Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems.

AIMS: To identify changes in the bacterial community, at the phylum level brought about by varied crop management. METHODS AND RESULTS: Next-generation sequencing methods were used to compare the taxonomic structure of the bacterial community within 24 agricultural soils managed with either organic or conventional methods, over a 3-year period. Relative abundance of the proportionately larger phyla (e.g. Acidobacteria and Actinobacteria) was primarily affected by sample year rather than crop management. Changes of abundance in these phyla were correlated with changes in pH, organic nitrogen and soil basal respiration. Crop management affected some of the less dominant phyla (Chloroflexi, Nitrospirae, Gemmatimonadetes) which also correlated with pH and organic N. CONCLUSION: Soil diversity can vary with changing environmental variables and soil chemistry. If these factors remain constant, soil diversity can also remain constant even under changing land use. SIGNIFICANCE AND IMPACT OF THE STUDY: The impact of crop management on environmental variables must be considered when interpreting bacterial diversity studies in agricultural soils. Impact of land use change should always be monitored across different sampling time points. Further studies at the functional group level are necessary to assess whether management-induced changes in bacterial community structure are of biological and agronomic relevance.

Serotonin toxicity from antidepressant overdose and its association with the T102C polymorphism of the 5-HT2A receptor.

Serotonin toxicity results from serotonin excess in the central nervous system from serotonergic drugs. Previous studies suggest an association between T102C polymorphism of the serotonin 2A (5-hydroxytryptamine 2A) receptor gene and serotonergic adverse effects with serotonergic drugs. We aimed to determine whether there is an association between the T102C polymorphism and serotonin toxicity in patients taking serotonergic drug overdoses. Ninety-five patients presenting with serotonergic drug overdoses were examined for serotonin toxicity and had blood collected for DNA analysis. A diagnosis of serotonin toxicity was made in 14 patients (15%) based on the Hunter Serotonin Toxicology Criteria. Four of the 14 patients (29%) with serotonin toxicity had the C/C genotype compared with 20/81 (25%) without serotonin toxicity. There were no differences in age or sex, but the median defined daily dose taken by patients with serotonin toxicity was 27 (14-84) compared with 18 (2-136) in patients without serotonin toxicity (P=0.06). There was no association between serotonin toxicity and the T102C polymorphism in patients taking a serotonergic drug overdose.

Magnetite-doped polydimethylsiloxane (PDMS) for phosphopeptide enrichment.

Reversible phosphorylation plays a key role in numerous biological processes. Mass spectrometry-based approaches are commonly used to analyze protein phosphorylation, but such analysis is challenging, largely due to the low phosphorylation stoichiometry. Hence, a number of phosphopeptide enrichment strategies have been developed, including metal oxide affinity chromatography (MOAC). Here, we describe a new material for performing MOAC that employs a magnetite-doped polydimethylsiloxane (PDMS), that is suitable for the creation of microwell array and microfluidic systems to enable low volume, high throughput analysis. Incubation time and sample loading were explored and optimized and demonstrate that the embedded magnetite is able to enrich phosphopeptides. This substrate-based approach is rapid, straightforward and suitable for simultaneously performing multiple, low volume enrichments.

Aerosol droplet optical trap loading using surface acoustic wave nebulization.

We demonstrate the use of surface acoustic wave nebulization (SAWN) to load optical traps. We show that the droplets sizes produced can be tuned by altering the RF frequency applied to the devices, which leads to more control over the sizes of trapped particles. Typically the size distribution of the liquid aerosols delivered using SAWN is smaller than via a standard commercial nebulization device. The ability to trap a range of liquids or small solid particles, not readily accessible using other ultrasonic devices, is also demonstrated both in optical tweezers and dual beam fiber traps.

Mask-less ultraviolet photolithography based on CMOS-driven micro-pixel light emitting diodes.

We report on an approach to ultraviolet (UV) photolithography and direct writing where both the exposure pattern and dose are determined by a complementary metal oxide semiconductor (CMOS) controlled micro-pixellated light emitting diode array. The 370 nm UV light from a demonstrator 8 x 8 gallium nitride micro-pixel LED is projected onto photoresist covered substrates using two back-to-back microscope objectives, allowing controlled demagnification. In the present setup, the system is capable of delivering up to 8.8 W/cm2 per imaged pixel in circular spots of diameter approximately 8 microm. We show example structures written in positive as well as in negative photoresist.

Comparison of Faxén's correction for a microsphere translating or rotating near a surface.

Boundary walls in microfluidic devices have a strong influence on the fluid flow and drag forces on moving objects. The Stokes drag force acting on a sphere translating in the fluid is increased by the presence of a neighboring wall by a factor given by Faxén's correction. A similar increase in the rotational drag is expected when spinning close to a wall. We use optical tweezers to confirm the translational drag correction and report the hitherto unmeasured rotational equivalent. We find that the corrections for the rotational motion is only required for particle-wall separations an order of magnitude shorter than that for the translational cases. These results are particularly significant in the use of optical tweezers for measuring viscosity on a picolitre scale.

Coenzyme Q10 and vitamin E deficiency in Friedreich's ataxia: predictor of efficacy of vitamin E and coenzyme Q10 therapy.

BACKGROUND AND PURPOSE: A pilot study of high dose coenzyme Q(10) (CoQ(10))/vitamin E therapy in Friedreich's ataxia (FRDA) patients resulted in significant clinical improvements in most patients. This study investigated the potential for this treatment to modify clinical progression in FRDA in a randomized double blind trial. METHODS: Fifty FRDA patients were randomly divided into high or low dose CoQ(10)/ vitamin E groups. The change in International Co-operative Ataxia Ratings Scale (ICARS) was assessed over 2 years as the primary end-point. A post hoc analysis was made using cross-sectional data. RESULTS: At baseline serum CoQ(10) and vitamin E levels were significantly decreased in the FRDA patients (P < 0.001). During the trial CoQ(10) and vitamin E levels significantly increased in both groups (P < 0.01). The primary and secondary end-points were not significantly different between the therapy groups. When compared to cross-sectional data 49% of all patients demonstrated improved ICARS scores. This responder group had significantly lower baseline serum CoQ(10) levels. CONCLUSIONS: A high proportion of FRDA patients have a decreased serum CoQ(10) level which was the best predictor of a positive clinical response to CoQ(10)/vitamin E therapy. Low and high dose CoQ(10)/vitamin E therapies were equally effective in improving ICARS scores.

Control of enteric pathogens in ready-to-eat vegetable crops in organic and 'low input' production systems: a HACCP-based approach.

Risks from pathogens such as Salmonella, Yersinia, Campylobacter and Escherichia coli O157 have been identified as a particular concern for organic and 'low input' food production systems that rely on livestock manure as a nutrient source. Current data do not allow any solid conclusions to be drawn about the level of this risk, relative to conventional production systems. This review describes six Risk Reduction Points (RRPs) where risks from enteric pathogens can be reduced in ready-to-eat vegetables. Changes can be made to animal husbandry practices (RRP1) to reduce inoculum levels in manure. Outdoor livestock management (RRP2) can be optimized to eliminate the risk of faecal material entering irrigation water. Manure storage and processing (RRP3), soil management practices (RRP4) and timing of manure application (RRP5), can be adjusted to reduce the survival of pathogens originating from manure. During irrigation (RRP6), pathogen risks can be reduced by choosing a clean water source and minimizing the chances of faecal material splashing on to the crop. Although preventive measures at these RRPs can minimize enteric pathogen risk, zero risk can never be obtained for raw ready-to-eat vegetables. Good food hygiene practices at home are essential to reduce the incidence of food-borne illnesses.

Effect of alternative treatments on seed-borne Didymella lycopersici in tomato.

AIMS: To quantify the phytotoxicity and effect of alternative seed treatments based on acidified nitrite and elicitors of plant resistance (Tillekur and Chitosan) against seed-borne inocula of Didymella lycopersici. METHODS AND RESULTS: Treatments tested were: nitrite [sodium nitrite in citric acid buffer (pH 2)] at 30, 100 and 300 mmol l(-1) and three exposure times (10, 20 and 30 min); Tillekur (in water) at 12.5, 25, 50, 100 and 200 mg ml(-1); Chitosan (in 0.05% acetic acid) at 2.5, 5, 10 and 50 mg ml(-1). Efficacy of treatments was determined in growth chamber experiments. Nitrite at 300 mmol l(-1) was completely effective, as was the fungicide, at controlling disease when applied for less than 20 min. Tillekur was as effective as the fungicide postemergence, but proved to be phytotoxic pre-emergence. Chitosan was significantly less effective than the other treatments. CONCLUSIONS: The high efficacy and low cost of acidified nitrite indicates that it is a suitable alternative to fungicides. SIGNIFICANCE AND IMPACT OF THE STUDY: There is currently a lack of effective seed treatments that can be used in organic and low-input crops. Treatments identified in this study can be considered as an effective alternative to chemical control against seed-borne fungal pathogens.

Lab-on-a-chip technologies for proteomic analysis from isolated cells.

Lab-on-a-chip systems offer a versatile environment in which low numbers of cells and molecules can be manipulated, captured, detected and analysed. We describe here a microfluidic device that allows the isolation, electroporation and lysis of single cells. A431 human epithelial carcinoma cells, expressing a green fluorescent protein-labelled actin, were trapped by dielectrophoresis within an integrated lab-on-a-chip device containing saw-tooth microelectrodes. Using these same trapping electrodes, on-chip electroporation was performed, resulting in cell lysis. Protein release was monitored by confocal fluorescence microscopy.

Creating tissue on chip constructs in microtitre plates for drug discovery.

We report upon a novel coplanar dielectrophoresis (DEP) based cell patterning system for generating transferrable hepatic cell constructs, resembling a liver-lobule, in culture. The use of paper reinforced gel substrates provided sufficient strength to enable these constructs to be transfered into 96-well plates for long term functional studies, including in the future, drug development studies. Experimental results showed that hepatic cells formed DEP field-induced structures corresponding to an array of lobule-mimetic patterns. Hepatic viability was observed over a period of 3 days by the use of a fluorescent cell staining technique, whilst the liver specific functionality of albumin secretion showed a significant enhancement due to the layer patterning of cell lines (HepG2/C3A), compared to 2D patterned cells and un-patterned control. This "build and transfer" concept could, in future, also be adapted for the layer-by-layer construction of organs-on-chip in microtitre formats.

Friedreich's ataxia: coenzyme Q10 and vitamin E therapy.

Since the identification of the genetic mutation causing Friedreich's ataxia (FRDA) our understanding of the mechanisms underlying disease pathogenesis have improved markedly. The genetic abnormality results in the deficiency of frataxin, a protein targeted to the mitochondrion. There is extensive evidence that mitochondrial respiratory chain dysfunction, oxidative damage and iron accumulation play significant roles in the disease mechanism. There remains considerable debate as to the normal function of frataxin, but it is likely to be involved in mitochondrial iron handling, antioxidant regulation, and/or iron sulphur centre regulation. Therapeutic avenues for patients with FRDA are beginning to be explored in particular targeting antioxidant protection, enhancement of mitochondrial oxidative phosphorylation, iron chelation and more recently increasing FRDA transcription. The use of quinone therapy has been the most extensively studied to date with clear benefits demonstrated using evaluations of both disease biomarkers and clinical symptoms, and this is the topic that will be covered in this review.

Desvenlafaxine overdose and the occurrence of serotonin toxicity, seizures and cardiovascular effects.

CONTEXT: Desvenlafaxine is used to treat major depression. Desvenlafaxine is also the active metabolite of venlafaxine. Venlafaxine overdose can cause serotonin toxicity, seizures and cardiovascular effects, but there is limited information on desvenlafaxine overdose. OBJECTIVE: We aimed at investigating the clinical effects and complications from desvenlafaxine overdose. MATERIALS AND METHODS: This was a retrospective observational study of desvenlafaxine overdoses over a six-year period. Demographic details, dose and timing of the overdose, together with clinical effects, treatment and complications were extracted from a local hospital network database or the medical records of patients following hospital admission with a desvenlafaxine overdose. RESULTS: There were 182 cases of desvenlafaxine overdose included in the study. From the 182 cases, 75 were desvenlafaxine (± alcohol) only ingestions and 107 included one or more co-ingested drugs. In single-agent desvenlafaxine ingestions, median age was 25 years (range: 13-68 years) with a median ingested dose of 800 mg (range: 250-3500 mg; interquartile range (IQR): 600-1400 mg), and 54/75 (72%) were female. The Glasgow Coma Score (GCS) was 15 in 68/74 (92%) patients, 13-14 in 5/74 (7%), and was seven in one patient following aspiration. Mild hypertension (systolic blood pressure [BP] > 140-180 mmHg) occurred in 23/71 patients (32%), and tachycardia occurred in 29/74 (39%) patients. There were no abnormal QT intervals and no QRS >120 m s. Serotonin toxicity was diagnosed by the treating physician in 7/75 (9%) patients, but only one of these met the Hunter Serotonin Toxicity Criteria. None of the 75 patients who took desvenlafaxine only (± alcohol) had seizures, were admitted to intensive care or died. In comparison, the 107 patients taking desvenlafaxine in overdose with other medications developed more pronounced toxicity. Generalised seizures occurred in 5/107 (5%), but in three of these cases co-ingestants were possible proconvulsants. Fifteen patients had a GCS ≤9 and none had an abnormal QT or QRS. Severe effects appeared to be associated with coingestants. CONCLUSION: Desvenlafaxine overdose causes minor effects with mild hypertension and tachycardia. The risk of seizures or serotonin toxicity is low.

The liquid-liquid diffusive extraction of hydrocarbons from a North Sea oil using a microfluidic format.

Extraction of a GC-amenable hydrocarbon fraction from oil by liquid-liquid diffusion across a laminar interface can be performed in a microfluidic format. Analysis of figures of merit, determined using standard analytical techniques, show this method to be an effective new tool for rapidly processing small quantities of oil and petroleum for GC analysis. Methods based upon similar microsystems devices could find widespread use in a variety of fields, including those associated with organic geochemistry and oil exploration and production, where the manipulation of petroleum constituents (greater than C14) is necessary for analytical purposes.

Visualization of Surface Acoustic Waves in Thin Liquid Films.

We demonstrate that the propagation path of a surface acoustic wave (SAW), excited with an interdigitated transducer (IDT), can be visualized using a thin liquid film dispensed onto a lithium niobate (LiNbO3) substrate. The practical advantages of this visualization method are its rapid and simple implementation, with many potential applications including in characterising acoustic pumping within microfluidic channels. It also enables low-cost characterisation of IDT designs thereby allowing the determination of anisotropy and orientation of the piezoelectric substrate without the requirement for sophisticated and expensive equipment. Here, we show that the optical visibility of the sound path critically depends on the physical properties of the liquid film and identify heptane and methanol as most contrast rich solvents for visualization of SAW. We also provide a detailed theoretical description of this effect.

Assessment of biocompatibility of 3D printed photopolymers using zebrafish embryo toxicity assays.

3D printing has emerged as a rapid and cost-efficient manufacturing technique to enable the fabrication of bespoke, complex prototypes. If the technology is to have a significant impact in biomedical applications, such as drug discovery and molecular diagnostics, the devices produced must be biologically compatible to enable their use with established reference assays and protocols. In this work we demonstrate that we can adapt the Fish Embryo Test (FET) as a new method to quantify the toxicity of 3D printed microfluidic devices. We assessed the biocompatibility of four commercially available 3D printing polymers (VisiJetCrystal EX200, Watershed 11122XC, Fototec SLA 7150 Clear and ABSplus P-430), through the observation of key developmental markers in the developing zebrafish embryos. Results show all of the photopolymers to be highly toxic to the embryos, resulting in fatality, although we do demonstrate that post-printing treatment of Fototec 7150 makes it suitable for zebrafish culture within the FET.

Human mitochondrial complex I dysfunction.

In humans, complex I dysfunction has been observed in a high percentage of patients with mitochondrial myopathy. Analysis of mitochondria from these patients suggests the function and assembly of complex I is particularly susceptible to abnormalities of mitochondrial DNA, involving either point mutations of tRNA genes or major deletions. The evidence for a complex I defect in Parkinson's disease is accumulating, although the cause of this deficiency or the role it plays in the events that culminate in dopaminergic cell death remains unresolved.

The molecular pathology of respiratory-chain dysfunction in human mitochondrial myopathies.

Some of the different molecular pathologies of respiratory-chain dysfunction in human mitochondrial myopathies will be reviewed in relation to the findings in 58 cases. Deletions of mitochondrial DNA were identified in 21 cases [36%]. There was some correlation between the sites of the deletion and the mitochondrial biochemistry in patients with defects of Complex I but not in cases with more extensive loss of respiratory chain activity. Complex I and Complex IV polypeptides were usually normal in deleted cases. Non-deleted cases, however, often showed specific subunit deficiencies which involved the products of both nuclear and mitochondrial genes. Immunoblots of respiratory-chain polypeptides in one case pointed to defective translocation of the Rieske precursor from the cytosol into the mitochondria. The pathogenic role of circulating autoantibodies to specific matrix proteins and the nature of the target antigens in two patients with mitochondrial encephalomyopathies and respiratory-chain dysfunction will also be discussed.

Mitochondrial DNA (mtDNA) diseases: correlation of genotype to phenotype.

This study examines the relationship of genotype to phenotype in 14 unselected patients who were found to harbour the A3243G transition in the mitochondrial transfer RNALeu(UUR) gene commonly associated with the syndrome of mitochondrial encephalopathy, lactic acidosis and strokes (MELAS). Only 6 of the 14 cases (43%) had seizures and recurrent strokes, the core clinical features of the MELAS phenotype. Of the remaining cases, four had an encephalomyopathy with deafness, ataxia and dementia, two had syndromes with progressive external ophthalmoplegia and two had limb weakness alone. Even within the MELAS subgroup, the majority of patients had one or more clinical manifestations considered to be atypical of the MELAS syndrome. They included developmental delay, ophthalmoparesis, pigmentary retinopathy and intestinal pseudo-obstruction. The proportion of mutant mitochondrial DNA (mtDNA) in muscle was generally higher in patients with recurrent strokes than in those without strokes, the highest levels being observed in MELAS cases with early onset disease. Studies of isolated muscle mitochondria identified a range of respiratory chain abnormalities mostly involving Complex I; immunoblots of Complex I in 3 of 10 cases showed selective loss of specific subunits encoded by nuclear genes. In the group as a whole, however, no clear correlations were observed between the severity or extent of the respiratory chain abnormality and clinical phenotype or the proportion of mutant mtDNA in biopsied skeletal muscle. These discrepancies suggest that, in patients harbouring the common MELAS3243 mutation, differences in heteroplasmy and the proportions of mutant mtDNA may not be the sole determinants of disease expression and that additional genetic mechanisms are involved in defining the range of clinical and biochemical phenotypes associated with this aberrant mitochondrial genome.

Ultrasonographic assessment of the rate of solid-phase gastric emptying in dogs.

Twelve healthy dogs were used in an ultrasonographic assessment of the effect of the composition of a solid meal on the rate of gastric emptying. The dogs were fasted for nine hours before they were fed either a standard or a high energy density test meal, in a cross-over study design. The gastric antrum was visualised with a 6.5 MHz microconvex transducer, and the area inside the elliptical shape defined by the craniocaudal and ventrodorsal diameters of the stomach was measured. Antral images were acquired at regular intervals for six hours after the ingestion of the test meal. Three indices to describe the rate of gastric emptying were computed: the gastric half-emptying time (t1/2), the time to 50 per cent maximal antral area (t50%), and the time of maximal antral area (tmax). The values of t50% and t1/2 calculated for the high energy density meals were significantly longer than for the standard meals, but there was no significant difference between the tmax values.