Influence of redox potential on the accumulation of poly(3-hydroxybutyrate) by Bacillus megaterium.

The main goal of the present study was to evaluate the oxidation-reduction potential (ORP) on the production of poly(3-hydroxybutyrate) (P(3HB)) by Bacillus megaterium. Each microorganism has an optimal ORP range, and changes to the culture medium's ORP may redistribute the cell's metabolic flux, as such, the measurement and control of the ORP profile allows one to, in a way, manipulate the microbial metabolism, affecting the expression of certain enzymes and allowing for better control over the fermentative process. The ORP tests were carried out in a fermentation vessel coupled with an ORP probe, containing 1 L of mineral medium added with agroindustry byproducts (60% v/v of confectionery wastewater, and 40% v/v of rice parboiling water). The system's temperature was kept at 30 °C, with an agitation speed of 500 rpm. The vessel's airflow rate was controlled via a solenoid pump based on the ORP probe's data. Different ORP values were evaluated to verify their impact on biomass and polymer production. Cultures using OPR levels of 0 mV displayed the highest amounts of total biomass (5.00 g L-1) when compared to - 20 mV and - 40 mV (2.90 g L-1 and 0.53 g L-1, respectively). Similar results were also found for P(3HB)-to-biomass ratio, with polymer concentration being reduced when using ORP levels below 0 mV and with a maximum amount of polymer-to-biomass ratio of 69.87% after 48 h of culture. Furthermore, it was possible to observe that the culture's pH can also affect total biomass and polymer concentration, albeit to a lesser extent. Thus, when considering the data found during this study, it is possible to observe that ORP values can greatly impact B. megaterium cell's metabolism. Furthermore, the measurement and control of ORP levels may be an invaluable asset when trying to maximize polymer production under different culture conditions.

Development of redox potential-driven fermentation process for recombinant protein expression.

OBJECTIVES: A redox potential-driven fermentation, maintaining dissolved oxygen at a prescribed level while simultaneously monitoring the changes of fermentation redox potential, was developed to guide the cultivation progress of recombinant protein expression. RESULTS: A recombinant E. coli harboring prolinase-expressing plasmid (pKK-PepR2) was cultivated using the developed process. Two distinct ORP valleys were noticeable based on recorded profile. The first ORP valley is equivalent to the timing for the addition of inducing agent, and the second ORP valley serves to guide the timing for cell harvesting. The final prolinase activity is 0.172 µmol/mg/min as compared to that of 0.154 µmol/mg/min where the optical density was employed to guide the timing of inducer addition and an empirically determined length of the cultivation. CONCLUSION: The developed process can be further modified to become an automatic operation.

Reconstruction and analysis of a three-compartment genome-scale metabolic model for Pseudomonas fluorescens.

With the versatile metabolic diversity, Pseudomonas fluorescens is a potential candidate in petroleum aromatic hydrocarbon (PAH) bioremediation. Genome-scale metabolic model (GSMM) can provide systematic information to guide the development of metabolic engineering strategy to improve microbial activity. In this study, a GSMM for P. fluorescens SBW25 was reconstructed, which is termed as lCW1057. The reconstruction was based on automatic reannotation and manual curation. The periplasmic compartment was constructed to better represent the proton gradient profile. The reconstructed proton transport chain has a P/O (ATP generated per atom oxygen consumed by the respiratory chain) ratio of 11/8. Flux balance analysis (FBA) was performed to explore the whole-cell metabolic flow. The model suggested that instead of Embden-Meyerhof-Parnas pathway, Entner-Doudoroff pathway was used in glycolytic metabolism of P. fluorescens, indicating that the growth of P. fluorescens is more energy dependent. Furthermore, P. fluorescens can use nitrate as the terminal electron acceptor for the glucose metabolism. The ß-ketoadipate pathway was involved in catechol metabolism. The uptake of oxygen is mandatory for the aromatic ring cleavage. The in silico and in vitro maximum specific growth rate was compared, resulting in 10% difference when catechol was used as the sole carbon source.

Metabolic flux analysis of Saccharomyces cerevisiae during redox potential-controlled very high-gravity ethanol fermentation.

A previously published genome-scale metabolic model namely iFF708 was modified to depict the metabolic flux distribution within Saccharomyces cerevisiae grown under a redox potential-controlled very high-gravity condition. The following modifications were made: electron transport chain (ETC) and oxidative phosphorylation, proton gradient and ATP transportation, and malate-aspartate shuttle. With these modifications, this model could describe the experimental data collected from the above-mentioned ethanol fermentation. As a result, the simulation unveiled that the P/O ratio is critical under microaerobic conditions and the malate-aspartate shuttle is inactivated due to the shortage of electron transport across mitochondria. In other words, the limited supply of oxygen suppresses the functionality of oxidative phosphorylation, tricarboxylic acid (TCA) cycle, and ETC. In terms of the glycolytic pathway, fluxes coming from glucose-6-phosphate and pyruvate nodes are insensitive to the changes of fermentation redox potential. As the initial glucose concentration is greater than 250 g/L, the interactive effect between the initial glucose concentration and redox potential level becomes noticeable.

Online monitoring lignocellulosic particles by focus beam reflectance measurement for efficient bioprocessing.

Lignocellulose presents a promising alternative to fossil fuels. Monitoring the mass and size changes of lignocellulosic particles without disrupting the process can assist in adjusting pretreatment and enzymatic hydrolysis, where conventional sieving methods fall short. A method utilizing focused beam reflectance measurement (FBRM) was developed to establish mathematical correlations between FBRM chord information (chord length and count) and particle characteristics (weight and size) quantified through sieving. Results indicate particle size exhibits a linear correlation with the square weighted median chord length (Lsqr) with R2 at 0.93. Further, real-time bulk particle mass can be predicted using Lsqr and chord count (R2 0.98). These correlations are applicable in range 53 µm to 358.5 µm. Real-time monitoring of enzymatic hydrolysis of corn stalks has demonstrated the practical applicability of FBRM. This study introduces a novel approach for online characterization of lignocellulosic particles, thereby enhancing lignocellulosic biorefineries.

Magnetic graphene oxide nanoflakes for dual RNA interfering delivery and gene knockdown in prostate and liver cancers.

The development of synthetic carriers for small interfering RNA (siRNA) and plasmids is crucial for effective gene therapy. In this study, we synthesized magnetic graphene oxide nanoflakes as carriers for siRNA delivery, with the goal of knockdown specific genes such as the green fluorescence protein (GFP). Our approach combined magnetically reduced graphene oxide with polyethylenimine (PEI) crosslinked to its surface using carbonyl diimidazole. To evaluate the adsorption capacity of the PEI-modified nanocomposite, we investigated its ability to bind two types of nucleic acids: short-hairpin (sh)RNA plasmids and siRNA targeting GFP. The nanocomposite exhibited significant adsorption, with maximum capacities of 426 ng/µg for shRNA and 71 ng/µg for siRNA, respectively. Simultaneous delivery of siRNA and shRNA using our designed nanocomposites was successfully achieved in human hepatoma and prostate cancer cells. Under magnetic guidance, the knockdown efficiencies reached 73.5 % in hepatoma cells for dual delivery of siRNA and shRNA. Our findings revealed that the nanocomplexes were internalized by the cells through a caveolae-dependent endocytosis mechanism. The demonstrated ability of the nanoflakes to efficiently transport siRNA and shRNA, with high loading capacity, controlled release, and magnetic targeting, resulted in effective GFP knockdown in vitro. These findings highlight the potential of magnetic graphene oxide nanoflakes as promising carriers for siRNA delivery and gene knockdown in therapeutic applications.

False positive reduction in protein-protein interaction predictions using gene ontology annotations.

BACKGROUND: Many crucial cellular operations such as metabolism, signalling, and regulations are based on protein-protein interactions. However, the lack of robust protein-protein interaction information is a challenge. One reason for the lack of solid protein-protein interaction information is poor agreement between experimental findings and computational sets that, in turn, comes from huge false positive predictions in computational approaches. Reduction of false positive predictions and enhancing true positive fraction of computationally predicted protein-protein interaction datasets based on highly confident experimental results has not been adequately investigated. RESULTS: Gene Ontology (GO) annotations were used to reduce false positive protein-protein interactions (PPI) pairs resulting from computational predictions. Using experimentally obtained PPI pairs as a training dataset, eight top-ranking keywords were extracted from GO molecular function annotations. The sensitivity of these keywords is 64.21% in the yeast experimental dataset and 80.83% in the worm experimental dataset. The specificities, a measure of recovery power, of these keywords applied to four predicted PPI datasets for each studied organisms, are 48.32% and 46.49% (by average of four datasets) in yeast and worm, respectively. Based on eight top-ranking keywords and co-localization of interacting proteins a set of two knowledge rules were deduced and applied to remove false positive protein pairs. The 'strength', a measure of improvement provided by the rules was defined based on the signal-to-noise ratio and implemented to measure the applicability of knowledge rules applying to the predicted PPI datasets. Depending on the employed PPI-predicting methods, the strength varies between two and ten-fold of randomly removing protein pairs from the datasets. CONCLUSION: Gene Ontology annotations along with the deduced knowledge rules could be implemented to partially remove false predicted PPI pairs. Removal of false positives from predicted datasets increases the true positive fractions of the datasets and improves the robustness of predicted pairs as compared to random protein pairing, and eventually results in better overlap with experimental results.

Prediction of protein-protein interactions using protein signature profiling.

Protein domains are conserved and functionally independent structures that play an important role in interactions among related proteins. Domain-domain interactions have been recently used to predict protein-protein interactions (PPI). In general, the interaction probability of a pair of domains is scored using a trained scoring function. Satisfying a threshold, the protein pairs carrying those domains are regarded as "interacting". In this study, the signature contents of proteins were utilized to predict PPI pairs in Saccharomyces cerevisiae, Caenorhabditis elegans, and Homo sapiens. Similarity between protein signature patterns was scored and PPI predictions were drawn based on the binary similarity scoring function. Results show that the true positive rate of prediction by the proposed approach is approximately 32% higher than that using the maximum likelihood estimation method when compared with a test set, resulting in 22% increase in the area under the receiver operating characteristic (ROC) curve. When proteins containing one or two signatures were removed, the sensitivity of the predicted PPI pairs increased significantly. The predicted PPI pairs are on average 11 times more likely to interact than the random selection at a confidence level of 0.95, and on average 4 times better than those predicted by either phylogenetic profiling or gene expression profiling.

Ultrahigh-Density 256-Channel Neural Sensing Microsystem Using TSV-Embedded Neural Probes.

Highly integrated neural sensing microsystems are crucial to capture accurate signals for brain function investigations. In this paper, a 256-channel neural sensing microsystem with a sensing area of 5 × 5 mm 2 is presented based on 2.5-D through-silicon-via (TSV) integration. This microsystem composes of dissolvable µ-needles, TSV-embedded µ-probes, 256-channel neural amplifiers, 11-bit area-power-efficient successive approximation register analog-to-digital converters, and serializers. This microsystem can detect 256 electrocorticography and local field potential signals within a small area of 5 mm × 5 mm. The neural amplifier realizes 57.8 dB gain with only 9.8 µW per channel. The overall power of this microsystem is only 3.79 mW for 256-channel neural sensing. A smaller microsystem with dimension of 6 mm × 4 mm has been also implanted into rat brain for somatosensory evoked potentials (SSEPs) recording by using contralateral and ipsilateral electrical stimuli with intensity from 0.2 to 1.0 mA, and successfully observed different SSEPs from left somatosensory cortex of a rat.

Topological properties of protein-protein and metabolic interaction networks of Drosophila melanogaster.

The underlying principle governing the natural phenomena of life is one of the critical issues receiving due importance in recent years. A key feature of the scale-free architecture is the vitality of the most connected nodes (hubs). The major objective of this article was to analyze the protein-protein and metabolic interaction networks of Drosophila melanogaster by considering the architectural patterns and the consequence of removal of hubs on the topological parameter of the two interaction systems. Analysis showed that both interaction networks follow a scale-free model, establishing the fact that most real world networks, from varied situations, conform to the small world pattern. The average path length showed a two-fold and a three-fold increase (changing from 9.42 to 20.93 and from 5.29 to 17.75, respectively) for the protein-protein and metabolic interaction networks, respectively, due to the deletion of hubs. On the contrary, the arbitrary elimination of nodes did not show any remarkable disparity in the topological parameter of the protein-protein and metabolic interaction networks (average path length: 9.42+/-0.02 and 5.27+/-0.01, respectively). This aberrant behavior for the two cases underscores the significance of the most linked nodes to the natural topology of the networks.

Variation of fermentation redox potential during cell-recycling continuous ethanol operation.

Fermentation redox potential was monitored during cell-recycling continuous ethanol operation. The cell-recycling system (CRS) was operated using two hollow fibre (HF) membranes (pore sizes 0.20 and 0.65µm) at three dilution rates (0.02, 0.04 and 0.08h-1). Saccharomyces cerevisiae NP 01 were recycled in the fermenter at a recycle ratio of 0.625. Aeration was provided at 2.5vvm for the first 4h and then further supplied continuously at 0.25vvm. As steady state was established, results showed that the fermentation redox potential was lower for processes employing CRS than those without. At the same dilution rates, the sugar utilization and ethanol production with CRS were higher than those without CRS. The highest fermentation efficiency (87.94g/l of ethanol, ∼90% of theoretical yield) was achieved using a 0.2-µm HF membrane CRS at a dilution rate of 0.02h-1. It was found that 7.53-10.07% of the carbon derived from glucose was incorporated into the yeast. Further, at the same dilution rates, yeast in the processes with CRS incorporated less carbon into ethanol than in those grown without CRS. This result suggests that processes involving CRS utilize more carbon for metabolite synthesis than biomass formation. This indicated that the processes with CRS could utilize more carbon for metabolite synthesis than biomass formation.

Redox potential driven aeration during very-high-gravity ethanol fermentation by using flocculating yeast.

Ethanol fermentation requires oxygen to maintain high biomass and cell viability, especially under very-high-gravity (VHG) condition. In this work, fermentation redox potential (ORP) was applied to drive the aeration process at low dissolved oxygen (DO) levels, which is infeasible to be regulated by a DO sensor. The performance and characteristics of flocculating yeast grown under 300 and 260 g glucose/L conditions were subjected to various aeration strategies including: no aeration; controlled aeration at -150, -100 and -50 mV levels; and constant aeration at 0.05 and 0.2 vvm. The results showed that anaerobic fermentation produced the least ethanol and had the highest residual glucose after 72 h of fermentation. Controlled aerations, depending on the real-time oxygen demand, led to higher cell viability than the no-aeration counterpart. Constant aeration triggered a quick biomass formation, and fast glucose utilization. However, over aeration at 0.2 vvm caused a reduction of final ethanol concentration. The controlled aeration driven by ORP under VHG conditions resulted in the best fermentation performance. Moreover, the controlled aeration could enhance yeast flocculating activity, promote an increase of flocs size, and accelerate yeast separation near the end of fermentation.

Metabolite profiles and growth characteristics of Rhizobium meliloti cultivated at different specific growth rates.

Rhizobium meliloti (ATCC 55340) was grown at different specific growth rates in a chemostat apparatus. Metabolic products, relating to the Embden-Meyerhof-Parnas (EMP) pathway and the tricarboxylic acid (TCA) cycle, were measured and quantified to probe the influence of specific growth rate on the distribution of important metabolites. The detection of propionate in the fermentation broth implies that the imbalance of reducing equivalents of FADH(2) and NADH + H(+) resulted in a partially reductive operation of the TCA cycle. Additionally, experimental results show that the specific growth rate plays an essential role in modulating the biomass concentration, the specific substrate uptake rate, the cell length, the specific exopolysaccharide (EPS) production rate, the distribution of EPS molecular weight, and the profiles of carbohydrate and organic acid. The specific EPS production rate (varying from 13.3 to 111 mg EPS/g-DW/h) follows a growth-associated pattern at the specific growth rate ranging from 0.06 to 0.20 h(-1) and switches into non-growth-associated mode when the specific growth rate is over 0.20 h(-1).

Global gene expression analysis of Saccharomyces cerevisiae grown under redox potential-controlled very-high-gravity conditions.

Redox potential (ORP) plays a pivotal role in yeast viability and ethanol production during very-high-gravity (VHG) ethanol fermentation. In order to identify the correlation between redox potential profiles and gene expression patterns, global gene expression of Saccharomyces cerevisiae was investigated. Results indicated that significant changes in gene expression occurred at the periods of 0 - 6 h and 30 - 36 h, respectively. Changes noted in the period of 0 - 6 h were mainly related to carbohydrate metabolism. In contrast, gene expression variation at 30 - 36 h could be attributed primarily to stress response. Although CDC19 was down-regulated, expression of PYK2, PDC6 and ADH2 correlated inversely with ORP. Meanwhile, expression of GPD1 decreased due to the depletion of dissolved oxygen in the fermentation broth, but expression of GPD2 correlated with ORP. Transcription of genes encoding heat shock proteins was characterized by uphill, downhill, valley and plateau expression profiles, accordingly to specific function in stress response. These results highlight the role of ORP in modulating yeast physiology and metabolism under VHG conditions.

Redox potential control and applications in microaerobic and anaerobic fermentations.

Many fermentation products are produced under microaerobic or anaerobic conditions, in which oxygen is undetectable by dissolved oxygen probe, presenting a challenge for process monitoring and control. Extracellular redox potentials that can be detected conveniently affect intracellular redox homeostasis and metabolism, and consequently control profiles of fermentation products, which provide an alternative for monitoring and control of these fermentation processes. This article reviews updated progress in the impact of redox potentials on gene expression, protein biosynthesis and metabolism as well as redox potential control strategies for more efficient production of fermentation products, taking ethanol fermentation by the yeast Saccharomyces under microaerobic conditions and butanol production by the bacterium Clostridium under anaerobic conditions as examples.

Very high gravity ethanol fermentation by flocculating yeast under redox potential-controlled conditions.

BACKGROUND: Very high gravity (VHG) fermentation using medium in excess of 250 g/L sugars for more than 15% (v) ethanol can save energy consumption, not only for ethanol distillation, but also for distillage treatment; however, stuck fermentation with prolonged fermentation time and more sugars unfermented is the biggest challenge. Controlling redox potential (ORP) during VHG fermentation benefits biomass accumulation and improvement of yeast cell viability that is affected by osmotic pressure and ethanol inhibition, enhancing ethanol productivity and yield, the most important techno-economic aspect of fuel ethanol production. RESULTS: Batch fermentation was performed under different ORP conditions using the flocculating yeast and media containing glucose of 201 ± 3.1, 252 ± 2.9 and 298 ± 3.8 g/L. Compared with ethanol fermentation by non-flocculating yeast, different ORP profiles were observed with the flocculating yeast due to the morphological change associated with the flocculation of yeast cells. When ORP was controlled at -100 mV, ethanol fermentation with the high gravity (HG) media containing glucose of 201 ± 3.1 and 252 ± 2.9 g/L was completed at 32 and 56 h, respectively, producing 93.0 ± 1.3 and 120.0 ± 1.8 g/L ethanol, correspondingly. In contrast, there were 24.0 ± 0.4 and 17.0 ± 0.3 g/L glucose remained unfermented without ORP control. As high as 131.0 ± 1.8 g/L ethanol was produced at 72 h when ORP was controlled at -150 mV for the VHG fermentation with medium containing 298 ± 3.8 g/L glucose, since yeast cell viability was improved more significantly. CONCLUSIONS: No lag phase was observed during ethanol fermentation with the flocculating yeast, and the implementation of ORP control improved ethanol productivity and yield. When ORP was controlled at -150 mV, more reducing power was available for yeast cells to survive, which in turn improved their viability and VHG ethanol fermentation performance. On the other hand, controlling ORP at -100 mV stimulated yeast growth and enhanced ethanol production under the HG conditions. Moreover, the ORP profile detected during ethanol fermentation with the flocculating yeast was less fluctuated, indicating that yeast flocculation could attenuate the ORP fluctuation observed during ethanol fermentation with non-flocculating yeast.

Ageing vessel configuration for continuous redox potential-controlled very-high-gravity fermentation.

The development of continuous very-high-gravity (VHG) fermentation is hindered by ineffective glucose uptake in order to result in zero discharge in the effluent stream. To overcome the problem, we proposed a continuous redox potential-controlled fermentation configuration, consisting of a Chemostat vessel connected with two ageing vessels installed in parallel, and the relevant design criteria are also specified. The Chemostat vessel is subjected to redox potential control to maintain yeast viability, and the ageing vessels are used to completely utilize glucose before discharging to next process unit. Two ageing vessels are scheduled alternatively, resulting in continuously-like operation. The size of ageing vessel is governed by the Chemostat size, dilution rate and filling time. The guideline to choose proper dilution rate is provided and the selection criterion of the proposed continuous configuration over batch fermentation is derived. The excess ethanol produced by the proposed continuous configuration over batch fermenter is quantified. As an illustration, a bio-ethanol plant is typically operated 8000 h per annum and the downtime between batches is 6h. Given that the fermenter size of 100 m(3) for both batch fermenter and Chemostat vessel, and glucose fed at 300 g/l, if the proposed continuous redox potential-controlled fermentation configuration (operated at 0.028 h(-1) and controlled at -50 mV) is selected, it will take 191 h for this configuration to outperform the batch counterpart, and the excess amount of ethanol being produced will be 1142 t.

Development of redox potential-controlled schemes for very-high-gravity ethanol fermentation.

Fermentation redox potential reflects the momentary physiological status of organisms. Controlling redox potential can modulate the redistribution of intracellular metabolic flux to favor the formation of the desired metabolite. Accordingly, we have developed three redox potential-controlled schemes to maximize their effects on the very-high-gravity (VHG) ethanol fermentation. They are aeration-controlled scheme (ACS), glucose-controlled feeding scheme (GCFS), and combined chemostat and aeration-controlled scheme (CCACS). These schemes can maintain fermentation redox potential at a prescribed level (i.e., -50, -100, and -150 mV) by supplementing sterile air, fresh glucose media, or a combination of sterile air and fresh glucose media into a fermenter to counteract the decline of redox potential due to yeast growth. When ACS was employed, the fermentation efficiency at -150 mV is superior to the other two redox potential levels especially when the initial glucose concentration is higher than 250 g/l. The redox potential-controlled period for ACS, GCFS, and CCACS at -150 mV under the same 200 g glucose/l condition was 2.5, 21.7 and 64.6h and the corresponding fermentation efficiency was 85.9,89.3 and 92.7%, respectively.

Development of t(50) and its application to evaluate very-high-gravity ethanol fermentation.

A three-parameter logistic growth model was modified to monitor the glucose uptake profile of yeast during very-high-gravity (VHG) ethanol fermentation. The modified model was used to define t(50) as a quantifier to differentiate among various fermentation conditions. There are two types of t(50); t(50)(g) is the time required to convert 50% of the initial glucose, and t(50)(e) is the time required to produce half of the final ethanol. A 2(4) factorial experimental design was implemented to illustrate the applicability of using t(50) to isolate active ingredients in VHG growth media. The analytical results obtained from the experimental design and from a modified model were compared, which demonstrated that t(50) could serve the proposed objectives. A shorter t(50) implies a faster fermentation. A tailing of the ethanol profile after t(50)(e) indicates that there is an inhibitory effect imposed on yeast, i.e., the stronger the tailing in the ethanol profile, the stronger the inhibitory effect. When t(50) is equal to or near to the halftime of the total course of the fermentation, a bell-shaped curve was seen for the glucose uptake rate or for the ethanol production rate, indicating that the inhibitory effect exerted on yeast was evenly distributed.