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informatics in biofuels


tracked within LIMS using barcodes all the way back to the seed


grown in nurseries,’ says David Benton, director of informatics and information technology at GLBRC.


The research pipeline begins


with seed planted in test plots. The biomass is then harvested, pre-treated – generally with alkali-based AFEX (ammonia fi bre expansion) or alkaline hydrogen peroxide – and subjected to enzymes for hydrolysis. Finally, the hydrolysate is used as the growth medium in fermentations with bacteria or yeast to produce ethanol. ‘When we run a fermentation we want


to be able to trace back and know exactly how the hydrolysis was carried out, what enzyme mixture was used, where the biomass originated, what pre-treatment was used, and also the genotype of the plant and the fi eld conditions the plants were grown in,’ says Benton. ‘Plants differ depending on where they’re grown and the nutrient levels of the soil, among other factors. We want to be able to trace all those elements through the process.’ GLBRC’s research in the biofuel synthesis


group is centred on AFEX-treated corn stover and switchgrass. The centre also runs sustainability research, which is based on a wider spectrum of plants, from a traditional corn/soybean rotation, an annual monoculture, to restored prairie, which is heterogeneous with around 20 species growing together. The sustainability group, however, operates its own informatics systems. The biomass production group grows


around half a ton of corn stover and half a ton of switchgrass biomass each year. This enters the reaction pipeline in small batches of 50- 100g. ‘There is a lot of biomass to track in the experimental workfl ow,’ says Benton. Ying Gao, head of the LIMS group at the centre, adds that another function of LIMS is to automate the workfl ow, which, she says, can be complex. This year, GLBRC’s experimental


fermentation facility has produced at least 20 batches of hydrolysate, each one around nine litres in volume and taking around one week to generate. During the hydrolysis process, glucose and xylose are monitored – the hydrolysate should have around six per cent glucose and three per cent xylose. ‘During fermentation we collect metabolomic samples, monitor sugar kinetics and how much ethanol has been produced, as well as collect samples for carbon and nitrogen analysis and heavy metal analysis,’ explains Yaoping Zhang, leader of the experimental fermentation facility at GLBRC.


www.scientific-computing.com ANALYSING


THIS DATA HELPS TO ASSESS THE STATE OF CELL CULTURES AND


DETERMINE WHAT THE BOTTLENECKS FOR


FERMENTATION MIGHT BE OR HOW THE STRAINS CAN BE FURTHER IMPROVED TO MAKE THE PROCESS MORE EFFICIENT


The quantities of around 50-60 different


compounds are measured for each batch of hydrolysate including amino acids, metals, chemical analysis and oxygen content. During the fermentation, the researchers want to know how these compounds change inside the cells and in the media. All along the research pipeline, and during fermentation, samples are collected and sent for multi-omics analysis, which are tracked using LIMS, both when the samples are sent and the returning results. There are also a number of tools used for


bioinformatics analysis. The researchers use R and Partek statistical software for analysing gene expression data, and also run a local Galaxy server for analysing next-generation sequence data. ‘Researchers would like to know how different conditions affect gene expression in different strains of yeast or how the genotype of a strain is linked to fermentation effi ciency,’ explains Yury Bukhman, head of the bioinformatics group at the centre. ‘Analysing this data helps to assess the state of cell cultures and determine what the bottlenecks for fermentation might be or how the strains can be further improved to make the process more effi cient.’ Benton adds that although ethanol is the standard biofuel, other fuels could work better.


Capturing data electronically As biofuel production is still in its infancy, most companies run R&D facilities. The US company POET operates 27 biorefi neries converting corn starch to ethanol. It is optimising its biorefi nery process through its POET Research division and has recently implemented Accelrys’ electronic laboratory notebook (ELN) across its laboratories. The data is now input into the ELN rather


than recorded in paper lab notebooks. ‘It’s a good tool for us because, fi rstly, it’s searchable, and secondly, we can share experiments and see what each other is working on and really


informatics for biofuels


tie those experiments together,’ states Kristi Plack, laboratory manager at POET Research. ‘Whereas, prior to implementing the ELN, results were sitting in a paper notebook on somebody’s desk – you’d refer to the notebook number, but you weren’t able to collaborate as well as you can with the electronic lab notebook.’ Last year, Accelrys merged with Symyx,


which increased its laboratory informatics offerings with the Symyx Notebook and other packages. Its modelling and simulation software, along with its informatics systems, are used in biofuel R&D. At POET, standard laboratory procedure


used to involve printing out data from chromatograms, spreadsheets and other documents, such as PDFs, to paste into paper notebooks. ‘Now, we’re taking this process and moving it directly into the ELN,’ Plack explains. ‘It saves us an entire step.’ Data is now available in real time,


with sample results taken throughout a fermentation fed directly into the ELN rather than collating them at the end of an experiment. POET Research runs experimental


procedures on scaled down versions of its production fermentation vessels. Samples are taken at different time points throughout a fermentation to monitor kinetics and ensure the yeast and enzymes are active at the right time. The spent corn material from the fermentation is dried and processed as distillers grain for animal feedstock, which, in itself, has to be the same quality or better with the modifi ed process. ‘We’ve got to ensure we’re not affecting the co-product from the experimental fermentation procedure,’ says Plack. The research involves aspects such as


investigating the inputs of the process and seeing if there are new raw materials available that would improve effi ciency, or whether a dose change would alter the cost of production. ‘On implementing the ELN, our number


one goal was to store experimental data and information electronically, so it could be archived daily and backed up,’ states Plack. ‘This allows us to search experiments and collaborate better; it’s really hard to go back and look at old notebooks, especially if the person is no longer at the company. Now we can search the data using key words. She adds: ‘We also believe that it will reduce


the number of experiments that are repeated between groups, simply because the scientist was unaware that the research had already been carried out,’ she continues. POET Research also plans to scan all its old paper notebooks into the ELN in PDF format


OCTOBER/NOVEMBER 2011 9


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