Bad plays a more significant role than Bid and Bim in mediating cell death signals in batch cultures of HEK 293 cells

The expression of three BH3-only proteins, Bad, Bid and Bim, were knocked down in HEK 293 cells using vectors that express corresponding siRNAs. When cultured in the presence of 10% (v/v) serum and a diminished glucose/nutrients environment, cells lacking any one of these BH3-only proteins showed delayed cell death compared to wild type cells. Remarkably, the culture life of Bad (−) cells was extended for an additional 5 days compared to WT HEK 293 cells. In the absence of serum, the suppression of either Bad, Bim or Bid expression delayed cell death under several stress conditions. Results presented in this paper offer an insight into the functions of BH3-only proteins in mediating the death signals under different stress conditions. Anup Padmanabhan and Sen Liu contributed equally to this work.     

Growth phase-dependent changes in the expression of global regulatory genes and associated metabolic pathways in Escherichia coli

Metabolic regulation in Escherichia coli was studied in terms of the changes in the expression of the global regulatory genes rpoD, rpoS, soxRS, cra, fadR, iclR and arcA at three different growth phases, in batch culture. The expression of rpoS and several rpoS-dependent metabolic pathway genes, such as tktB, talA, fumC, acnA, sucA, acs and sodC, were increased (∼1.5 to 2-fold) as the cells entered the late phase of growth. The changes in the expression of other global regulators and their effects on different metabolic pathway genes were less significant, as compared to rpoS, during the later phases of growth.     

In vitro study on gas generation and prebiotic effects of some carbohydrates and their mixtures

This study was carried out to examine the effect of inulin (IN), fructooligosaccharide (FOS), polydextrose (POL) and isomaltooligosaccharides (ISO), alone and in combination, on gas production, gas composition and prebiotic effects. Static batch culture fermentation was performed with faecal samples from three healthy volunteers to study the volume and composition of gas generated and changes in bacterial populations. Four carbohydrates alone or mixed with one another (50:50) were examined. Prebiotic index (PI) was calculated and used to compare the prebiotic effect. The high amount of gas produced by IN was reduced by mixing it with FOS. No reduction in gas generation was observed when POL and ISO mixed with other substrates. It was found that the mixture of IN and FOS was effective in reducing the amount of gas produced while augmenting or maintaining their potential to support the growth of bifidobacteria in faecal batch culture as the highest PI was achieved with FOS alone and a mixture of FOS and IN. It was also found that high volume of gas was generated in presence of POL and ISO and they had lower prebiotic effect. The results of this study imply that a mixture of prebiotics could prove effective in reducing the amount of gas generated by the gut microflora.     

Mean-variance performance optimization of response time in a tandem router network with batch arrivals

The end-to-end performance of a simple wireless router network with batch arrivals is optimized in an M/G/1 queue-based, analytical model. The optimization minimizes both the mean and variance of the transmission delay (or ‘response time’), subject to an upper limit on the rate of losses and finite capacity queueing and recovery buffers. Losses may be due to either full buffers or corrupted data. The queueing model is also extended to higher order moments beyond the mean and variance of the response time. The trade-off between mean and variance of response time is assessed and the optimal ratio of arrival-buffer size to recovery-buffer size is determined, which is a critical quantity, affecting both loss rate and transmission time. Graphs illustrate performance in the near-optimal region of the critical parameters. Losses at a full buffer are inferred by a time-out whereas corrupted data is detected immediately on receipt of a packet at a router, causing a N-ACK to be sent upstream. Recovery buffers hold successfully transmitted packets so that on receiving a N-ACK, the packet, if present, can be retransmitted, avoiding an expensive resend from source. The impact of the retransmission probability is investigated similarly: too high a value leads to congestion and so higher response times, too low and packets are lost forever.

Improvement of a β-glucanase activity test by taking into account the batch reactor balance of the test system

Activity tests of enzymes are often applied for determining their concentration. In the easiest case, just one product concentration is measured after a given time. This often leads to nonlinear dependences of the apparent activity with enzyme protein concentration. A general solution of this problem consists in using the balance equation of the assay system, which commonly represents a batch reactor. Here, the balance equation of the batch for a general Michaelis Menten-type reaction kinetics is used as the calibration function. The correlation of the apparent activity and enzyme concentration was established by capturing the enzyme by means of metal chelate interaction owing to a hexahistidine tag attached to the β-glucanase.     

Bio-kinetic analysis on treatment of textile dye wastewater using anaerobic batch reactor

An anaerobic digestion technique was applied to textile dye wastewater aiming at the colour and COD removal. Pet bottles of 5 L capacity were used as reactor which contains methanogenic sludge of half a liter capacity which was used for the treatment of combined synthetic textile dye and starch wastewater at different mixing ratios of 20:80, 30:70, 40:60, 50:50 and 60:40 with initial COD concentrations as 3520, 3440, 3360, 3264 and 3144 mg L⁻¹, respectively. The reactor was maintained at room temperature (30 ± 3 °C) with initial pH of 7. The maximum COD and colour removal were 81.0% and 87.3% at an optimum mixing ratio of 30:70 of textile dye and starch wastewaters. Both Monod’s and Haldane’s models were adopted in this study. The kinetic constants of cell growth under Haldane’s model were satisfactory when compared to Monod’s model. The kinetic constants obtained by Haldane’s model were found to be in the range of μ_max = 0.037-0.146 h⁻¹, K_s = 651.04-1372.88 mg L⁻¹ and K_i = 5681.81-18727.59 mg L⁻¹.     

Multi-objective optimization of glycopeptide antibiotic production in batch and fed batch processes

Fermentation optimization involves potentially conflicting multiple objectives such as product concentration and production media cost. Simultaneous optimization of these objectives would result in a multiobjective optimization problem, which is characterized by a set of multiple solutions, knows as pareto optimal solutions. These solutions gives flexibility in evaluating the trade-offs and selecting the most suitable operating policy. Here, ε-constraint approach was used to generate the pareto solutions for two objectives: product concentration and product per unit cost of media, for batch and fed batch operations using process model for Amycolatopsis balhimycina, a glycopeptide antibiotic producer. This resulted in a set of several pareto optimal solutions with the two objectives ranging from (0.75 g l⁻¹, 3.97 g $^-1) to (0.44 g l⁻¹, 5.19 g $^-1) for batch and from (1.5 g l⁻¹, 5.46 g $^-1) to (1.1 g l⁻¹, 6.34 g $^-1) for fed batch operations. One pareto solution each for batch and for fed batch mode was experimentally validated.     

Fermentative hydrogen production from fresh leachate in batch and continuous bioreactors

This research for the first time investigated hydrogen production from the fresh leachate originated from municipal solid wastes. We found that fermentation of the leachate generated H₂ and was very much enhanced in the presence of extra phosphate in the batch reactor. The continuous expanded granular sludge bed (EGSB) reactor started to generate H₂ at day 20 and continued to 176 days with 120 mg/l of extra phosphate present. The highest chemical oxygen demand (COD) removal efficiency (66.9%) was achieved at liquid up-flow velocity of 3.7 m/h and hydraulic retention time of 12 h. Under proposed optimal operation conditions, the mean H₂ production rate reached up to 2155 ml/(l day). We also found that over 80% liquid metabolites were acetic acid and ethanol, suggesting the ethanol-type fermentation was dominant in the bioreactor. These findings indicate that the fresh leachate can be used as the source for continuous hydrogen production.     

Biogas production from different substrates in an experimental Continuously Stirred Tank Reactor anaerobic digester

Different mixtures were digested in a single-stage, batch, mixed, laboratory scale mesophilic anaerobic digester at the Biomass Research Centre Laboratory (University of Perugia). The yield and the composition of biogas from the different substrates were evaluated and the cumulative curves were estimated. Two experimental campaigns were carried out, the first on three mixtures (chicken, pig and bovine manures), the second on animal and vegetal biomasses (chicken and cow manure, olive husk) with different inocula (rumen fluid and digested sludge). In the first campaign pig manure mixture showed the maximum biogas production (0.35 Nm³/kg) and energy content (1.35 kWh/kg VS); in the second one the differences in produced biogas from the different inocula were analyzed: olive husk with piggery manure anaerobically digested as inoculum showed the higher biogas (0.28 Nm³/kg VS) and methane yield (0.11 Nm³/kg VS), corresponding to an energetic content of 1.07 kWh/kg VS. All data obtained from the laboratory scale anaerobic digester are comparable to the values in literature for several biomass and in particular for olive husk, dairy manure and chicken manure.     

Batch cultures of supplemented whey permeate using Lactobacillus helveticus: unstructured model for biomass formation, substrate consumption and lactic acid production

The Luedeking and Piret expression can not account for the cessation of production observed at the end of batch; so an empiric term has been previously added to this equation which accounted in a global way for possible substrate limitations. In the model developed in this work, a carbon substrate limitation appeared explicitly in the production expression. Assuming a sigmoidal variation with time of specific growth rate previously validated, the new production model matched well the entire experimental production kinetics. It has been successfully tested for a wide range of nitrogen supplementations, i.e. from an almost total coupling between growth and production for largely supplemented media, to a high decoupling in case of few available nitrogen. Since all the parameters of this model have an obvious biologic meaning, it may be an unvaluable tool for the comprehension of the phenomenon. The model accounted also well for the variation of the specific production rate versus specific growth rate, avoiding the noise due to the direct differentiation of experimental data.