Integration of holographic sensors into microfluidics for the real-time pH sensing of L. casei metabolism

We describe developments in the integration of analyte specific holographic sensors into PDMS-based microfluidic devices for the purpose of continuous, low-impact monitoring of extra-cellular change in micro-bioreactors. Holographic sensors respond to analyte concentration via volume change, which makes their reduction in size and integration into spatially confined fluidics difficult. Through design and process modification many of these constraints have been addressed, and a microfluidics-based device capable of real-time monitoring of the pH change caused by Lactobacillus casei fermentation is presented as a general proof-of-concept for a wide array of possible devices.

Role of RNA polymerase IV in plant small RNA metabolism.

In addition to the three RNA polymerases (RNAP I-III) shared by all eukaryotic organisms, plant genomes encode a fourth RNAP (RNAP IV) that appears to be specialized in the production of siRNAs. Available data support a model in which dsRNAs are generated by RNAP IV and RNA-dependent RNAP 2 (RDR2) and processed by DICER (DCL) enzymes into 21- to 24-nt siRNAs, which are associated with different ARGONAUTE (AGO) proteins for transcriptional or posttranscriptional gene silencing. However, it is not yet clear what fraction of genomic siRNA production is RNAP IV-dependent, and to what extent these siRNAs are preferentially processed by certain DCL(s) or associated with specific AGOs for distinct downstream functions. To address these questions on a genome-wide scale, we sequenced approximately 335,000 siRNAs from wild-type and RNAP IV mutant Arabidopsis plants by using 454 technology. The results show that RNAP IV is required for the production of >90% of all siRNAs, which are faithfully produced from a discrete set of genomic loci. Comparisons of these siRNAs with those accumulated in rdr2 and dcl2 dcl3 dcl4 and those associated with AGO1 and AGO4 provide important information regarding the processing, channeling, and functions of plant siRNAs. We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors.

SIMULATION OF THE ANAEROBIC DIGESTION OF FOOD WASTE

This study has established that the use of a computer model, the Anaerobic Digestion Model 1, is suitable for investigation of the stability and energy balance of the anaerobic digestion of food waste. In simulations, digestion of undiluted food waste was less stable than that of sewage sludge or mixtures of the two, but gave much higher average methane yields per volume of digester. In the best case scenario simulations, food waste resulted in the production of 5.3 Nm3 of methane per day per m3 of digester volume, much higher than that of sewage sludge alone at 1.1 Nm3 of methane per day per m3. There was no substantial difference in the yield per volatile solids added. Food waste, however, did not sustain a stable digestion if its cation content was below a certain level. Mixing food waste and sewage sludge allowed digestion with a lower cation content. The changes in composition of food waste feedstock caused great variation in biogas output and even more so volatile fatty acid concentration, which lowered the digestion stability. Modelling anaerobic digestion allowed simulation of failure scenarios and gave insights into the importance of the cation/anion balance and the magnitude of variability in feedstocks.