Self-reproduction and doubling time limits of different cellular subsystems.

Ribosomes which can self-replicate themselves practically autonomously in beneficial physicochemical conditions have been recognized as the central organelles of cellular self-reproduction processes. The challenge of cell design is to understand and describe the rates and mechanisms of self-reproduction processes of cells as of coordinated functioning of ribosomes and the enzymatic networks of different functional complexity that support those ribosomes. We show that doubling times of proto-cells (ranging from simplest replicators up to those reaching the size of E. coli) increase rather with the number of different cell component species than with the total numbers of cell components. However, certain differences were observed between cell components in increasing the doubling times depending on the types of relationships between those cell components and ribosomes. Theoretical limits of doubling times of the self-reproducing proto-cells determined by the molecular parameters of cell components and cell processes were in the range between 6-40 min.

Protein Turnover in Epithelial Cells and Mucus along the Gastrointestinal Tract Is Coordinated by the Spatial Location and Microbiota.

The gastrointestinal tract is covered by a single layer of epithelial cells that, together with the mucus layers, protect the underlying tissue from microbial invasion. The epithelium has one of the highest turnover rates in the body. Using stable isotope labeling, high-resolution mass spectrometry, and computational analysis, we report a comprehensive dataset of the turnover of more than 3,000 and the expression of more than 5,000 intestinal epithelial cell proteins, analyzed under conventional and germ-free conditions across five different segments in mouse intestine. The median protein half-life is shorter in the small intestine than in the colon. Differences in protein turnover rates along the intestinal tract can be explained by distinct physiological and immune-related functions between the small and large intestine. An absence of microbiota results in an approximately 1 day longer protein half-life in germ-free animals.

Model-based metabolism design: constraints for kinetic and stoichiometric models.

The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms. Some constraints (mass balance, energy balance, and steady-state assumption) serve as a basis for many modelling approaches. There are others (total enzyme activity constraint and homeostatic constraint) proposed decades ago, but which are frequently ignored in design development. Several new approaches of cellular analysis have made possible the application of constraints like cell size, surface, and resource balance. Constraints for kinetic and stoichiometric models are grouped according to their applicability preconditions in (1) general constraints, (2) organism-level constraints, and (3) experiment-level constraints. General constraints are universal and are applicable for any system. Organism-level constraints are applicable for biological systems and usually are organism-specific, but these constraints can be applied without information about experimental conditions. To apply experimental-level constraints, peculiarities of the organism and the experimental set-up have to be taken into account to calculate the values of constraints. The limitations of applicability of particular constraints for kinetic and stoichiometric models are addressed.

Step-wise temperature decreasing cultivates a biofilm with high nitrogen removal rates at 9°C in short-term anammox biofilm tests.

The anaerobic ammonium oxidation (anammox) and nitritation-anammox (deammonification) processes are widely used for N-rich wastewater treatment. When deammonification applications move towards low temperature applications (mainstream wastewater has low temperature), temperature effect has to be studied. In current research, in a deammonification moving bed biofilm reactor a maximum total nitrogen removal rate (TNRR) of 1.5 g N m(-2 )d(-1) (0.6 kg N m(-3 )d(-1)) was achieved. Temperature was gradually lowered by 0.5°C per week, and a similar TNRR was sustained at 15°C during biofilm cultivation. Statistical analysis confirmed that a temperature decrease from 20°C down to 15° did not cause instabilities. Instead, TNRR rose and treatment efficiency remained stable at lower temperatures as well. Quantitative polymerase chain reaction analyses showed an increase in Candidatus Brocadia quantities from 5 × 10(3) to 1 × 10(7) anammox gene copies g(-1) total suspended solids (TSS) despite temperature lowered to 15°C. Fluctuations in TNRR were rather related to changes in influent [Formula: see text] concentration. To study the short-term effect of temperature on the TNRR, a series of batch-scale experiments were performed which showed sufficient TNRRs even at 9-15°C (1.24-3.43 mg N g(-1 )TSS h(-1), respectively) with anammox temperature constants (Q10) ranging 1.3-1.6. Experiments showed that a biofilm adapted to 15°C can perform N-removal most sufficiently at temperatures down to 9°C as compared with biofilm adapted to higher temperature. After biomass was adapted to 15°C, the decrease in TNRR in batch tests at 9°C was lower (15-20%) than that for biomass adapted to 17-18°C.

Start-up of low-temperature anammox in UASB from mesophilic yeast factory anaerobic tank inoculum.

Robust start-up of the anaerobic ammonium oxidation (anammox) process from non-anammox-specific seeding material was achieved by using an inoculation with sludge-treating industrial [Formula: see text]-, organics- and N-rich yeast factory wastewater. N-rich reject water was treated at 20°C, which is significantly lower than optimum treatment temperature. Increasing the frequency of biomass fluidization (from 1-2 times per day to 4-5 times per day) through feeding the reactor with higher flow rate resulted in an improved total nitrogen removal rate (from 100 to 500 g m(-3)d(-1)) and increased anammox bacteria activity. As a result of polymerase chain reaction (PCR) tests, uncultured planctomycetes clone 07260064(4)-2-M13-_A01 (GenBank: JX852965) was identified from the biomass taken from the reactor. The presence of anammox bacteria after cultivation in the reactor was confirmed by quantitative PCR (qPCR); an increase in quantity up to ∼2×10(6) copies g VSS(-1) during operation could be seen in qPCR. Statistical modelling of chemical parameters revealed the roles of several optimized parameters needed for a stable process.

Protein turnover forms one of the highest maintenance costs in Lactococcus lactis.

Protein turnover plays an important role in cell metabolism by regulating metabolic fluxes. Furthermore, the energy costs for protein turnover have been estimated to account for up to a third of the total energy production during cell replication and hence may represent a major limiting factor in achieving either higher biomass or production yields. This work aimed to measure the specific growth rate (µ)-dependent abundance and turnover rate of individual proteins, estimate the ATP cost for protein production and turnover, and compare this with the total energy balance and other maintenance costs. The lactic acid bacteria model organism Lactococcus lactis was used to measure protein turnover rates at µ = 0.1 and 0.5 h(-1) in chemostat experiments. Individual turnover rates were measured for ~75% of the total proteome. On average, protein turnover increased by sevenfold with a fivefold increase in growth rate, whilst biomass yield increased by 35%. The median turnover rates found were higher than the specific growth rate of the bacterium, which suggests relatively high energy consumption for protein turnover. We found that protein turnover costs alone account for 38 and 47% of the total energy produced at µ = 0.1 and 0.5 h(-1), respectively, and gene ontology groups Energy metabolism and Translation dominated synthesis costs at both growth rates studied. These results reflect the complexity of metabolic changes that occur in response to changes in environmental conditions, and signify the trade-off between biomass yield and the need to produce ATP for maintenance processes.

Nitritating-anammox biomass tolerant to high dissolved oxygen concentration and C/N ratio in treatment of yeast factory wastewater.

Maintaining stability of low concentration (< 1 g L(-1)) floccular biomass in the nitritation-anaerobic ammonium oxidation (anammox) process in the sequencing batch reactor (SBR) system for the treatment of high COD (> 15,000 mg O2 L(-1)) to N (1680 mg N L(-1)) ratio real wastewater streams coming from the food industry is challenging. The anammox process was suitable for the treatment of yeast factory wastewater containing relatively high and abruptly increased organic C/N ratio and dissolved oxygen (DO) concentrations. Maximum specific total inorganic nitrogen (TIN) loading and removal rates applied were 600 and 280 mg N g(-1) VSS d(-1), respectively. Average TIN removal efficiency over the operation period of 270 days was 70%. Prior to simultaneous reduction of high organics (total organic carbon > 600mg L(-1)) and N concentrations > 400 mg L(-1), hydraulic retention time of 15 h and DO concentrations of 3.18 (+/- 1.73) mg O2 L(-1) were applied. Surprisingly, higher DO concentrations did not inhibit the anammox process efficiency demonstrating a wider application of cultivated anammox biomass. The SBR was fed rapidly over 5% of the cycle time at 50% volumetric exchange ratio. It maintained high free ammonia concentration, suppressing growth of nitrite-oxidizing bacteria. Partial least squares and response surface modelling revealed two periods of SBR operation and the SBR performances change at different periods with different total nitrogen (TN) loadings. Anammox activity tests showed yeast factory-specific organic N compound-betaine and inorganic N simultaneous biodegradation. Among other microorganisms determined by pyrosequencing, anammox microorganism (uncultured Planctomycetales bacterium clone P4) was determined by polymerase chain reaction also after applying high TN loading rates.

Nutritional requirements and media development for Lactococcus lactis IL1403.

Lactic acid bacteria are extensively used in food technology and for the production of various compounds, but they are fastidious in nutrient requirements. In order to elucidate the role of each component precisely, defined multicomponent media are required. This study focuses on determining nutrient auxotrophies and minimizing media components (amino acids, vitamins, metal ions, buffers and additional compounds) for the cultivation of Lactococcus lactis subsp. lactis IL1403, using microtitre plates and test tubes. It was shown that glutamine and asparagine were the most important media components for achieving higher biomass yields while the branched-chain amino acids were necessary to increase specific growth rate. The amino acid and glucose ratio was reduced to achieve minimal residual concentration of amino acids in the medium after the growth of cells, whereas the specific growth rate and biomass yield of cells were not considerably affected. As the percentage of each consumed amino acid compared to initial amount is larger than measurement error, these optimized media are important for achieving more precise data about amino acid utilization and metabolism.

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins.

Regulation levels of the gene expression cascade controlling protein levels and metabolic fluxes for cells to achieve faster growth have not been elaborated in acceptable detail. Furthermore, there is need for specific growth rate (µ) dependent absolute quantitative transcriptome and proteome data to understand the molecular relationships for enabling cells to modify µ. We address these questions, for the first time, by presenting regulatory strategies for more efficient metabolism of Escherichia coli at higher µ by statistical covariance analysis of genome-wide intracellular mRNA and protein concentrations coupled to metabolic flux analysis in the steady state range of µ = 0.11-0.49 h(-1). Our analyses show dominating post-transcriptional control of protein abundances and post-translational control of flux rates. On average, E. coli achieved five-times faster growth through 3.7-fold increase of apparent catalytic rates of enzymes (kapp) and 2.5-fold increased translation rates, demonstrating the relevance of post-translational regulation for increasing flux throughput. Interestingly, pathways carrying the highest flux showed both high protein abundance and kapp values. Furthermore, co-regulation analysis of enzymatic capacities revealed tightly coupled regulatory dependencies of protein synthesis and RNA precursor synthesis, substrate utilization, biosynthetic and energy generation pathways carrying the highest flux. We also observed metabolic pathway and COG specific protein and metabolic flux control levels, protein expression costs and genome-wide principles for translation efficiency and transcription unit polarity. This work contributes to the much needed quantitative understanding of coordinated gene expression regulation and metabolic flux control. Our findings will also advance modeling and metabolic engineering of industrial strains.

Increased biomass yield of Lactococcus lactis by reduced overconsumption of amino acids and increased catalytic activities of enzymes.

Steady state cultivation and multidimensional data analysis (metabolic fluxes, absolute proteome, and transcriptome) are used to identify parameters that control the increase in biomass yield of Lactococcus lactis from 0.10 to 0.12 C-mol C-mol(-1) with an increase in specific growth rate by 5 times from 0.1 to 0.5 h(-1). Reorganization of amino acid consumption was expressed by the inactivation of the arginine deiminase pathway at a specific growth rate of 0.35 h(-1) followed by reduced over-consumption of pyruvate directed amino acids (asparagine, serine, threonine, alanine and cysteine) until almost all consumed amino acids were used only for protein synthesis at maximal specific growth rate. This balanced growth was characterized by a high glycolytic flux carrying up to 87% of the carbon flow and only amino acids that relate to nucleotide synthesis (glutamine, serine and asparagine) were consumed in higher amounts than required for cellular protein synthesis. Changes in the proteome were minor (mainly increase in the translation apparatus). Instead, the apparent catalytic activities of enzymes and ribosomes increased by 3.5 times (0.1 vs 0.5 h(-1)). The apparent catalytic activities of glycolytic enzymes and ribosomal proteins were seen to follow this regulation pattern while those of enzymes involved in nucleotide metabolism increased more than the specific growth rate (over 5.5 times). Nucleotide synthesis formed the most abundant biomonomer synthetic pathway in the cells with an expenditure of 6% from the total ATP required for biosynthesis. Due to the increase in apparent catalytic activity, ribosome translation was more efficient at higher growth rates as evidenced by a decrease of protein to mRNA ratios. All these effects resulted in a 30% decrease of calculated ATP spilling (0.1 vs 0.5 h(-1)). Our results show that bioprocesses can be made more efficient (using a balanced metabolism) by varying the growth conditions.

In situ determination of nerve agents in various matrices by portable capillary electropherograph with contactless conductivity detection.

Rapid, efficient and robust methods for sampling and extracting genuine nerve agents sarin, soman and VX were developed for analyzing these compounds on various solid matrices, such as concrete, tile, soil and vegetation. A portable capillary electrophoretic (CE) system with contactless conductometric detection was used for the in situ analysis of the extracted samples. A 7.5 mM MES/HIS-based separation electrolyte accomplished the analysis of target analytes in less than 5 min. The overall duration of the process including instrument start-up, sample extraction and analysis was less than 10 min, which is the fastest screening of nerve agents achieved with liquid phase separation methods to date. The procedure can easily be performed by a person in a protective suit and is therefore suitable for real-life applications. The CE results were validated by an independent GC-MS method and a satisfactory correlation was obtained. The use of a proper sampling strategy with two internal standards and "smart" data-processing software can overcome the low reproducibility of CE. This has a significant impact on the potential acceptance of portable CE instrumentation for the detection and analysis of genuine chemical warfare agents (CWA).

Thermal marks as a signal processing aid for a portable capillary electropherograph.

The interpretation of raw signals in capillary CE can be challenging if there are unknown peaks, or the signal is corrupt due to baseline fluctuations, EOF velocity drift, etc. Signal processing could be required before results can be interpreted. A suite of signal processing algorithms has been developed for CE data analysis, specifically for use in field experiments for the detection of nerve agents using portable CE instruments. Everything from baseline correction and electropherogram alignment to peak matching and identification is included in these programs. Baseline correction is achieved by interpolating a new baseline according to points found using all local extremes, by applying an appropriate outliers test. Irreproducible migration times are corrected by compensating for EOF drift, measured with the aid of thermal marks. Thermal marks are small disturbances in the capillary created by punctual heating that move with the velocity of EOF. Peaks in the sample electropherogram are identified using a fuzzy matching algorithm, by comparing peaks from the sample electropherogram to peaks from a reference electropherogram.

Improving precision of manual hydrodynamic injection in capillary electrophoresis with contactless conductivity detection.

Reproducible injection in capillary electrophoresis has been difficult to achieve with manual injection techniques using simple injection devices, such as gravity injection (siphoning) or hydrodynamic sample splitting. We demonstrate that the injection reproducibility can be improved using very simple means. With hydrodynamic sample splitter, a passive micro-metering valve can be inserted in-line to regulate the sample flow rate through the splitter interface. A significant improvement of both reproducibility and repeatability was achieved. The reproducibility of RSD of the peak areas improved from 25.4% to 4.4%, while the repeatability was below 4.1% when micro-metering valve was used. Additional simple correction that can be used to further improve the variability of injected sample volumes in any hydrodynamic injection mode in CE with conductivity detection was proposed and verified. The measured EOF peak can serve as a simple indicator of the injected volume and can be effectively used for additional correction. By a linear function between the injection volume and the peak area of the EOF, the RSD values of peak areas for both manual gravity injection and hydrodynamic sample splitter were further improved below 2% RSD. The linearity of the calibration curve was also significantly improved. The proposed correction works even with slight differences in matrix composition, as demonstrated on the analysis aqueous soil extract of model mixture of five nerve agent degradation products.

A portable capillary electropherograph equipped with a cross-sampler and a contactless-conductivity detector for the detection of the degradation products of chemical warfare agents in soil extracts.

A fully portable CE device equipped with a capacitively coupled contactless-conductivity detector and a cross-injection device is put to the test in laboratory conditions. The portable device is capable of working on batteries for at least 4 h. After that, its performance is strongly affected by the drop in the high-voltage output and analysis may be interrupted if its length exceeds a reasonable time. The concentration of the BGE affects both ionic strength and conductivity. Choosing an optimal concentration of BGE is therefore about finding a good compromise between selectivity and sensitivity. All experiments were performed using a mixture of histidine and MES with a concentration of 15 mM as BGE. The performance of the cross-injection device is optimized by the use of internal standards. Satisfactory reproducibility is gained as the RSD of peak areas is reduced to 8% or less. LODs for different phosphonic acids are in the range of 2.5-9.7 microM. For the analysis of adsorption of phosphonic acids in sand and loamy soil samples, calibration curves are constructed. Linearity in a measured concentration range of 10-100 microM is excellent, as the squares of correlation constants are approximately 1. The concentration analysis of phosphonic acids in soil extracts demonstrates that their adsorption curves in sand and loamy soil follow different adsorption isotherms.

Monitoring of the electroosmotic flow of ionic liquid solutions in non-aqueous media using thermal marks.

The possibility of applying a new method employing thermal marks to measuring the rate of the electroosmotic flow (EOF) in non-aqueous capillary electrophoresis (NACE) was investigated. The thermal marks were monitored by using a contactless conductivity detection. During one experiment and in between the series of experiments the reproducibility of the method was excellent. The EOF rate was measured 4-7 times during one experiment, the precision of measurement being around 0.5%. In this study, the influence of 1-butyl-3-methyl-imidazolium salts in organic solvents on the rate of the EOF was investigated. Various organic solvents were mixed with an ionic liquid of various concentrations and the EOF rate was measured using thermal marks. The accuracy of the method was compared with that of the neutral marker one. Five benzoic acid derivatives were separated while the EOF was monitored. The relative standard deviations of the corrected effective mobilities of the above analytes were in the range of 1.0-6.1%.