Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.

BACKGROUND: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras. RESULTS: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript. CONCLUSIONS: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras

Inactivation of viable Ascaris eggs during faecal sludge co-composting with chicken feathers and market waste

Faecal Sludge (FS) contains high concentrations of pathogenic microorganisms that are 10–100 times higher than those in domestic wastewater. Proper and sustainable treatment is required to inactivate these pathogens if FS is to be recycled in agriculture, so as to minimise public health and environmental risks. Composting is one of the common low-cost technologies of sanitising FS in Urban Africa; however, it is associated with longer pathogen inactivation periods that make it commercially uneconomical. This study investigated the effect of different organic wastes types and their mixing ratios with FS on the inactivation efficiency of viable Ascaris eggs (suum and lumbricoides) during composting. Dewatered FS was mixed with market waste (MW), chicken feathers (CF) and sawdust (SD) in different ratios. Compost piles of FS:MW:SD and FS:CF:SD both in volumetric ratios of 1:2:1 and 1:3:1 were set-up in duplicate (3m3 each), composted and monitored weekly for viable Ascaris eggs presence for a period of 15 weeks. The results suggest that the organic waste types have a significant effect on the temperature evolution and pathogen inactivation efficiency while their mixing ratios do not. Piles containing CF achieved the shortest pathogen survival period of 4 weeks compared with 6–8 weeks for those with MW. The temperature–time factor was found to be the most important variable responsible for viable Ascaris eggs inactivation. However, other mechanisms such as microbial antagonism or antibiotic action induced by indigenous microorganisms and toxic by-products such as free ammonia were found to have also played an important role in Ascaris eggs inactivation. All piles attained 100% Ascaris eggs inactivation from FS, and therefore, the compost was safe for use in agriculture. The study findings suggest that composting of FS with CF can reduce Ascaris eggs inactivation periods by 42%, which may thus reduce the operational costs of FS treatment facilities

Improving the biomethane yield from food waste by boosting hydrogenotrophic methanogenesis

Anaerobic digestion of food waste is usually impacted by high levels of VFAs, resulting in low pH and inhibited methane production from acetate (acetoclastic methanogenesis); however, this could be harnessed for improving methane production via hydrogenotrophic methanogenesis (biomethanation). In this study, batch anaerobic digestion of food waste was conducted to enhance biomethanation by supplying hydrogen gas (H2), using a gas mixture of 5%-H2 and 95%-N2. The addition of H2 influenced a temporal microbial shift in substrate utilisation from dissolved organic nutrients to H2 and CO2 and was perceived to have enhanced the hydrogenotrophic methanogenic activity. As a result, with the release of hydrogen as degradation progressed (secondary fermentation) hydrogenotrophic methanogenesis was further enriched. This resulted in an enhancement of the upgrading of the biogas, with a 12.1% increase in biomethane (from 417.6 to 468.3 NmL-CH4/gVSadded) and 38.9% reduction in CO2 (from 227.1 to 138.7 NmL-CO2/gVSadded). Furthermore, the availability of hydrogen gas at the start of the process promoted faster propionate degradation, by the enhanced activity of the H2-utilisers, thereby, reducing likely propionate-induced inhibitions. The high level of acidification from VFAs production helped to prevent excessive pH increases from the enhanced hydrogenotrophic methanogenic activity. Therefore, it was found that the addition of hydrogen gas to AD reactors treating food waste showed great potential for enhanced methane yield and biogas upgrade, supported by VFAs-induced pH buffer. This creates the possibility to optimise hydrogenotrophic methanogenesis towards obtaining biogas of the right quality for injection into the gas grid

A Simple and Non-destructive Method for Chlorophyll Quantification of Chlamydomonas Cultures Using Digital Image Analysis

Growing interest in the use of microalgae as a sustainable feedstock to support a green, circular, bio-economy has led to intensive research and development initiatives aimed at increasing algal biomass production covering a wide range of scales. At the heart of this lies a common need for rapid and accurate methods to measure algal biomass concentrations. Surrogate analytical techniques based on chlorophyll content use solvent extraction methods for chlorophyll quantification, but these methods are destructive, time consuming and require careful disposal of the resultant solvent waste. Alternative non-destructive methods based on chlorophyll fluorescence require expensive equipment and are less suitable for multiple sampling of small cultures which need to be maintained under axenic growth conditions. A simple, inexpensive and non-destructive method to estimate chlorophyll concentration of microalgal cultures in situ from digital photographs using the RGB color model is presented. Green pixel intensity and chlorophyll a, b and total chlorophyll concentration, measured by conventional means, follow a strong linear relationship (R2 = 0.985–0.988). In addition, the resulting standard curve was robust enough to accurately estimate chlorophyll concentration despite changes in sample volume, pH and low concentrations of bacterial contamination. In contrast, use of the same standard curve during nitrogen deprivation (causing the accumulation of neutral lipids) or in the presence of high quantities of bacterial contamination led to significant errors in chlorophyll estimation. The low requirement for equipment (i.e., a simple digital camera, available on smartphones) and widely available standard software for measuring pixel intensity make this method suitable for both laboratory and field-based work, particularly in situations where sample, qualified personnel and/or equipment is limited. By following the methods described here it should be possible to produce a standard curve for chlorophyll analysis in a wide range of testing conditions including different microalga cultures, culture vessel and photographic set up in any particular laboratory

Valorisation of macroalgae via the integration of hydrothermal carbonisation and anaerobic digestion

This study investigates the integration of hydrothermal carbonisation (HTC) with anaerobic digestion (AD) as a valorisation route for two macroalgae species; S. latissima (SL) and F. serratus (FS). HTC reactions were conducted at temperatures of 150°C, 200°C and 250°C, with resulting hydrochars, process waters and hydrothermal slurries assessed for biomethane potential yields. Un-treated SL generated similar biomethane levels compared to all SL slurries. Whereas all FS slurries improved biomethane yields compared to un-treated FS. Hydrochars represent a greater energy carrier if used as a solid fuel, rather than a feedstock for anaerobic digestion. Integrating HTC and AD, through hydrochar combustion and process water digestion has a greater energetic output than anaerobic digestion of the un-treated macroalgae. Treatment at 150°C, with separate utilisation of products, can improve the energetic output of S. latissima and F. serratus by 47 % and 172 % respectively, compared to digestion of the un-treated macroalgae

Simulating Pathogen Transport within a Naturally Ventilated Hospital Ward

Understanding how airborne pathogens are transported through hospital wards is essential for determining the infection risk to patients and healthcare workers. This study utilizes Computational Fluid Dynamics (CFD) simulations to explore pathogen transport within a six-bed Nightingale hospital ward. Grid independence of a ward model was addressed using the Grid Convergence Index (GCI) from solutions obtained using three fully-structured grids. Pathogens were simulated using source terms in conjunction with a scalar transport equation and a RANS turbulence model. Errors were found to be less than 4% in the prediction of air velocities but an average of 13% was seen in the scalar field. A parametric study into the pathogen release point illustrated that its distribution is strongly influenced by the local velocity field and the degree of mixing present

Hydrothermal carbonization of sewage digestate at wastewater treatment works: Influence of solid loading on characteristics of hydrochar, process water and plant energetics

Nowadays the sludge treatment is recognized as a priority challenge to the wastewater industry due to the increasing volumes produced and tighter environmental controls for its safe disposal. The most cost-effective process for sewage sludge is the anaerobic digestion but raw digestate still contains high levels of organic matter that can be transformed into an energy carrier by using processes like Hydrothermal Carbonization (HTC). In this work, the influence of solid loading (2.5, 5.0, 10.0, 15.0, 17.5, 20.0, 25.0 and 30.0% solids w/w) on the composition of hydrochar and process water was studied, together with an evaluation of product yields, solubilisation of organic carbon and biomethane potential of process waters from HTC processing (250 °C, 30- minute reaction time). Hydrochar yields ranged from 64 to 88%wt, whereas the concentration of soluble organic carbon increased from 2.6 g/L in the raw digestate to a maximum of 72.3 g/L in the process water following HTC at the highest solid loading. Furthermore, process modelling with Aspen Plus shows that the integration of AD with HTC to wastewater treatment works provides a significant positive energy balance when process water and hydrochar are considered as fuel sources for cogeneration

Ammonia volatilisation in waste stabilisation ponds: a cascade of misinterpretations?

Ammonia volatilisation has generally been reported as, or assumed to be, the main nitrogen removal mechanism in waste stabilisation ponds (WSP). Nitrogen removal via ammonia volatilisation is based on two observations: (a) in-pond pH values can reach high values (>9, even >10), so increasing the proportion of the total ammonia present as the un-ionized form or free ammonia (NH(3)); and (b) in-pond temperatures can also be high, so improving the mass transfer rate of free ammonia to the atmosphere. Consequently, one of the most widely accepted models for ammonia removal in WSP is that reported by Pano & Middlebrooks in 1982, which was developed to reflect the occurrence of these two observations. This work reports how simple mathematical models for ammonia volatilisation in WSP, in spite of the possibility of their giving good predictions, may not accurately describe the main pathways and mechanisms involved in ammonia removal in WSP

An Effective Surrogate Tracer Technique for S. aureus Bioaerosols in a Mechanically Ventilated Hospital Room Replica Using Dilute Aqueous Lithium Chloride

Finding a non-pathogenic surrogate aerosol that represents the deposition of typical bioaerosols in healthcare settings is beneficial from the perspective of hospital facility testing, general infection control and outbreak analysis. This study considers aerosolization of dilute aqueous lithium chloride (LiCl) and sodium chloride (NaCl) solutions as surrogate tracers capable of representing Staphylococcus aureus bioaerosol deposition on surfaces in mechanically ventilated rooms. Tests were conducted in a biological test chamber set up as a replica hospital single patient room. Petri dishes on surfaces were used to collect the Li, Na and S. aureus aerosols separately after release. Biological samples were analyzed using cultivation techniques on solid media, and flame atomic absorption spectroscopy was used to measure Li and Na atom concentrations. Spatial deposition distribution of Li tracer correlated well with S. aureus aerosols (96% of pairs within a 95% confidence interval). In the patient hospital room replica, results show that the most contaminated areas were on surfaces 2 m away from the source. This indicates that the room’s airflow patterns play a significant role in bioaerosol transport. NaCl proved not to be sensitive to spatial deposition patterns. LiCl as a surrogate tracer for bioaerosol deposition was most reliable as it was robust to outliers, sensitive to spatial heterogeneity and found to require less replicates than the S. aureus counterpart to be in good spatial agreement with biological results

Microalgae Growth and Phosphorus Uptake of Chlamydomonas Reinhardtii 11/32C under Different Inorganic Nitrogen Sources

Microalgae have been shown to be effective in utilizing both nitrogen and phosphorus from a wide range of wastewaters. This ability enhances the potential role that microalgae may have not only in wastewater bioremediation, but also in algal biomass production as an alternative feedstock for biofertiliser and biofuel production. This study was conducted to investigate the nutrient recovery from wastewater through microalgae biological uptake. The green microalgae of C. reinhardtii 11/32C used in this study and cultivated in Bold’s Basal Media (BBM). The algae culture was placed in a 2 liter of photobioreactor for approximately in 14 days. The results revealed that green microalgae can recover up to 5.9 % and 1.3% of N and P in their cell, respectively