From genomes to systems

A report on the 2nd Conference of the Consortium for Post-Genome Science (CPGS) 'Genomes to Systems', Manchester, UK, 1-3 September 2004

Effect of ammonium and high light intensity on the accumulation of lipids in Nannochloropsis oceanica (CCAP 849/10) and Phaeodactylum tricornutum (CCAP 1055/1).

BACKGROUND: Microalgae accumulate lipids when exposed to stressful conditions such as nutrient limitation that can be used to generate biofuels. Nitrogen limitation or deprivation is a strategy widely employed to elicit this response. However, this strategy is associated with a reduction in the microalgal growth, leading to overall poor lipid productivities. Here, we investigated the combined effect of a reduced source of nitrogen (ammonium) and super-saturating light intensities on the growth and induction of lipid accumulation in two model but diverse microalgal species, Phaeodactylum tricornutum and Nannochloropsis oceanica. We hypothesized that the lower energy cost of assimilating ammonium would allow the organisms to use more reductant power for lipid biosynthesis without compromising growth and that this would be further stimulated by the effect of high light (1000 µmol m-2 s-1) stress. We studied the changes in growth and physiology of both species when grown in culture media that either contained nitrate or ammonium as the nitrogen source, and an additional medium that contained ammonium with tungsten in place of molybdenum and compared this with growth in media without nitrogen. We focused our investigation on the early stages of exposure to the treatments to correspond to events relevant to induction of lipid accumulation in these two species. RESULTS: At super-saturating light intensities, lipid productivity in P. tricornutum increased twofold when grown in ammonium compared to nitrogen free medium that increased further when tungsten was present in the medium in place of molybdenum. Conversely, N. oceanica growth and physiology was not compromised by the high light intensities used, and the use of ammonium had a negative effect on the lipid productivity, which was even more marked when tungsten was present. CONCLUSIONS: Whilst the use of ammonium and super-saturating light intensities in P. tricornutum was revealed to be a good strategy for increasing lipid biosynthesis, no changes in the lipid productivity of N. oceanica were observed, under these conditions. Both results provide relevant direction for the better design of processes to produce biofuels in microalgae by manipulating growth conditions without the need to subject them to genetic engineering manipulation

Influence of washing and quenching in profiling the metabolome of adherent mammalian cells: A case study with the metastatic breast cancer cell line MDA-MB-231

Metabolome characterisation is a powerful tool in oncology. To obtain a valid description of the intracellular metabolome, two of the preparatory steps are crucial, namely washing and quenching. Washing must effectively remove the extracellular media components and quenching should stop the metabolic activities within the cell, without altering the membrane integrity of the cell. Therefore, it is important to evaluate the efficiency of the washing and quenching solvents. In this study, we employed two previously optimised protocols for simultaneous quenching and extraction, and investigated the effects of a number of washing steps/solvents and quenching solvent additives, on metabolite leakage from the adherent metastatic breast cancer cell line MDA-MB-231. We explored five washing protocols and five quenching protocols (including a control for each), and assessed for effectiveness by detecting ATP in the medium and cell morphology changes through scanning electron microscopy (SEM) analyses. Furthermore, we studied the overall recovery of eleven different metabolite classes using the GC-MS technique and compared the results with those obtained from the ATP assay and SEM analysis. Our data demonstrate that a single washing step with PBS and quenching with 60% methanol supplemented with 70 mM HEPES (−50 °C) results in minimum leakage of intracellular metabolites. Little or no interference of PBS (used in washing) and methanol/HEPES (used in quenching) on the subsequent GC-MS analysis step was noted. Together, these findings provide for the first time a systematic study into the washing and quenching steps of the metabolomics workflow for studying adherent mammalian cells, which we believe will improve reliability in the application of metabolomics technology to study adherent mammalian cell metabolism

Bioenergy Technologies for a Net Zero Transition:Outcomes of UK-India Bioenergy Research Scoping

The report is part of scoping exercise led by UK Research and Innovation (UKRI)’s Engineering and Physical Sciences Research Council (EPSRC) and Biotechnology and Biological Sciences Research Council (BBSRC) and commissioned to Supergen Bioenergy Hub. The report is for UKRI, funded by UKRI India. UKRI launched in April 2018. UKRI is a non-departmental public body sponsored by the Department for Business, Energy and Industrial Strategy (BEIS). Our organisation brings together the seven disciplinary research councils, Research England, which is responsible for supporting research and knowledge exchange at higher education institutions in England, and the UK’s innovation agency, Innovate UK. Our nine councils work together in innovative ways to deliver an ambitious agenda, drawing on our great depth and breadth of expertise and the enormous diversity of our portfolio. http://www.ukri.org UKRI India plays a key role in enhancing the research and innovation collaboration between the UK and India. Since 2008, the UK and Indian governments, and third parties, have together invested over £330 million in co-funded research and innovation programmes. This investment has brought about more than 258 individual projects. The projects were funded by over 15 funding agencies, bringing together more than 220 lead institutions from the UK and India. These research projects have generated more than £450 million in further funding, mainly from public bodies but also from non-profit organisations and commercial entities, attesting the relevance of these projects. www.ukri.org/india This work was commissioned to inform UKRI/UKRI India priorities and pathways for innovation development in bioenergy with UK-India partnerships

Monitoring submerged mycelial bioprocesses using near-infrared spectroscopy

Available from British Library Document Supply Centre- DSC:DXN055914 / BLDSC - British Library Document Supply CentreSIGLEGBUnited Kingdo

Deconvolution of near-infrared spectral information for monitoring mycelial biomass and other key analytes in a submerged fungal bioprocess

Near-infrared spectroscopy is a promising technique for the rapid monitoring of submerged culture bioprocesses. However, despite the key role of mycelial (filamentous fungal and bacterial) micro-organisms in the manufacture of antibiotics and other valuable therapeutics, there is little information on the application of the technique to monitor mycelial bioprocesses. In part, this is due to the complex and spectroscopically challenging matrices, which result from the growth of these micro-organisms. Moreover, there is a particular lack of any detailed mechanistic information on how models for the prediction of the concentration of key analytes (e.g. biomass, substrates, product) can be constructed, evaluated and improved using the spectral data arising from such complex matrices. We investigated the near-infrared spectra of culture fluid from a submerged fungal bioprocess, for monitoring the concentrations of mycelial biomass and other key analytes. Several empirical models were developed for predicting the concentration of the analytes, using multivariate statistical techniques. Despite the filamentous nature of the biomass and the resulting complexity of the spectral variations, empirical models could be developed for the prediction of this analyte, using biomass ‘specific’ information. SEP values of <1 g/l could be achieved on external validation, for models developed in the concentration range of 0–20 g/l. The concentrations of the substrates, total sugars (as glucose equivalents) and ammonium, could also be predicted, simultaneously. However, the product (penicillin) and by product (extracellular proteins) levels had to be monitored on the cell free culture fluid, due to their relatively low concentration. Here we report upon how the spectral information can be deconvoluted for predicting the levels of the analytes and upon how the ‘analyte specific’ information in the spectral data can be used to inform and assist the modelling process, in order to increase confidence in exactly what is being modelled