources of energy dissipation.The dissipated energy is modulated on the period P_{sh} = ({P_{orb}}^{-1}-{P_{prec}}^{-1}^{-1} with which the orientation of the disc relative to the mass donor repeats. This superhump modulation in dissipation energy has a variation in amplitude of ~10% relative to the total dissipation energy and evolves, repeating exactly only after a full disc precession cycle. A sharp component in the light curve is associated with centrifugally expelled material falling back and impacting the disc. Synthetic trailed spectrograms reveal two distinct "S-wave" features, produced respectively by the stream gas and the disc gas at the stream-disc impact shock. These S-waves are non-sinusoidal, and evolve with disc precession phase. We identify the spiral density wave emission in the trailed spectrogram. Instantaneous Doppler maps show how the stream impact moves in velocity space during an orbit. In our maximum entropy Doppler tomogram the stream impact region emission is distorted, and the spiral density wave emission is uppressed. A significant radial velocity modulation of the whole line profile occurs on the disc precession period. We compare our SPH simulation with a simple 3D model: the former is appropriate for comparison with emission lines while the latter is preferable for skewed absorption lines from precessing discs.Comment: See http://physics.open.ac.uk/FHMR/ for associated movie (avi) files. The full paper is in MNRAS press. Limited disk space limit of 650k, hence low resolution figure file

Evaluating the potential of biochar for reducing bioavailable heavy metal fractions in polluted soil

Previous studies have proposed biochar as a natural adsorbent material with potential to be used in the remediation of polluted soils. Its application for adsorption of pollutants may reduce the bioavailability of harmful compounds in the soil media by limiting its chemical distribution and reducing the risk of uptake by organisms. Therefore, biochar has been suggested for the attenuation of heavy metals (HMs) in soil, minimizing the possibility of accumulation through the trophic chain (Figure ). Please click on the file below for full content of the abstract

Multispectral imaging for presymptomatic analysis of light leaf spot in oilseed rape

Background: The use of spectral imaging within the plant phenotyping and breeding community has been increasing due its utility as a non-invasive diagnostic tool. However, there is a lack of imaging systems targeted specifically at plant science duties, resulting in low precision for canopy-scale measurements. This study trials a prototype multispectral system designed specifically for plant studies and looks at its use as an early detection system for visually asymptomatic disease phases, in this case Pyrenopeziza brassicae in Brassica napus. The analysis takes advantage of machine learning in the form of feature selection and novelty detection to facilitate the classification. An initial study into recording the morphology of the samples is also included to allow for further improvement to the system performance. Results: The proposed method was able to detect light leaf spot infection with 92% accuracy when imaging entire oilseed rape plants from above, 12 days after inoculation and 13 days before the appearance of visible symptoms. False colour mapping of spectral vegetation indices was used to quantify disease severity and its distribution within the plant canopy. In addition, the structure of the plant was recorded using photometric stereo, with the output influencing regions used for diagnosis. The shape of the plants was also recorded using photometric stereo, which allowed for reconstruction of the leaf angle and surface texture, although further work is needed to improve the fidelity due to uneven lighting distributions, to allow for reflectance compensation. Conclusions: The ability of active multispectral imaging has been demonstrated along with the improvement in time taken to detect light leaf spot at a high accuracy. The importance of capturing structural information is outlined, with its effect on reflectance and thus classification illustrated. The system could be used in plant breeding to enhance the selection of resistant cultivars, with its early and quantitative capability

A combined phase I and II open label study on the effects of a seaweed extract nutrient complex on osteoarthritis

Background: Isolated fucoidans from brown marine algae have been shown to have a range of anti-inflammatory effects. Purpose: This present study tested a Maritech® extract formulation, containing a blend of extracts from three different species of brown algae, plus nutrients in an open label combined phase I and II pilot scale study to determine both acute safety and efficacy in osteoarthritis of the knee. Patients and methods: Participants (n = 12, five females [mean age, 62 ± 11.06 years] and seven males [mean age, 57.14 ± 9.20 years]) with a confirmed diagnosis of osteoarthritis of the knee were randomized to either 100 mg (n = 5) or 1000 mg (n = 7) of a Maritech® extract formulation per day. The formulation contained Maritech® seaweed extract containing Fucus vesiculosis (85% w/w), Macrocystis pyrifera (10% w/w) and Laminaria japonica (5% w/w) plus vitamin B6, zinc and manganese. Primary outcome was the average comprehensive arthritis test (COAT) score which is comprised of four sub-scales: pain, stiffness, difficulty with physical activity and overall symptom severity measured weekly. Safety measures included full blood count, serum lipids, liver function tests, urea, creatinine and electrolytes determined at baseline and week 12. All adverse events were recorded. Results: Eleven participants completed 12 weeks and one completed 10 weeks of the study. Using a multilevel linear model, the average COAT score was reduced by 18% for the 100 mg treatment and 52% for the 1000 mg dose at the end of the study. There was a clear dose response effect seen between the two treatments (P≤0.0005) on the average COAT score and each of the four COAT subscales (pain, stiffness, difficulty with physical activity and overall symptom severity) (P≤0.05). The preparation was well tolerated and the few adverse events were unlikely to be related to the study medication. There were no changes in blood parameters measured over the course of the study with the exception of an increase in serum albumin which was not clinically significant. Conclusion: The seaweed extract nutrient complex when taken orally over twelve weeks decreased the symptoms of osteoarthritis in a dose-dependent manner. It was demonstrated to be safe to use over the study period at the doses tested. The efficacy of the preparation now needs to be demonstrated in a phase III randomized controlled trial (RCT). Australian and New Zealand Clinical Trials Register: ACTRN12607000229471

A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community

Most microorganisms in nature are uncultured with unknown functionality. Sequence-based metagenomics alone answers 'who/what are there?' but not 'what are they doing and who is doing it and how?'. Function-based metagenomics reveals gene function but is usually limited by the specificity and sensitivity of screening strategies, especially the identification of clones whose functional gene expression has no distinguishable activity or phenotypes. A 'biosensor-based genetic transducer' (BGT) technique, which employs a whole-cell biosensor to quantitatively detect expression of inserted genes encoding designated functions, is able to screen for functionality of unknown genes from uncultured microorganisms. In this study, BGT was integrated with Stable isotope probing (SIP)-enabled Metagenomics to form a culture-independent SMB toolbox. The utility of this approach was demonstrated in the discovery of a novel functional gene cluster in naphthalene contaminated groundwater. Specifically, metagenomic sequencing of the (13)C-DNA fraction obtained by SIP indicated that an uncultured Acidovorax sp. was the dominant key naphthalene degrader in-situ, although three culturable Pseudomonas sp. degraders were also present in the same groundwater. BGT verified the functionality of a new nag2 operon which co-existed with two other nag and two nah operons for naphthalene biodegradation in the same microbial community. Pyrosequencing analysis showed that the nag2 operon was the key functional operon in naphthalene degradation in-situ, and shared homology with both nag operons in Ralstonia sp. U2 and Polaromonas naphthalenivorans CJ2. The SMB toolbox will be useful in providing deep insights into uncultured microorganisms and unravelling their ecological roles in natural environments

A combined Phase I and II open-label study on the immunomodulatory effects of seaweed extract nutrient complex

Background: Isolated fucoidans from brown marine algae have been shown to have a range of immune-modulating effects. This exploratory study aimed to determine whether a seaweed nutrient complex containing a blend of extracts from three different species of brown algae plus nutrients is safe to administer and has biological potential as an immune modulator. The study was undertaken as an open-label combined Phase I and II study. Methods: Participants (n = 10) were randomized to receive the study medication at either a 100 mg (n = 5) or 1000 mg (n = 5) dose over 4 weeks. The primary outcome measurement was in vivo changes in lymphocyte subsets. The secondary outcome measures were ex vivo changes in T-lymphocyte (CD4 and CD8) activation, phagocytosis of granulocytes and monocytes, T helper 1/T helper 2 cytokines, and serum oxygen radical absorbance capacity. Results: The preparation was found to be safe over the 4 weeks at both doses tested. There were no clinically relevant changes to blood measurements of hemopoietic, hepatic, or renal function. Immunomodulatory measurements showed no dose response between the two doses. The combined results from the two doses demonstrated a significant increase in cytotoxic T cell numbers and phagocytic capacity in monocytes, and a significant decrease in levels of the inflammatory cytokine interleukin 6. A separate analysis of the 100 mg dose (n = 5) alone showed a significant linear component over time (P \u3c 0.05) for phagocytosis by both granulocytes and monocytes. Conclusion: The seaweed nutrient complex was safe to use when taken orally over 4 weeks. The preparation was demonstrated to have potential as an immune modulator, and this bioactivity deserves further exploration

Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon.

SlyA is a member of the MarR family of bacterial transcriptional regulators. Previously, SlyA has been shown to directly regulate only two operons in Escherichia coli K-12 MG1655, fimB and hlyE (clyA). In both cases SlyA activates gene expression by antagonizing repression by the nucleoid associated protein H-NS. Here the transcript profiles of aerobic glucose-limited steady-state chemostat cultures of E. coli K-12 MG1655, slyA mutant and slyA over-expression strains are reported. The transcript profile of the slyA mutant was not significantly different to that of the parent; however, that of the slyA expression strain was significantly different from that of the vector control. Transcripts representing 27 operons were increased in abundance, whereas 3 were decreased. Of the 30 differentially regulated operons, 24 have been previously associated with sites of H-NS binding, suggesting that antagonism of H-NS repression is a common feature of SlyA-mediated transcription regulation. Direct binding of SlyA to DNA located upstream of a selection of these targets permitted the identification of new operons likely to be directly regulated by SlyA. Transcripts of four operons coding for cryptic adhesins exhibited enhanced expression and this was consistent with enhanced biofilm formation associated with the SlyA over-producing strain