Non-growing Phase Research Articles

Growth Phase Contribution in Dictating Drug Transport and Subcellular Accumulation inside Escherichia coli.

Depending upon nutrient availability, bacteria transit to multiple growth phases. The transition from the active to nongrowing phase results in reduced drug efficacy and, in some cases, even multidrug resistance. However, due to multiple alterations in the cell envelope, probing the drug permeation kinetics during growth phases becomes perplexing, especially across the Gram-negative bacteria's complex dual membrane envelope. To advance the understanding of drug permeation during the life cycle of Gram-negative bacteria, we sought to address two underlying objectives: (a) how changes are occurring inside the bacterial envelope during growth and (b) how the drug permeation and accumulation vary across both the membranes and in subcellular compartments during growth. Both objectives are met with the help of nonlinear optical technique second-harmonic generation spectroscopy (SHG). Specifically, using SHG, we probed the transport kinetics and accumulation of a quaternary ammonium compound (QAC), malachite green, inside Escherichia coli in various growth phases. Further insight about another QAC molecule, propidium iodide, is accomplished using fluorescence microscopy. Results indicate that actively growing cells have faster drug transport and higher cytoplasmic accumulation than slow- or nongrowing cells. In this regard, the rpoS gene plays a crucial role in limiting drug transport across the saturation phase cultures. Moreover, within a particular growth phase, membrane permeability undergoes gradual changes much before the subsequent growth phase commences. These outcomes signify the importance of reporting the growth phase and rate in drug efficacy studies.

The Conjugation Window in an Escherichia coli K-12 Strain with an IncFII Plasmid.

Many studies have examined the role that conjugation plays in disseminating antibiotic resistance genes in bacteria. However, relatively little research has quantitively examined and modeled the dynamics of conjugation under growing and nongrowing conditions beyond a couple of hours. We therefore examined growing and nongrowing cultures of Escherichia coli over a 24-h period to understand the dynamics of bacterial conjugation in the presence and absence of antibiotics with pUUH239.2, an IncFII plasmid containing multiantibiotic- and metal-resistant genes. Our data indicate that conjugation occurs after E. coli cells divide and before they have transitioned to a nongrowing phase. The result is that there is only a small window of opportunity for E. coli to conjugate with pUUH239.2 under both growing and nongrowing conditions. Only a very small percentage of the donor cells likely are capable of even undergoing conjugation, and not all transconjugants can become donor cells due to molecular regulatory controls and not being in the correct growth phase. Once a growing culture enters stationary phase, the number of capable donor cells decreases rapidly and conjugation slows to produce a plateau. Published models did not provide accurate descriptions of conjugation under nongrowing conditions. We present here a modified modeling approach that accurately describes observed conjugation behavior under growing and nongrowing conditions.IMPORTANCE There has been growing interest in horizontal gene transfer of antibiotic resistance plasmids as the antibiotic resistance crisis has worsened over the years. Most studies examining conjugation of bacterial plasmids focus on growing cultures of bacteria for short periods, but in the environment, most bacteria grow episodically and at much lower rates than in the laboratory. We examined conjugation of an IncFII antibiotic resistance plasmid in E. coli under growing and nongrowing conditions to understand the dynamics of conjugation under which the plasmid is transferred. We found that conjugation occurs in a narrow time frame when E. coli is transitioning from a growing to nongrowing phase and that the conjugation plateau develops because of a lack of capable donor cells in growing cultures. From an environmental aspect, our results suggest that episodic growth in nutrient-depleted environments could result in more conjugation than sustained growth in a nutrient rich environment.

Small-Molecule Inhibition of Bacterial Biofilm.

Antibiotic resistance is a massive and serious threat to human welfare and healthcare. Apart from being genetically resistant to antibiotics, the other important mechanism by which bacteria can evade antibiotics is multidrug tolerance. Here cells enter into a transiently nongrowing phase, and as a result, latent infection remains inside the host, causing disease recurrence. Biofilm-derived antibiotic tolerance and persister formation of the pathogenic bacteria inside the host remain a serious issue of treatment failure and recurrent chronic infection in the case of all major pathogens. As a result, new chemotherapeutic agents are sought that specifically inhibit biofilm formation or maturation as well as cause the dispersion of mature biofilms, thus allowing the conventional drugs to kill sensitive cells residing inside. This mini-review attempts to analyze different small-molecule-based chemical approaches that have been used to enable bacterial biofilm inhibition at different steps of maturation.

Temporal inactivation enhances robustness in an evolving system.

We study the robustness of an evolving system that is driven by successive inclusions of new elements or constituents with m random interactions to older ones. Each constitutive element in the model stays either active or is temporarily inactivated depending upon the influence of the other active elements. If the time spent by an element in the inactivated state reaches TW, it gets extinct. The phase diagram of this dynamic model as a function of m and TW is investigated by numerical and analytical methods and as a result both growing (robust) as well as non-growing (volatile) phases are identified. It is also found that larger time limit TW enhances the system’s robustness against the inclusion of new elements, mainly due to the system’s increased ability to reject ‘falling-together’ type attacks. Our results suggest that the ability of an element to survive in an unfavourable situation for a while, either as a minority or in a dormant state, could improve the robustness of the entire system.

Modeling of growth kinetics for an isolated marine bacterium, Oceanimonas sp. BPMS22 during the production of a trypsin inhibitor

Protease inhibitors significantly control physiologically relevant protease activities. Protease inhibitors from marine microbial sources are unique due to their rough living environmental conditions. In the present study, a protein protease inhibitor (PI) was produced from marine Oceanimonas sp. BPMS22. Seven different media were screened for the growth of the bacterium and production of PI. Different carbon and nitrogen sources were screened and optimized for the specific protease inhibitor activity. Three different growth models were checked for the best fit of the bacterial growth. A modified Gompertz model was selected as the best model for the growth of Oceanimonas sp. BPMS22 with the maximum specific growth rate of 0.165 hr−1 and doubling time of 4.2 hr. The production of PI takes place during the non-growing phase of the bacterial growth. A kinetic model for the production of PI during non-growing phase was used for studying various process parameters. From the model, the maximum trypsin inhibitor formation rate of 0.3802 IU per mg of biomass per hour was observed at 49.91 hr.

Identifying genomic targets for protein over-expression by \u201comics\u201d analysis of Quiescent Escherichia coli cultures

BackgroundA cellular stress response is triggered upon induction of recombinant protein expression which feedback inhibits both growth as well as protein synthesis. In order to separate these two effects, it was decided to study “quiescent cultures” which continue to be metabolically active and express recombinant proteins even after growth cessation. The idea was to identify and up-regulate genes which are responsible for protein synthesis in the absence of growth. This would ensure that, even if growth were adversely affected post induction, there would be no attendant reduction in the protein expression capability of the cells. This strategy allowed us to design host strains, which did not grow better post induction but had significantly higher levels of protein expression.ResultsA quiescent Escherichia coli culture, which is able to sustain recombinant protein expression in the absence of growth, was analyzed by transcriptomic and proteomic profiling. Many genes involved in carbon utilization, biosynthesis of building blocks and stress protection were found to be up-regulated in the quiescent phase. Analysis of the global regulators showed that fis, which tends to get down-regulated as the cells enter stationary phase, remained up-regulated throughout the non-growing quiescent phase. The downstream genes regulated by fis like carB, fadB, nrfA, narH and queA were also up-regulated in the quiescent phase which could be the reason behind the higher metabolic activity and protein expression ability of these non-growing cells. To test this hypothesis, we co-expressed fis in a control culture expressing recombinant l-asparaginase and observed a significantly higher buildup of l-asparaginase in the culture medium.ConclusionsThis work represents an important breakthrough in the design of a superior host platform where a gene not directly associated with protein synthesis was used to generate a phenotype having higher protein expression capability. Many alternative gene targets were also identified which may have beneficial effects on expression ability.

A mean-field analysis of the simple model of evolving open systems

A recently reported mechanism of letting evolving systems grow only if the interactions in it is moderately sparse is reviewed and examined. It is shown that the mean field analysis, which is known to give a good simple understanding for this transition from growing to non-growing phase but with about 30% difference in its position, is well improved by taking only mean field type information from the simulation of the original model. This supports the validity of the understanding for the mechanism of the transition, obtained from the mean field analysis. The transition stems from an essential balance of two effects: although having more interactions makes each node robust, it also increases the impact of the loss of a node.

Use of non-growing Lactococcus lactis cell suspensions for production of volatile metabolites with direct relevance for flavour formation during dairy fermentations.

BackgroundLactococcus lactis is a lactic acid bacterium that has been used for centuries in the production of a variety of cheeses, as these bacteria rapidly acidify milk and greatly contribute to the flavour of the fermentation end-products. After a short growth phase during cheese ripening L. lactis enters an extended non-growing state whilst still strongly contributing to amino acid-derived flavour formation. Here, a research approach is presented that allows investigation of strain- and amino acid-specific flavour formation during the non-growing state.ResultsNon-growing cells of five selected L. lactis strains were demonstrated to degrade amino acids into flavour compounds that are relevant in food fermentations and differs greatly from production of flavour compounds using growing cells. As observed earlier in other research set-ups and with other microorganisms, addition of NADH, α-ketoglutarate and pyridoxal-5-phosphate was demonstrated to be essential for optimal flavour formation, suggesting that intracellular pools of these substrates are too low for the significant production of the flavour compounds. Production of flavours during the non-growing phase strongly depends on the individual amino acids that were supplied, on the presence of other amino acids (mixtures versus single compounds), and on the strain used. Moreover, we observed that the plasmid-free model strains L. lactis MG1363 and IL1403 produce relatively low amounts of flavour components under the various conditions tested.ConclusionsBy using this simplified and rapid approach to study flavour formation by non-growing lactic acid bacteria, lengthy ripening periods are no longer required to assess the capacity of strains to produce flavours in the long, non-growing state of dairy fermentation. In addition, this method also provides insight into the conversion of single amino acids versus the conversion of a mixture of amino acids as produced during protein degradation. The generated results are complementary to earlier generated datasets using growing cells, allowing assessment of the full flavour forming potential of strains used as starter cultures in industrial food fermentation processes.

Use of a continuous multistage bioreactor to mimic winemaking fermentation

Continuous fermentation set-ups are of great interest for studying the physiology of microorganisms. In winemaking conditions, yeasts go through a growth phase and a stationary phase during which more than half of the sugar is fermented. A comprehensive study of wine-yeast physiology must therefore include yeasts in a non-growing phase. This condition is impossible to achieve within a chemostat, which led us to design a multi-stage fermentation device. In this study, we evaluated the ability of such a device to reproduce, in a series of steady states, the conditions of batch fermentation. Two-stage and four-stage fermentations were carried out with two different strains of Saccharomyces cerevisiae. The main characteristics of the fermentation process (biomass growth, by-product content of the medium) were compared with those observed in batch mode at the same stage of fermentation, which was defined by glucose uptake. The four-stage configuration showed a better ability to reproduce batch fermentation characteristics than the two-stage set-up. It also allowed to uncouple the variations of environmental parameters and proved to be a promising tool to gain new insights into yeast metabolism during alcoholic fermentation.

On the non-equilibrium phase transition in evaporation–deposition models

We study a system of diffusing–aggregating particles with deposition and evaporation ofmonomers. By combining theoretical and numerical methods, we establish a clearerunderstanding of the non-equilibrium phase transition known to occur in such systems. Thetransition is between a growing phase in which the total mass increases for alltime and a non-growing phase in which the total mass is bounded. In addition toderiving rigorous bounds on the position of the transition point, we show that thegrowing phase is in the same universality class as diffusion–aggregation models withdeposition but no evaporation. In this regime, the flux of mass in mass space becomesasymptotically constant (as a function of mass) at large times. The magnitude ofthis flux depends on the evaporation rate but the fact that it is asymptoticallyconstant does not. The associated constant flux relation exactly determines thescaling of the two-point mass correlation function with mass in all dimensionswhile higher order mass correlation functions exhibit nonlinear multi-scaling indimension less than two. If the deposition rate is below some critical value, a differentstationary state is reached at large times characterized by a global balance betweenevaporation and deposition with a scale-by-scale balance between the mass fluxes dueto aggregation and evaporation. Both the mass distribution and the flux decayexponentially in this regime. Finally, we develop a scaling theory of the model near thecritical point, which yields non-trivial scaling laws for the critical two-point masscorrelation function with mass. These results are well supported by numericalmeasurements.

The preshaving protocol in body hair-to-scalp transplant to identify hair in anagen phase

Introduction:The use of body donor hair for transplanting to the bald scalp is termed body hair transplant. In recent times, robust body hair has been used as an adjunct to scalp donor hair to augment the donor hair supply. A large percentage of body hair are in telogen and, as single hair units.Aims:To devise a non invasive protocol to identify the body donor hair in anagen phase prior to extraction.Materials and Methods:Hairs are shaved flush with the skin, four days prior to extraction. On fourth day, the actively growing hair follicles as well as non growing hairs were extracted and phase of hair growth determined. Results: Nineteen out 22 extracted hair follicles in nongrowing phase were found to be the telogen phase.Conclusion:Preshaving the body donor areas is a simple non invasive method of isolating the hair in anagen phase.

Tobacco pollen tubes as cellular models for ion dynamics: improved spatial and temporal resolution of extracellular flux and free cytosolic concentration of calcium and protons using pHluorin and YC3.1 CaMeleon

The presence of both calcium (Ca2+) and proton (H+) apical gradients is necessary for polarized cell elongation to occur in pollen tubes. So far, most of these studies have been carried out in lily pollen tubes, using chemical probes. Yet, lily is a refractory model for molecular genetics, with no easy protocol available for the construction of stable transgenic lines. Tobacco, however, is well suited for both transformation and cell biology, with sexual organs that are accessible, easy to handle and visualize. Pollen tubes are in an ideal size range for sub-cellular imaging analyses using modern microscopy techniques. Ion homeostasis in tobacco pollen tubes has not been precisely characterized so far. Here, we characterize the H+ and Ca2+ spatial and temporal patterns in tobacco pollen tubes by the use of two fluorescent genetic probes, pHluorin and the YC3.1 yellow CaMeleon, and direct measurement of extracellular flux by ion-sensitive vibrating probes. A distinct 0.4 pH unit acidic gradient was found to stretch from the tip up to 40 μm into the tube shank. This gradient intensity displayed 1–4 min period oscillations and is reduced in the non-growing phase of an oscillatory cycle. Furthermore, sub-membrane and sub-apical alkaline domains were detected. Extracellular H+ fluxes oscillated between 10 and 40 pmol cm−2 s−1. Fourier and continuous wavelet analyses showed tubes with one or two major oscillatory components in both extra and intracellular H+ oscillations. Cytosolic Ca2+ was imaged by confocal microscopy, showing a V-shaped 40 μm gradient extending from the tip, from 0.2 to 1.0 μM, which oscillates with a 1–4 min period, but with only one major oscillatory component. Extracellular Ca2+ fluxes oscillate in most pollen tubes, between 2 and 50 pmol cm−2 min−1 and, like in H+, with one or two major oscillatory peaks. A combination of confocal and widefield microscopy showed that H+ and Ca2+ displayed different patterns and shapes inside the cell, sometimes suggesting a structurally complementary role for these 2 second messengers in the growth process. These data suggest that fluxes at the apex of the pollen tube are directly responsible for establishment and maintenance of the gradient.

Pharmacodynamic Effects of Telavancin against Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Strains in the Presence of Human Albumin or Serum and in an In Vitro Kinetic Model

Telavancin is a novel bactericidal lipoglycopeptide with multiple mechanisms of action against gram-positive pathogens. The aim of this study was to describe the dynamics of the antimicrobial effect of telavancin against two strains of Staphylococcus aureus (methicillin susceptible and methicillin resistant) in an in vitro kinetic model with simulated human pharmacokinetics. Also, static experiments were performed to determine the rate and extent of killing by telavancin in the presence and absence of human albumin and human serum. Experiments in broth and in nutrient-depleted medium were performed to study the rate and extent of killing by telavancin of bacteria in different growth phases. In the in vitro kinetic model regrowth was noted at 24 h for both strains when exposed to initial concentrations below 5 mg/liter. There was a >3-log(10) killing at all concentrations from 0.5x MIC and above at 24 h both in broth and in the presence of 40-g/liter human albumin. In contrast to the methicillin-susceptible strain, the methicillin-resistant strain in 40-g/liter human albumin showed a regrowth at concentrations of 0.5x MIC and 1x MIC at 24 h. At all the other concentrations >3-log(10) killing was seen at 24 h. Concordant results were seen in 50% human serum. At a target area under the curve/MIC ratio of 50 (corresponding to the human dose of 10 mg/kg of body weight, administered intravenously), >3-log(10) killing was observed at 6 to 8 h. Unlike most antibiotics, telavancin was able to kill both strains in a nongrowing phase.

Benzo(a)pyrene-induced changes in p53 and related proteins in mouse skin.

Benzo(a)pyrene-induced changes in p53 and related proteins in mouse skin.

Kinetic phase diagram for crystallization of bimodal mixtures of oligomers as predicted by computer simulations

We analyze the crystallization process of mixtures of long and short oligomers such as n-alkanes using a Sadler–Gilmer-type growth algorithm. The short chains are assumed to crystallize only in a fully stretched conformation, while the long chains take a pathway over a folded state. Increasing the concentration of long chains from zero to unity, the zero-growth temperature, which separates the stable growing phase from the non-growing phase, first decreases for low concentrations of long chains, reaching a minimum value at intermediate concentrations, and increases again for higher concentrations, as a result a growth-gap appears. Here, mixing long chains into the short chain liquid stops the growth process completely until it resumes at higher concentrations of long chains. This effect is explained by the particular kinetic pathway, the long chains take into the crystalline state. Since the folded state has to be passed at first, long chains are more likely to be desorbed again. At low concentrations, the long chains thus effectively dilute the short chain liquid leading to a decrease of the zero-growth temperature. At higher concentrations, the transition into the stretched state of the long chains leads more frequently to bonded pairs, which stabilizes the growth again due to the higher binding energy among fully stretched long chains.

Establishment of pulmonary alveolar type II cell line from p53-deficient mice.

We obtained a pulmonary alveolar type II epithelial cell line, MAC7, derived from the lung of p53-deficient mice (p53 -/-). When this cell line was passaged for long periods of time, the epithelial cells grew at a high rate for over 50th passage and never entered the non-growing senescent phase characteristic of the normal cells (p53 +/+). Each pulmonary epithelial outgrowth was characterized morphologically and immunocytochemically, and the growth and viability of the outgrowths were examined by MTT assay. Expression of surfactant-associated protein, SP-B, was detected, and transmission electron microscopy demonstrated a type II phenotype containing lamellar bodies and phospholipids. These findings indicate that MAC7 cells retain the morphological and physiological properties of alveolar type II epithelial cells. This cell line should be useful in experimental systems for studying lung pathology.

Co-expression of bcl-2 and bag-1, apoptosis suppressing genes, prolonged viable culture period of hybridoma and enhanced antibody production.

Human bcl-2 and bag-1 DNA were introduced into mouse hybridoma 2E3- O cells and expressed. The expression of bcl-2 in BCMGneo-bcl2 transfectants was confirmed by ELISA and that of bag-1 in pZeo-bag1 was confirmed by western blotting. In batch cultures, the over-expression of bcl-2 prolonged the culture period by 2 days and co-expression of bcl-2 and bag-1 prolonged the culture period by 3 days. The delayed increase in the dead cell number in culture of the bcl-2 and bag-1 cotransfectant indicated the additional antiapoptosis effect of bcl-2 and bag-1 cotransfection in comparison with the bcl-2 only transfection. The bcl-2 transfectants (2E3O-Bcl2) produced antibody twofold per batch culture in comparison with 2E3-O cells transfected with BCMGSneo (2E3O-Mock). Enhancement of this MoAb production was due to the improved survival of the cells and was not due to stimulation of antibody production rate per cell by Bcl-2 expression. And the bcl-2 and bag-1 co-transfectant (2E3O-Bcl2-BAG1) produced antibody approximately fourfold of 2E3O-Mock per batch culture. Enhancement of this MoAb production was due to the improved survival of the cells and was partly due to stimulation of MoAb production rate per cell in the non-growing phase by the cotransfection. The method to engineer hybridoma cells genetically with bcl-2 and bag-1 for increasing viability and productivity would be widely applied for improving antibody productivity of hybridoma cultures.

Kojic acid production by Aspergillus flavus using gelatinized and hydrolyzed sago starch as carbon sources.

Direct conversion of gelatinized sago starch into kojic acid by Aspergillus flavus strain having amylolytic enzymes was carried out at two different scales of submerged batch fermentation in a 250-mL shake flask and in a 50-L stirred-tank fermentor. For comparison, fermentations were also carried out using glucose and glucose hydrolyzate from enzymic hydrolysis of sago starch as carbon sources. During kojic acid fermentation of starch, starch was first hydrolyzed to glucose by the action of alpha-amylase and glucoamylase during active growth phase. The glucose remaining during the production phase (non-growing phase) was then converted to kojic acid. Kojic acid production (23.5 g/L) using 100 g/L sago starch in a shake flask was comparable to fermentation of glucose (31.5 g/L) and glucose hydrolyzate (27.9 g/L) but in the 50-L fermentor was greatly reduced due to non-optimal aeration conditions. Kojic acid production using glucose was higher in the 50-L fermentor than in the shake flask.

Cell growth and the regulation of prostaglandin synthesis

Prostaglandin (PG) synthesis was determined in human embryo lung fibroblasts (HELF) during active, slowed and nongrowing phases. Bradykinin and ascorbic acid were used to induce PG synthesis. The cells were also exposed to arachidonic acid, a PG precursor. During active growth, PGE 2 synthesis in response to stimulation by either bradykinin or ascorbic acid was low. As growth slowed the cellular response changed. During quiescence bradykinin and ascorbic acid stimulated PG production markedly while the conversion of free arachidonic acid to PGE 2 also increased markedly. This change in response by quiescent cells was not due to an increase in cell density. When growing and quiescent cells at the same cell density were compared, the growing cells showed very little response to bradykinin while the quiescent cells were very responsive. The change in response was also not due to any differences in arachidonic acid concentrations in the culture medium during growth and non-growth.