Anaerobic digestion of dried/shredded food waste in a periodic anaerobic baffled reactor

The objective of the current work is to study the impact of the operational parameters' variation (HRT, OLR and T) on biomethane productivity in a periodic anaerobic baffled reactor (PABR). The feedstock used was a biomass product named food residue biomass (FORBI), which is dried and shredded source-separated household food waste. The PABR is an innovative, high-rate bioreactor. Apart from the hydraulic retention time (HRT) and the organic loading rate (OLR), an important operational parameter is the switching period (T) of the feeding compartment: when T is high, the bioreactor operation is similar to an anaerobic baffled reactor (ABR), while when it is low, the operation approaches that of an upflow anaerobic sludge blanket reactor (UASBR). Nine distinct experimental phases were conducted, during which the operational parameters of the PABR were consecutively modified: the HRT varied from 9 to 2.5 days, T between 2 days and 1 and finally the OLR from 1.24 g_COD/L_bioreactor^*d to 8.08 g_COD/L_bioreactor^*d. The maximum biomethane yield was 384 L_CH4/kg_FORBI corresponding to the operation at HRT = 5 d, OLR = 2.14 g_COD/L_bioreactor^*d and T = 2 days. Similar efficiency (333 L_CH4/kg-_FORBI) was achieved at higher OLR (4.53 g_COD/L_bioreactor^*d).

Protein structure topological comparison, discovery and matching service

We describe a fold level fast protein comparison and motif matching facility based on the TOPS representation of structure. This provides an update to a previous service at the EBI, with a better graph matching with faster results and visualization of both the structures being compared against and the common pattern of each with the target domain.

AVAILABILITY

Web service at http://balabio.dcs.gla.ac.uk/tops or via the main TOPS site at http://www.tops.leeds.ac.uk. Software is also available for download from these sites.

Role of the conserved lysine 80 in stabilisation of NF-kappaB p50 DNA binding

The transcriptional rate of a variety of genes involved in acute-phase response, inflammation, lymphocytic activation, and cell growth or differentiation, is regulated by the DNA binding activity of the inducible transcription factor NF-kappaB. NF-kappaB p50 homodimers bind specifically to DNA, via base and backbone contacts mediated by residues in the flexible loops which link secondary structure elements in both of its two distinct domains. However, it has been suggested that additional contacts which stabilise DNA binding are made by lysine residues located in the C-terminus of the flexible loop which connects A and B beta-sheets of the N-terminal domain of p50. To determine the importance of each of the lysine residues in this region (K77, K79, K80), a series of mutated p50 proteins were generated in which the lysines were changed to alanines. The DNA binding properties of these mutants were analysed by gel electrophoresis DNA binding assays and surface plasmon resonance. This study revealed that the C-terminus of AB loop interacts with DNA through an additional lysine-phosphate backbone ionic bond which makes a significant contribution to the binding energy, thus stabilising the complex. The lysine residue responsible for this interaction is K80 which is conserved in all NF-kappaB/Rel/Dorsal molecules.

Inducible degradation of I kappa B alpha in vitro and in vivo requires the acidic C-terminal domain of the protein

After exposure of cells to tumor necrosis factor (TNF), I kappa B alpha is rapidly degraded by a proteolytic activity that is required for nuclear localization and activation of transcription factor NF-kappa B. To investigate this problem, we have developed a cell-free system to study the degradation of I kappa B alpha initiated in vivo. In this in vitro system, characteristics of endogenous I kappa B alpha degradation were comparable to those observed in vivo. Recombinant I kappa B alpha, when added to lysates from cells exposed to TNF, was specifically degraded by a cellular proteolytic activity; however, it was stable in extracts from unstimulated cells. Inhibition characteristics of the proteolytic activity responsible for I kappa B alpha degradation suggest the involvement of a serine protease. Analysis of mutated forms of I kappa B alpha in the in vitro system demonstrated that an I kappa B alpha species which was unable to interact with NF-kappa B was still efficiently degraded. In contrast, deletion of the C-terminal 61 amino acids from I kappa B alpha rendered the protein resistant to proteolytic degradation. Expression of I kappa B alpha mutated forms in COS-7 cells confirmed the importance of the C-terminal domain for the degradation of the protein in vivo following cell activation. Thus, it is likely that the acidic, negatively charged region represented by the C-terminal 61 amino acids of the protein contains residues critical for TNF-inducible degradation of I kappa B alpha.