GeneMill officially launched on 4th February 2016 and is an open access academic facility located at The University of Liverpool that has been established for the high-throughput construction and testing of synthetic DNA constructs. GeneMill provides end-to-end design, construction and phenotypic characterization of small to large gene constructs or genetic circuits/pathways for academic and industrial applications. Thus, GeneMill is equipping the scientific community with easy access to the validated tools required to explore the possibilities of Synthetic Biology.

3D reconstituted respiratory epithelia have emerged as better in vitro models for toxicological testing compared to cell lines due to the conservation of key morphological features and functions. MucilAir™ is a commercially available human airway epithelia system that can potentially maintain functional attributes for up to a year, however, detailed mucociliary characteristics and xenobiotic metabolism relevant to inhaled pro-toxicant bioactivation is lacking. Here, we assessed in MucilAir™ some key biomarkers that are characteristic of the respiratory epithelia including morphology, function and xenobiotics metabolism. The end points that were measured included targeted proteomics using a panel of 243 airway surface liquid (ASL) proteins, cilia beat frequency (CBF), a qRT-PCR screen of xenobiotic metabolizing enzymes, and CYP2A6/13, CYP1A1/1B1 activity. Comparison of ASL proteomics with human sputum identified key proteins common to both matrices, but present at different levels. Xenobiotic metabolism gene profiling demonstrated strong similarities with the normal human lung and did not reveal any consistent changes when assessed over a 6 month period. Inducibility and activity of CYP1A1/1B1 and activity of CYP2A6/2A13 were present at one month in culture and maintained in one tested MucilAir™ donor for several months. In conclusion, MucilAir™ presented important morphological and metabolic characteristics of a mucociliary epithelium in short and long term culture. MucilAir™ is therefore a potentially useful model to test repeated sub-cytotoxic doses of toxicants.

The heathland lichen Cladonia portentosa was collected from sites in mainland Britain differing either in rates of wet N deposition or in annual mean N concentration in rainfall based on a modelled data set. Methanolic extracts of thalli were analyzed by liquid chromatography time-of-flight mass spectrometry to yield metabolic profiles. Differences between sites in metabolite concentration were quantified using multivariate statistical tools and used to identify potential biomarker molecules. The abundances of three structurally related betaine lipids showed an increase with increasing modelled N deposition to a threshold of 22.3 kg ha(-1) year(-1) after which they remained constant. In contrast, the abundance of a phosphatidylcholine (PC) lipid showed concomitant decrease. Correlations of the identified biomarkers with N deposition and precipitation were stronger than those with N concentrations. The results presented in this study clearly show that N enrichment associated with tissue P limitation changes lipid composition, leading to shifts from PCs to betaine lipids, and that these lipids identified have the potential to be used as biomarkers for nitrogen enrichment.

Nitrogen availability has profound ecological consequences in nutrient-limited systems. In terrestrial settings these would include the upland heaths, sand dunes and blanket bogs of temperate latitudes. Understanding the physiological consequences of nitrogen enrichment is a first critical step in predicting possible consequences. Results are presented from a metabolic fingerprinting study using Fourier transform-infrared spectroscopy (FTIR) to detect biochemical differences in the lichen Cladonia portentosa collected from 25 sites across mainland Britain varying in their nitrogen input. Partial least-squares regression analysis of the FTIR data demonstrated that changes in broad biochemical classes were consistently correlated with mean annual wet inorganic nitrogen deposition loads. These results demonstrated a direct coupling of a broad range of metabolic processes in C. portentosa to nitrogen deposition.

Chemical properties have been used as a way of following the composting process and compost maturity, however, their analysis is very time consuming as each must be separately determined. By developing a more rapid method to predict these properties, time and cost would be saved. This study investigates the use of Fourier Transform mid-Infrared Spectroscopy (FT-IR) for this purpose. FT-IR spectra and measured values of several chemical properties from a variety of compost mixtures were used to produce calibrated models using partial least-squares regression analysis which predicted the known chemical properties. These models displayed a range of accuracies that for most properties was more than sufficient to follow at least broad dynamic changes associated with maturation. The best calibrations were achieved for total C, total N, LOI, lignin, and cellulose with r(2) values within the range 56-77%. Some degree of calibration was achieved for available-P and NH(4)(+)-N, with r(2) values of between 40% and 57%. No useful calibration could be achieved for NO(3)(-) or pH.

Levels of lignin and hydroxycinnamic acid wall components in three genera of forage grasses (Lolium, Festuca and Dactylis) have been accurately predicted by Fourier-transform infrared spectroscopy using partial least squares models correlated to analytical measurements. Different models were derived that predicted the concentrations of acid detergent lignin, total hydroxycinnamic acids, total ferulate monomers plus dimers, p-coumarate and ferulate dimers in independent spectral test data from methanol extracted samples of perennial forage grass with accuracies of 92.8%, 86.5%, 86.1%, 59.7% and 84.7% respectively, and analysis of model projection scores showed that the models relied generally on spectral features that are known absorptions of these compounds. Acid detergent lignin was predicted in samples of two species of energy grass, (Phalaris arundinacea and Pancium virgatum) with an accuracy of 84.5%.

The effect of alkali metals on the thermal degradation of biomass during combustion and pyrolysis has been investigated for 19 Lolium and Festuca grass varieties. These samples have been grown under the same conditions, but has been genetically mutated to give varying lignin contents in the range 2–6% measured by Klason. These grasses also have a high alkali metal content resulting in a high ash content. In order to compare the Lolium and Festuca grasses willow chip and switchgrass were also studied to act as a reference fuels. All samples were subjected to different washing conditions to investigate the effect of decreasing the metal content. The resulting biomass samples were studied for pyrolysis characteristics using thermogravimetric analysis (TGA) and pyrolysis gas chromatography–mass spectrometry (pyroprobe-GC/MS) and for combustion characteristics by TGA. A strong catalytic effect of metals, particularly potassium, was observed in both pyrolysis and combustion. Also, it was found that as the lignin content increases, the metal content (especially potassium and sodium) decreases. Furthermore, the char yield from pyrolysis (measured at 773K from TGA pyrolysis traces) increases as metals increase, and hence char yield increases as the lignin content decreases. Py-GCMS showed that peak intensities varied for untreated and treated samples; in particular the levoglucosan yield is higher and the hydroxyacetaldehyde yield is lower for treated (low metal content) samples. This supports previous work mechanisms by Liden et al. in which alkali metals promote an ionic route that favours ring-scission and hydroxyacetaldehyde formation.

Few experiments have yet been performed to explore the potential ecological impacts of genetic modification in long-lifespan species such as trees. In this paper, we review the available data on GM trees with modified lignin focussing on the results of the first long-term field trials of such trees. These trials evaluated poplars expressing antisense transgenes to reduce the expression of the lignin biosynthesis genes cinnamyl alcohol dehydrogenase (CAD) or caffeic acid/5-hydroxyferulic acid O-methyltransferase (COMT) with the aim of producing trees with improved pulping characteristics. The trees were grown for 4 years at two sites in France and England, and their ecological impacts and agronomic performance were assessed. Modifications to lignin in the poplars were maintained over the 4 years of the trial. The trees remained healthy throughout and growth was normal. The lignin modifications had no unexpected biological or ecological impacts. Interactions with leaf-feeding insects, microbial pathogens and soil organisms were unaltered although the short-term decomposition of transgenic roots was slightly enhanced. Investigation of the ecological impacts of the GM trees was curtailed by the early termination of the field trial when it was attacked and largely destroyed by anti-GM protestors. To supplement our work on the decomposition of GM plant materials with modified lignin, we have therefore turned to the study of transgenic tobacco lines where we can perform more comprehensive and controlled analyses of the biological and ecological effects of lignin-gene suppression.

A rapid method for the analysis of biomass feedstocks was established to identify the quality of the pyrolysis products likely to impact on bio-oil production. A total of 15 Lolium and Festuca grasses known to exhibit a range of Klason lignin contents were analysed by pyroprobe–GC/MS (Py–GC/MS) to determine the composition of the thermal degradation products of lignin. The identification of key marker compounds which are the derivatives of the three major lignin subunits (G, H, and S) allowed pyroprobe-GC/MS to be statistically correlated to the Klason lignin content of the biomass using the partial least-square method to produce a calibration model. Data from this multivariate modelling procedure was then applied to identify likely “key marker” ions representative of the lignin subunits from the mass spectral data. The combined total abundance of the identified key markers for the lignin subunits exhibited a linear relationship with the Klason lignin content. In addition the effect of alkali metal concentration on optimum pyrolysis characteristics was also examined. Washing of the grass samples removed approximately 70% of the metals and changed the characteristics of the thermal degradation process and products. Overall the data indicate that both the organic and inorganic specification of the biofuel impacts on the pyrolysis process and that pyroprobe–GC/MS is a suitable analytical technique to asses lignin composition.

Two energy crops (switchgrass and reed canary grass) have been processed using ball mills and divided into two size fractions (<90μm and 90–600μm) and analysed using an array of analytical techniques including proximate and ultimate analysis, metal analysis, calorific value determination, and plant component analysis (cellulose, lignin and hemicellulose contents). The results indicate that smaller particles of the two grasses have a significantly higher concentration of inorganic matter and moisture content than larger particles. In contrast the larger size fractions had a higher carbon content, and lower nitrogen content, with a resulting higher calorific value. The volatile content was also higher in the larger size fraction. The composition of the organic content varied between the two size fractions, most noticeable was the difference in cellulose concentration which was approximately 50% higher in the >90μm sample. Two laboratory scale techniques, thermogravimetric analysis (TGA) and pyrolysis–GC–MS (py–GC–MS), were used to study the significance of these differences in thermal conversion. In py–GC–MS of reed canary grass, and switchgrass to a lesser extent, the amounts of cellulose and lignin decomposition products were higher for the larger particle size fraction. The differences in cellulose contents were also apparent from the TGA studies, where different mass losses were seen in the cellulose decomposition region of the two size fractions. From the results of these two techniques it was concluded that the differences in ash, and therefore catalytic metal contents, between the two size fractions, resulted in lower pyrolysis temperatures, lower char combustion temperatures, and higher yields of catalytic pyrolysis decomposition products for the smaller size fractions. The implications of the results are discussed in terms of the bio-oil quality in fast pyrolysis and the predicted behaviour of the ash in combustion. It is suggested that pre-treatment by milling is one route that might be used routinely as a feedstock quality improvement strategy in integrated biomass conversion processes.

Thain, S. C., Morris, P., Hawkins, S., Morris, C., Donnison, I. S. (2005). Screening of perennial grasses and a mutant maize collection by Fourier-Transform InfraRed Spectroscopy (FTIR) spectroscopy for improved biofuel traits. Page 173 in: Humphreys, M. O. (Ed.), Molecular Breeding for the Genetic Improvement of Forage Crops and Turf. Proceedings of the 4th International Symposium on the Molecular Breeding of Forage and Turf. XXth International Grassland Congress, July 2005, Aberystwyth, Wales.

Ethylene controls multiple physiological processes in plants, including cell elongation. Consequently, ethylene synthesis is regulated by internal and external signals. We show that a light-entrained circadian clock regulates ethylene release from unstressed, wild-type Arabidopsis (Arabidopsis thaliana) seedlings, with a peak in the mid-subjective day. The circadian clock drives the expression of multiple ACC SYNTHASE genes, resulting in peak RNA levels at the phase of maximal ethylene synthesis. Ethylene production levels are tightly correlated with ACC SYNTHASE 8 steady-state transcript levels. The expression of this gene is controlled by light, by the circadian clock, and by negative feedback regulation through ethylene signaling. In addition, ethylene production is controlled by the TIMING OF CAB EXPRESSION 1 and CIRCADIAN CLOCK ASSOCIATED 1 genes, which are critical for all circadian rhythms yet tested in Arabidopsis. Mutation of ethylene signaling pathways did not alter the phase or period of circadian rhythms. Mutants with altered ethylene production or signaling also retained normal rhythmicity of leaf movement. We conclude that circadian rhythms of ethylene production are not critical for rhythmic growth.

The expression of CHALCONE SYNTHASE(CHS) expression is an important control step in the biosynthesis of flavonoids, which are major photoprotectants in plants. CHS transcription is regulated by endogenous programs and in response to environmental signals. Luciferase reporter gene fusions showed that the CHS promoter is controlled by the circadian clock both in roots and in aerial organs of transgenic Arabidopsis plants. The period of rhythmicCHS expression differs from the previously described rhythm of chlorophyll a/b-binding protein (CAB) gene expression, indicating thatCHS is controlled by a distinct circadian clock. The difference in period is maintained in the wild-type Arabidopsis accessions tested and in the de-etiolated 1 andtiming of CAB expression 1 mutants. These clock-affecting mutations alter the rhythms of both CABand CHS markers, indicating that a similar (if not identical) circadian clock mechanism controls these rhythms. The distinct tissue distribution of CAB andCHS expression suggests that the properties of the circadian clock differ among plant tissues. Several animal organs also exhibit heterogeneous circadian properties in culture but are believed to be synchronized in vivo. The fact that differing periods are manifest in intact plants supports our proposal that spatially separated copies of the plant circadian clock are at most weakly coupled, if not functionally independent. This autonomy has apparently permitted tissue-specific specialization of circadian timing.

BACKGROUND:Circadian clocks regulate the gene expression, metabolism and behaviour of most eukaryotes, controlling an orderly succession of physiological processes that are synchronised with the environmental day/night cycle. Central circadian pacemakers that control animal behaviour are located in the brains of insects and rodents, but the location of such a pacemaker has not been determined in plants. Peripheral plant and animal tissues also maintain circadian rhythms when isolated in culture, indicating that these tissues contain circadian clocks. The degree of autonomy that the multiple, peripheral circadian clocks have in the intact organism is unclear.RESULTS:We used the bioluminescent luciferase reporter gene to monitor rhythmic expression from three promoters in transgenic Arabidopsis and tobacco plants. The rhythmic expression of a single gene could be set at up to three phases in different anatomical locations of a single plant, by applying light/dark treatments to restricted tissue areas. The initial phases were stably maintained after the entraining treatments ended, indicating that the circadian oscillators in intact plants are autonomous. This result held for all the vegetative plant organs and for promoters expressed in all major cell types. The rhythms of one organ were unaffected by entrainment of the rest of the plant, indicating that phase-resetting signals are also autonomous.CONCLUSIONS:Higher plants contain a spatial array of autonomous circadian clocks that regulate gene expression without a localised pacemaker. Circadian timing in plants might be less accurate but more flexible than the vertebrate circadian system.

Developmental and physiological responses are regulated by light throughout the entire life cycle of higher plants. To sense changes in the light environment, plants have developed various photoreceptors, including the red/far-red light-absorbing phytochromes and blue light-absorbing cryptochromes. A wide variety of physiological responses, including most light responses, also are modulated by circadian rhythms that are generated by an endogenous oscillator, the circadian clock. To provide information on local time, circadian clocks are synchronized and entrained by environmental time cues, of which light is among the most important. Light-driven entrainment of the Arabidopsis circadian clock has been shown to be mediated by phytochrome A (phyA), phytochrome B (phyB), and cryptochromes 1 and 2, thus affirming the roles of these photoreceptors as input regulators to the plant circadian clock. Here we show that the expression of PHYB::LUC reporter genes containing the promoter and 5' untranslated region of the tobacco NtPHYB1 or Arabidopsis AtPHYB genes fused to the luciferase (LUC) gene exhibit robust circadian oscillations in transgenic plants. We demonstrate that the abundance of PHYB RNA retains this circadian regulation and use a PHYB::Luc fusion protein to show that the rate of PHYB synthesis is also rhythmic. The abundance of bulk PHYB protein, however, exhibits only weak circadian rhythmicity, if any. These data suggest that photoreceptor gene expression patterns may be significant in the daily regulation of plant physiology and indicate an unexpectedly intimate relationship between the components of the input pathway and the putative circadian clock mechanism in higher plants.