Machine learning modeling and additive explanation techniques for glutathione production from multiple experimental growth conditions of Saccharomyces cerevisiae

Glutathione (GSH) production is of great industrial interest due to its essential properties. This study aimed to use machine learning (ML) methods to model GSHproduction under different growth conditions of Saccharomyces cerevisiae, namely cultivation time, culture volume, pressure, and magnetic field application. Different ML and regression models were evaluated for their statistics to select the most robust model. Results showed that eXtreme Gradient Boosting (XGB) was the best predictive performance model. From the best model, additive explanation techniques were used to identify the feature importance of process. According to variable analysis, the best conditions to obtain the highest GSH concentrations would be cultivation times of 72-96 h, low magnetic field intensity (3.02 mT), low pressure (0.5 kgf.cm-2), and high culture volume (3.5 L). XGB use and additive explanation techniques proved promising for determining process optimization conditions and selecting the essential process variables.

strain E1 under stress conditions

Phthalates esters (PAEs) are a kind of polymeric material additives widely been added into plastics to improve products' flexibility. It can easily cause environmental pollution which are hazards to public health. In this study, we isolated an efficient PAEs degrading strain, Janthinobacterium sp. E1, and determined its degradation effect of di-2-ethylhexyl phthalate (DEHP) under stress conditions. Strain E1 showed an obvious advantage in pollutants degradation under various environmental stress conditions. Degradation halo clearly occurred around the colony of strain E1 on agar plate supplemented with triglyceride. Strain E1's esterase is a constitutively expressed intracellular enzyme. The esterase purified from strain E1 showed a higher catalytic effect on short-chain PAEs than long-chain PAEs. The input of DEHP, DBP (dibutyl phthalate) and DMP (dimethyl phthalate) into the tested soil did not change the species composition of soil prokaryotic community, but altered the dominant species in specific environmental conditions. And the community diversity and richness decreased to a certain extent. However, the diversity and richness of the microbial community were improved after the contaminated soil was treated with the strain E1. Our results also suggested that strain E1 exhibited a tremendous potential in environmental bioremediation in the real environment, which provides a new insight into the elimination of the pollutants contamination in the urban environment.

Cellular and physiological roles of sigma factors in Vibrio spp.: A comprehensive review

Vibrio species are motile gram-negative bacteria commonly found in aquatic environments. Vibrio species include pathogenic as well as non-pathogenic strains. Pathogenic Vibrio species have been reported in invertebrates and humans, whereas non-pathogenic strains are involved in symbiotic relationships with their eukaryotic hosts. These bacteria are also able to adapt to fluctuations in temperature, salinity, and pH, in addition to oxidative stress, and osmotic pressure in aquatic ecosystems. Moreover, they have also developed protective mechanisms against the immune systems of their hosts. Vibrio species accomplish adaptation to changing environments outside or inside the host by altering their gene expression profiles. To this end, several sigma factors specifically regulate gene expression, particularly under stressful environmental conditions. Moreover, other sigma factors are associated with biofilm formation and virulence as well. This review discusses different types of sigma and anti-sigma factors of Vibrio species involved in virulence and regulation of gene expression upon changes in environmental conditions. The evolutionary relationships between sigma factors with various physiological roles in Vibrio species are also discussed extensively.

Forced Degradation Studies, Elucidation of Degradation Pathways and Degradation Kinetics of Xylopic Acid via LC and LC-MS/MS Analyses

Stability studies of active pharmaceutical ingredients (APIs) remain an essential quality requirement of the pharmaceutical industry. Stability data of an API could guide in the choice of its processing technique, packaging method and storage conditions. Here, we sought to determine the stability or otherwise of xylopic acid (XA) under various stress conditions as stipulated by the International Conference on Harmonization (ICH). XA is a diterpene kaurene isolate of the African spice, Xylopia aethiopica (Annonaceae) that is credited with diverse biological activities. XA was subjected to various stress conditions (hydrolytic, oxidative, photolytic and thermal) and its degradation products characterized. Seven degradation products were identified and tentatively characterized by LC-MS/MS analysis. The probable degradation pathways for the seven degradation products were then predicted. Using a simple and validated UHPLC-DAD method, the degradation kinetics of XA under the different stress conditions were comprehensively assessed. The degradation of XA under all the stress conditions followed the first order reaction kinetics. XA was found to be less stable in strongly acidic or strongly basic solutions as well as in an oxidizing agent (hydrogen peroxide). The stability of XA was also found to be pH- and temperature-dependent. Its stability was however not affected by UV-light irradiation.

Microbial exopolysaccharide: Sources, stress conditions, properties and application in food and environment: A comprehensive review

Microbial glucan or exopolysaccharides (EPS) have caught an eye of researchers from decades. The unique characteristics of EPS make it suitable for various food and environmental applications. This review overviews the different types of exopolysaccharides, sources, stress conditions, properties, characterization techniques and applications in food and environment. The yield and production condition of EPS is a major factor affecting the cost and its applications. Stress conditions are very important as it stimulates the microorganism for enhanced EPS production and affects its properties. As far as application is concerned specific properties of EPS such as, hydrophilicity, less oil uptake behavior, film forming ability, adsorption potential have applications in both food and environment sector. Novel and improved method of production, feed stock and right choice of microorganisms with stress conditions are critical for desired functionality and yield of the EPS.

Tumor heterogeneity: An oncogenic driver of PDAC progression and therapy resistance under stress conditions

Pancreatic ductal adenocarcinoma (PDAC) is a clinically challenging disease usually diagnosed at advanced or metastasized stage. By this year end, there are an expected increase in 62,210 new cases and 49,830 deaths in the United States, with 90% corresponding to PDAC subtype alone. Despite advances in cancer therapy, one of the major challenges combating PDAC remains tumor heterogeneity between PDAC patients and within the primary and metastatic lesions of the same patient. This review describes the PDAC subtypes based on the genomic, transcriptional, epigenetic, and metabolic signatures observed among patients and within individual tumors. Recent studies in tumor biology suggest PDAC heterogeneity as a major driver of disease progression under conditions of stress including hypoxia and nutrient deprivation, leading to metabolic reprogramming. We therefore advance our understanding in identifying the underlying mechanisms that interfere with the crosstalk between the extracellular matrix components and tumor cells that define the mechanics of tumor growth and metastasis. The bilateral interaction between the heterogeneous tumor microenvironment and PDAC cells serves as another important contributor that characterizes the tumor-promoting or tumor-suppressing phenotypes providing an opportunity for an effective treatment regime. Furthermore, we highlight the dynamic reciprocating interplay between the stromal and immune cells that impact immune surveillance or immune evasion response and contribute towards a complex process of tumorigenesis. In summary, the review encapsulates the existing knowledge of the currently applied treatments for PDAC with emphasis on tumor heterogeneity, manifesting at multiple levels, impacting disease progression and therapy resistance under stress.

The new isolated Archaea strain improved grain yield, metabolism and quality of wheat plants under Co stress conditions

Heavy metal (e.g. cobalt) pollution causes a serious of environmental and agricultural problems. On the other hand, plant growth-promoting microorganisms enhance plant growth and mitigate heavy metal stress. Herein, we isolated and identified the unclassified species strain NARS9, belong to Haloferax,. Cobalt (Co, 200 mg/kg soil) stress mitigating impact of the identified on wheat grains yield, primary and secondary metabolism and grain quality was investigated. Co alone significantly induced Co accumulation in wheat grain (260%), and consequently reduced wheat yield (130%) and quality. Haloferax NARS9 alone significantly enhanced grain chemicals composition (i.e., total sugars (89%) and organic acids (e.g., oxalic and isobutyric acids), essential amino acids (e.g., threonine, lysine, and histidine) and unsaturated fatty acids (e.g. eicosenoic, erucic and tetracosenoic acids). Interestingly, Co stress induced wheat grain yield, reduction were significantly mitigated by Haloferax NARS9 treatment by 26% compared to Co stress alone. Under Co stress, Haloferax NARS9 significantly increased sugar metabolism including sucrose and starch levels and their metabolic enzymes (i.e. invertases, sucrose synthase, starch synthase). This in turn increased organic acid (e.g. oxalic (70%) and malic acids (60%)) and amino acids. levels and biosynthetic enzymes, e.g. glutamine synthetase and threonine synthase. Increased sugars levels by Haloferax NARS9 under Co treatment also provided a route for the biosynthesis of saturated fatty acids, particularly palmitic and stearic acids. Furthermore, Haloferax NARS9 treatment supported the wheat nutritive value through increasing minerals (Ca, Fe, Mn, Zn) and antioxidants i.e., polyphenol, flavonoids, ASC and GSH and total polyamines by 50%, 110%, 400%, 30%, and 90% respectively). These in parallel with the increase in the activity of (phenylalanine ammonia-lyase (110%) in phenolic metabolism). Overall, this study demonstrates the potentiality of Haloferax NARS9 in harnessing carbon and nitrogen metabolism differentially in wheat plants to cope with Co toxicity. Our results also suggested that the use of Haloferax NARS9 in agricultural fields can improve growth and nutritional value of wheat grains.

Development and Validation of Stability Indicating RP-HPLC Method for the Determination of Related Substances in novel nitroimidazole anti TB drug, Pretomanid Drug Substance: Robustness by Design Expert and application to the Stability Studies

A stability-indicating RP-HPLC method was developed for the related substances of the novel anti TB drug, Pretomanid. Critical quality attributes were evaluated and established for the robust method conditions by using quality by design-based design of experiments. Forced degradation were carried out under acidic, basic, thermal, oxidative, and photolytic stress conditions. Pretomanid degrades when treated with base, and no significant degradation was observed by other stress conditions. The impurities separation was achieved on Baker bond C18 (150 mm × 4.6 mm, 3μm) with the mobile phase of 0.1% of orthophosphoric acid and acetonitrile in a time gradient mode. The HPLC method was validated according to ICH tripartite guidelines. LOD and LOQ of Pretomanid and all the impurities were 0.1 μg ml^-1 and 0.4 μg ml^-1 respectively. The method was found to be linear with a correlation coefficient >0.99, precise (% RSD < 5.0), robust and accurate (% recovery 85-115%). Stability studies were evaluated according to ICH-Q1A and found stable in all the storage conditions.

The role of polyhydroxyalkanoates in adaptation of Cupriavidus necator to osmotic pressure and high concentration of copper ions

Polyhydroxyalkanoates (PHA) are abundant microbial polyesters accumulated in the form of intracellular granules by numerous prokaryotes primarily as storage of carbon and energy. Apart from their storage function, the presence of PHA also enhances the robustness of the microbial cells against various stressors. In this work, we investigated the role of PHA in Cupriavidus necator, a model organism concerning PHA metabolism, for adaptation to osmotic pressure and copper ions. In long-term laboratory evolution experiments, the bacterial culture was cultivated in presence of elevated doses of sodium chloride or copper ions (incubations lasted 78 passages for Cu²⁺ and 68 passages for NaCl) and the evolved strains were compared with the wild-type strain in terms of growth and PHA production capacity, cell morphology (investigated by various electron microscopy techniques), activities of selected enzymes involved in PHA metabolism and other crucial metabolic pathways, the chemical composition of bacterial biomass (determined by infrared and Raman spectroscopy) and also considering robustness against various stressors. The results confirmed the important role of PHA metabolism for adaptation to both tested stressors.

tuberculosis H37Ra

BACKGROUND

Hormone-sensitive lipase (HSL) is a neutral lipase capable of hydrolysing various kinds of lipids. In comparison to single human Hormone Sensitive Lipase (hHSL), that is induced under nutritional stress, twelve serine hydrolases are annotated as HSL in Mycobacterium tuberculosis (mHSL). Mycobacterium is exposed to multiple stresses inside the host. Therefore, the present study was carried out to investigate if mHSL are also expressed under stress condition and if there is any correlation between various stress conditions and expression pattern of mHSL.

METHODS AND RESULTS

The expression pattern of mHSL under different environmental conditions (in-vitro and ex-vivo) were studied using qRT-PCR in M. tuberculosis H37Ra strain with 16 S rRNA as internal control. Out of 12, only two genes (lipU and lipY) were expressed at very low level in mid log phase culture under aerobic conditions, while 9 genes were expressed at stationary phase of growth. Ten mHSLs were expressed post-infection under ex-vivo conditions in time dependent manner. LipH and lipQ did not express at any time point under ex-vivo condition. The relative expression of most of the genes under individual stress was much higher than observed in ex-vivo conditions. The expression pattern of genes varied with change in stress condition.

CONCLUSIONS

Different sets of mHSL genes were expressed under different individual stress conditions pointing towards the requirement of different mHSL to combat different stress conditions. Overall, most of the mHSLs have demonstrated stress dependent expression pointing towards their role in intracellular survival of mycobacteria.

Assembly of Bacillus subtilis Dynamin into Membrane-Protective Structures in Response to Environmental Stress Is Mediated by Moderate Changes in Dynamics at a Single Molecule Level

Dynamin-like proteins are membrane-associated GTPases, conserved in bacteria and in eukaryotes, that can mediate nucleotide-driven membrane deformation or membrane fusion reactions. Bacillus subtilis' DynA has been shown to play an important role in protecting cells against chemicals that induce membrane leakage, and to form an increased number of membrane-associated structures after induction of membrane stress. We have studied the dynamics of DynA at a single molecule level in real time, to investigate how assembly of stress-induced structures is accompanied by changes in molecule dynamics. We show that DynA molecule displacements are best described by the existence of three distinct populations, a static mode, a low-mobility, and a fast-mobile state. Thus, DynA is most likely freely diffusive within the cytosol, moves along the cell membrane with a low mobility, and arrests at division sites or at stress-induced lesions at the membrane. In response to stress-inducing membrane leakage, but not to general stress, DynA molecules become slightly more static, but largely retain their mobility, suggesting that only few molecules are involved in the repair of membrane lesions, while most molecules remain in a dynamic mode scanning for lesions. Our data suggest that even moderate changes in single molecule dynamics can lead to visible changes in protein localization patterns.

The study of stress conditions on growth and proteome of Raoultella planticola: a new emerging pathogen

All bacteria can survive and adapt to different stresses, such as fluctuations in temperature, pH oxidative, and osmotic pressure occurring in their surrounding environments. This study aims to evaluate the effects of a variety of stress conditions on the growth, and proteome of Raoultella planticola PTCC 1598. R. planticola cells were exposed to different values of temperatures, sodium chloride, pH, and hydrogen peroxide stresses. Among the stress conditions, oxidative stress, upon exposure to hydrogen peroxide (H₂O₂) at 4000 ppm concentration was selected for proteomics analysis in detail. Approximately, 1400 spots were identified in two-dimensional gel electrophoresis (2-DE). Among the identified spots, 85 spots were repeatable using 2D-Platinum software and eye confirmation and, nine protein spots were differentially expressed. Among nine proteins, six proteins identified successfully with an MASCOT score greater than 40 (p < 0.05) were 2,3-dihydroxybenzoate-2,3-dehydrogenase (oxidoreductase family), hypothetical protein G787-04832, periplasmic D-galactose-binding protein, uridine phosphorylase (glycosyltransferases), a single peptide match to cysteine-binding periplasmic protein, and NADP(H) nitroreductase. All identified proteins showed decreased level expression. Based on the obtained results, we concluded that hydrogen peroxide as an antiseptic compound could affect cell growth and proteomics of R. planticola. Therefore, we recommend using an antiseptic solution containing H₂O₂ to prevent the spread of R. planticola as a new emerging pathogen.

The underexplored role of diverse stress factors in microbial biopolymer synthesis

Polyhydroxyalkanoates (PHA) are microbial polyesters which, apart from their primary storage role, enhance the stress robustness of PHA accumulating cells against various stressors. PHA also represent interesting alternatives to petrochemical polymers, which can be produced from renewable resources employing approaches of microbial biotechnology. During biotechnological processes, bacterial cells are exposed to various stressor factors such as fluctuations in temperature, osmolarity, pH-value, elevated pressure or the presence of microbial inhibitors. This review summarizes how PHA helps microbial cells to cope with biotechnological process-relevant stressors and, vice versa, how various stress conditions can affect PHA production processes. The review suggests a fundamentally new strategy for PHA production: the fine-tuned exposure to selected stressors, which might be used to boost PHA production and even to tailor their structure.

Pomegranate seed oil nanoemulsion enriched by α-tocopherol; the effect of environmental stresses and long-term storage on its physicochemical properties and oxidation stability

In this study, pomegranate seed oil (PSO) nanoemulsions loading different amounts of α-tocopherol (0-40%) were produced. The nanoemulsions were fabricated by ultra-sonication method and the influence of thermal treatment (20-90 °C), pH (2-8) and ionic strength (0-500 mM NaCl) were investigated on physicochemical properties of all treatments. Moreover, the oxidative stability and α-tocopherol degradation were also assessed on optimal enriched nanoemulsion formulation during 50-day storage. The droplet diameter, viscosity, antioxidant activity, encapsulation efficiency and loading capacity of optimal formulation were 37.5 nm, 514 cp, 92%, 3.45% and 92.5%, respectively. The peroxide value changed in the range of 4.5-5.3 and 6.7-10.5 meq O₂/kg in loaded and unloaded nanoemulsions, respectively. Transmission electron microscopy demonstrated spherical morphology of nanoemulsion droplets with diameter average of 40 nm. This study suggested that PSO nanoemulsion loading α-tocopherol could be introduced as delivery system with favorable features under severe environmental conditions.

Stress induced modifications in photosystem II electron transport, oxidative status, and expression pattern of acc D and rbc L genes in an oleaginous microalga Desmodesmus sp

The study aimed at understanding the biochemical and molecular level modifications in Desmodesmus sp. under lipid inducing stress conditions. The low-temperature (5 °C) incubation and nitrogen starvation reduced the PS II electron transport in microalga with a maximum reduction of 50-57% in ET₀/ABS values. The PS II electron transport recovered in UV treated cultures after an initial reduction of 87-93% in ET₀/ABS values. A 2.7-4.4 fold increase in ROS and MDA levels was observed under low-temperature incubation, and nitrogen starvation. The UV treatment caused 1.3-2.4 fold higher ROS and MDA levels than control. The low-temperature incubated, nitrogen starved, and UV treated cultures showed 2.4-4 fold higher acc D gene expression. A higher rbc L gene expression was observed under low-temperature stress. The study showed modifications in PS II electron transport, oxidative status, and expression of acc D and rbc L genes under stress conditions.

Unraveling Brazilian bioethanol yeasts as novel starters for high-gravity brewing

High-gravity (HG) brewing has broader application to succeed on beer differentiation and production optimization. However, such process imposes a handicap to yeasts, which must be able to deal with stressful conditions in fermentation. In this work, we assessed different physiological traits of 24 Saccharomyces cerevisiae strains isolated from Brazilian bioethanol distilleries for the selection of novel starters for HG brewing. Five yeast strains were selected with ability to overcome different stressors under HG beer fermentation, showing high fermentability rates, resilience to ethanol stress, low production of foam and hydrogen sulfide, as well as similar flocculation rates to brewer's yeasts. After five fermentation recycles, most strains sustained a viability rate higher than 90% and were able to efficiently accumulate trehalose and glycogen, besides presenting no detectable petite mutants at the final stage. In the sensory analysis, the beers obtained from the five selected strains showed greater aromatic complexity, with predominance of 'spicy', 'dried' and 'fresh fruits' descriptors. In conclusion, this study sheds light on the potential of yeast strains from Brazilian bioethanol process to produce distinctive specialty beers, aside from proposing an effective selection methodology based on relevant physiological attributes for HG brewing process.

Comparison of stress conditions to induce viable but non-cultivable state in Salmonella

Salmonella can enter on the viable but non-culturable state (VBNC), characterized by the loss of ability to grow in routine culture media hindering detection by conventional methods and underestimation of the pathogen. Despite advances in research done so far, studies comparing conditions that lead Salmonella into the VBNC state are scarce. The main objective of this study was to evaluate different stresses to induce Salmonella to the VNBC state. Osmotic (1.2 M NaCl), acid (peracetic acid, 5.66 mg/mL) and oxidative (hydrogen peroxide, 1.20 mg/mL) stress were used at 4 °C to induce Salmonella enterica serovars Enteritidis and Typhimurium to the VBNC state. The culturability loss was monitored in the brain heart infusion (BHI) broth and agar, and the viability was determined by fluorescence microscopy, using the Live/Dead® kit, and by flow cytometry. Besides, the morphological characterization by atomic force microscopy (AFM) was performed. Storage in 1.2 M NaCl at 4 °C induced the VBNC state in Salmonella cells for periods longer than 121 days, and the percentage of viable cells has reached above 80.9%. More aggressive stress conditions promoted by peracetic acid and hydrogen peroxide induced the VBNC state in periods of, at most 0.14 day, and resulted in percentages of 8.5% to 45.5% viable cells, respectively. The counts of viable cells in the flow cytometer corroborate the results obtained by microscopic counts. The VBNC cells obtained in 1.2 M NaCl at 4 °C showed morphological changes, reducing the size and changing the morphology from bacillary to coccoid. No morphological change was observed on the cells stressed by acid or oxidant compounds.

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

BACKGROUND

Pseudomonas putida is a promising candidate for the industrial production of biofuels and biochemicals because of its high tolerance to toxic compounds and its ability to grow on a wide variety of substrates. Engineering this organism for improved performances and predicting metabolic responses upon genetic perturbations requires reliable descriptions of its metabolism in the form of stoichiometric and kinetic models.

RESULTS

In this work, we developed kinetic models of P. putida to predict the metabolic phenotypes and design metabolic engineering interventions for the production of biochemicals. The developed kinetic models contain 775 reactions and 245 metabolites. Furthermore, we introduce here a novel set of constraints within thermodynamics-based flux analysis that allow for considering concentrations of metabolites that exist in several compartments as separate entities. We started by a gap-filling and thermodynamic curation of iJN1411, the genome-scale model of P. putida KT2440. We then systematically reduced the curated iJN1411 model, and we created three core stoichiometric models of different complexity that describe the central carbon metabolism of P. putida. Using the medium complexity core model as a scaffold, we generated populations of large-scale kinetic models for two studies. In the first study, the developed kinetic models successfully captured the experimentally observed metabolic responses to several single-gene knockouts of a wild-type strain of P. putida KT2440 growing on glucose. In the second study, we used the developed models to propose metabolic engineering interventions for improved robustness of this organism to the stress condition of increased ATP demand.

CONCLUSIONS

The study demonstrates the potential and predictive capabilities of the kinetic models that allow for rational design and optimization of recombinant P. putida strains for improved production of biofuels and biochemicals. The curated genome-scale model of P. putida together with the developed large-scale stoichiometric and kinetic models represents a significant resource for researchers in industry and academia.

The impact of physiological stress conditions on protein structure and trypsin inhibition of serine protease inhibitor Kazal type 1 (SPINK1) and its N34S variant

One of the most common mutations in the serine protease inhibitor Kazal type 1 (SPINK1) gene is the N34S variant which is strongly associated with chronic pancreatitis. Although it is assumed that N34S mutation constitutes a high-risk factor, the underlying pathologic mechanism is still unknown. In the present study, we investigated the impact of physiological stress factors on SPINK1 protein structure and trypsin inhibitor function using biophysical methods. Our circular dichroism spectroscopy data revealed differences in the secondary structure of SPINK1 and N34S mutant suggesting protein structural changes induced by the mutation as an impairment that could be disease-relevant. We further confirmed that both SPINK1 (K_D of 0.15 ± 0.06 nM) and its N34S variant (K_D of 0.08 ± 0.02 nM) have similar binding affinity and inhibitory effect towards trypsin as shown by surface plasmon resonance and trypsin inhibition assay studies, respectively. We found that stress conditions such as altered ion concentrations (i.e. potassium, calcium), temperature shifts, as well as environmental pH lead to insignificant differences in trypsin inhibition between SPINK1 and N34S mutant. However, we have shown that the environmental pH induces structural changes in both SPINK1 constructs in a different manner. Our findings suggest protein structural changes in the N34S variant as an impairment of SPINK1 and environmental pH shift as a trigger that could play a role in disease progression of pancreatitis.

Different stress tolerance of spray and freeze dried Lactobacillus casei Shirota microcapsules with different encapsulating agents

In this study, the effects of encapsulation with maltodextrin and reconstituted skim milk (RSM) and their binary and ternary blends with gum arabic (GA) by spray and freeze drying methods on viability of probiotic Lactobacillus casei Shirota under different stress conditions were evaluated. All microcapsules showed high survival ratios (7.91-9.37 log cfu/g) after microencapsulation. The viability of microencapsulated cells was significantly higher than free cells when exposed to stress conditions. Spray dried microcapsules exposed to low pH showed small decrease in the viability of cells compared to freeze dried microcapsules, but freeze drying microcapsules showed higher protective effect at 85 and 90 °C. After exposure to 3% bile salt, almost 2.5 log decreases in the encapsulated cell counts were determined for both methods. The results indicated that using RSM:GA mixture as an encapsulating agent showed the higher cell protection against high temperature, acidic pH and bile salts.

Contribution of transposable elements in the plant's genome

Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.

Stable symbiotic nitrogen fixation under water-deficit field conditions by a stress-tolerant alfalfa microsymbiont and its complete genome sequence

We here characterized the stress-tolerant alfalfa microsymbiont Sinorhizobium meliloti B401. B401-treated plants showed high nitrogen fixation rates under humid and semiarid environments. The production of glycine betaine in isolated bacteroids positively correlated with low precipitation levels, suggesting that this compound acts as a critical osmoprotectant under field conditions. Genome analysis revealed that strain B401 contains alternative pathways for the biosynthesis and uptake of glycine betaine and its precursors. Such genomic information will offer substantial insight into the environmental physiology of this biotechnologically valuable nitrogen-fixing bacterium.

Effect of Some Growth Factors on Tissue Transglutaminase Overexpression Induced by β-Amyloid in Olfactory Ensheathing Cells

Herein, we assessed in a particular glial cell type, called olfactory ensheathing cells (OECs), the effect of some growth factors (GFs) on tissue transglutaminase (TG2) overexpression induced by amyloid-beta (Aβ) with native full-length peptide 1-42 or by fragments, 25-35 or 35-25, as control. Previously, we demonstrated that TG2 overexpression induced by some stressors was down-regulated by GFs exposure in OECs. To monitor cell viability, an MTT test was used, while TG2 expression was examined using immunocytochemical and Western blot analysis. We also considered the involvement of the TG2-mediated apoptotic pathway. Vimentin expression was evaluated as well. Reactive oxygen species and reduced glutathione levels were utilized to test the oxidative intracellular status. Lactate dehydrogenase released into the medium, as a marker of necrotic cell death, was evaluated. We found that in OECs exposed to Aβ(1-42) or Aβ(25-35) for 24 h, TG2 expression increased, and we observed that the protein appeared prevalently localized in the cytosol. The pre-treatment with GFs, basic fibroblast growth factor (bFGF) or glial-derived neurotrophic factor (GDNF), down-regulated the TG2 level, which was prevalently limited to the nuclear compartment. Vimentin expression and caspase cleavage showed a significant enhancement in Aβ(1-42) and Aβ(25-35) exposed cells. The pre-treatment with bFGF or GDNF was able to restore the levels of the proteins to control values, and the intracellular oxidative status modified by the exposure to Aβ(1-42) or Aβ(25-35). Our data suggest that both bFGF or GDNF could be an innovative mechanism to contrast TG2 expression, which plays a key role in Alzheimer's disease.

Simultaneous production of triacylglycerol and high-value carotenoids by the astaxanthin-producing oleaginous green microalga Chlorella zofingiensis

The production of lipids and astaxanthin, a high-value carotenoid, by Chlorella zofingiensis was investigated under different culture conditions. Comparative analysis revealed a good correlation between triacylglycerol (TAG) and astaxanthin accumulation in C. zofingiensis. Stress conditions promoted cell size and weight and induced the accumulation of neutral lipids, especially TAG and astaxanthin, with a concomitant decrease in membrane lipids. The highest contents of TAG and astaxanthin achieved were 387 and 4.89mgg(-1) dry weight, respectively. A semi-continuous culture strategy was developed to optimize the TAG and astaxanthin productivities, which reached 297 and 3.3mgL(-1)day(-1), respectively. Additionally, astaxanthin accumulation was enhanced by inhibiting de novo fatty acid biosynthesis. In summary, our study represents a pioneering work of utilizing Chlorella for the integrated production of lipids and high-value products and C. zofingiensis has great potential to be a promising production strain and serve as an emerging oleaginous model alga.

Expression of virulence and stress response genes in Aeromonas hydrophila under various stress conditions

Aeromonas hydrophila has emerged as an important human pathogen as it causes gastroenteritis and extra-intestinal infections. Information regarding the influence of environmental stresses on gene expression profile of A. hydrophila is lacking. The impact of nutrient replenishment, nutrient deprivation, acid stress, and cold shock on housekeeping, general stress-response, and virulence genes was studied using quantitative real-time PCR in two A. hydrophila strains, CECT 839^T , and A331. These sub-lethal stresses invoked significant changes in the expression of these genes in a strain-dependent manner. Overall, nutrient replenishment and deprivation significantly induced the expression of housekeeping (rpoD), general stress regulators (uspA and rpoS), and virulence (aer) genes, indicating their importance in regulating the survival and virulence of A. hydrophila under these stress conditions. rpoS gene was significantly induced under cold shock; whereas, acid stress significantly induced the expression of uspA gene. This is the first study to investigate the effect of environmental parameters on the expression of stress-response and virulence genes in A. hydrophila strains.

AealRACK1 expression and localization in response to stress in C6/36 HT mosquito cells

The Receptor for Activated C Kinase 1 (RACK1), a scaffold protein member of the tryptophan-aspartate (WD) repeat family, folds in a seven-bladed β-propeller structure that permits the association of proteins to form active complexes. Mosquitoes of the genus Aedes sp., are vectors of virus producing important diseases such as: dengue, chikungunya and yellow fever. Based on the highly conserved gene sequence of AeaeRACK1 of the mosquito Aedes aegypti we characterized the mRNA and protein of the homologous AealRACK1 from the Ae. albopictus-derived cell line C6/36 HT. Two protein species differing in MW/pI values were observed at 35kDa/8.0 and 36kDa/6.5. The behavior of AealRACK1 was studied inducing stress with serum deprivation and the glucocorticoid dexamethasone. Both stressors induced increase of the expression of AealRACK1 mRNA and proteins. In serum-deprived cells AealRACK1 protein was located cortically near the plasma membrane in contrast to dexamethasone-treated cells where the protein formed a dotted pattern in the cytoplasm. In addition, 33 protein partners were identified by immunoprecipitation and mass spectrometry. Most of the identified proteins were ribosomal, involved in signaling pathways and stress responses. Our results suggest that AealRACK1 in C6/36 HT cells respond to stress increasing its synthesis and producing phosphorylated activated form.

BIOLOGICAL SIGNIFICANCE

Insect cells adapt to numerous environmental stressors, including chemicals and invasion of pathogenic microorganisms among others, coordinating cellular and organismal responses. Individual cells sense the environment using receptors that trigger signaling pathways that regulate expression of specific effector proteins and/or cellular responses as movement or secretion. In the coordination of responses to stress, scaffold proteins are pivotal molecules that recruit other proteins forming active complexes. The Receptor for Activated C Kinase 1 (RACK1) is the best studied member of the conserved tryptophan-aspartate (WD) repeat family. RACK1 folds in a seven-bladed β-propeller structure and it could be activated during stress, participating in different signaling pathways. The presence and activities of RACK1 in mosquitoes had not been documented before, in this work the molecule is demonstrated in an Aedes albopictus-derived cell line and its reaction to stress is observed under the effect of serum deprivation and the presence of glucocorticoid analog dexamethasone, a chemical used to cause stress in vitro.

Control of mRNA turnover: implication of cytoplasmic RNA granules

The control of mRNA turnover is essential for the cell to rationalize its mRNA content both under physiological conditions and upon stress. Several mechanisms involved in the control of mRNA turnover have been elucidated. These include surveillance mechanisms such as nonsense-mediated decay, non-stop mediated decay and non-go-mediated decay that eliminate aberrant mRNAs, and regulatory mechanisms including AU-mediated decay, GU-mediated decay, and CDE-mediated decay that ensure mRNA plasticity. In general, the mechanisms of RNA decay rely on interactions between specific cis-acting RNA elements and selected RNA-binding proteins that either prevent the degradation of mRNA targets or induce the recruitment of decaying effectors leading to mRNA degradation. Formation of cytoplasmic RNA granules including processing bodies, stress granules, UV granules, and exosome granules have recently emerged as an additional mechanism that control mRNA turnover of selected mRNAs. Here we will review briefly review the main mechanisms that control mRNA decay and highlight possible implication of RNA granules in such mechanisms.

Stability-indicating HPLC method for posaconazole bulk assay

A stability-indicating liquid chromatographic (LC) method was developed for the determination of posaconazole in bulk. Chromatographic separation was achieved using an isocratic elution in a reversed-phase system, with a mobile phase composed of methanol-water (75:25, v/v), at 1.0 mL min(-1) flow. Samples were exposed to degradation under thermal, oxidative and acid/basic conditions, and no interference in the analysis was observed. System suitability was evaluated and results were satisfactory (N = 4,900.00 tailing factor 1.04; RSD between injections = 0.65). The retention time of posaconazole was about 8.5 min and the method was validated within the concentration range 5-60 μg mL(-1) (r = 0.9996). Adequate results were obtained for repeatability (RSD % = 0.86-1.22), inter-day precision (RSD % = 1.21) and accuracy (98.13% mean recovery). Robustness was also determined to be satisfactory after evaluation. The proposed method was successfully applied to posaconazole bulk quantification, showing the method is useful for determination of the drug in routine analysis.

Simple and sensitive stability-indicating ion chromatography method for the determination of cyclopropylamine in nevirapine and moxifloxacin hydrochloride drug substances

A simple and sensitive ion chromatography method has been developed for the determination of cyclopropylamine (CPA) in nevirapine (NEV) and moxifloxacin HCl (MOX) pharmaceutical drug substances. Efficient chromatographic separation was achieved on a Metrosep C4, 5 μm (250 mm × 4.0 mm) column. The mobile phase consists of 5 mM hydrochloric acid containing 10% (v/v) acetonitrile and was delivered in an isocratic mode at a flow rate of 0.9 mL min⁻¹ at 27°C. A conductometric detector was used for the detection of the analyte. The drug substances were subjected to stress conditions including oxidation, thermal, photolytic and humidity for the evaluation of the stability-indicating nature of the method. The method was validated for specificity, precision, linearity, accuracy and solution stability. The limit of detection (LOD) and limit of quantification (LOQ) values are 0.10 μg mL⁻¹ and 0.37 μg mL⁻¹ respectively. The linearity range of the method is between 0.37 μg mL⁻¹ and 1.5 μg mL⁻¹ and the correlation coefficient is found to be 0.9971. The average recoveries of CPA in NEV and MOX are 97.0% and 98.0%, respectively.

A validated stability-indicating liquid-chromatographic method for ranitidine hydrochloride in liquid oral dosage form

A selective, specific and stability-indicating gradient reverse phase high-performance liquid chromatographic (HPLC) method was developed for the determination of Ranitidine in presence of its impurities, forced degradation products and placebo substances such as saccharide and parabens. Ultraviolet detection was performed at 230 nm. Separate portions of the drug product and ingredients were exposed to stress conditions to induce oxidative, acidic, basic, hydrolytic, thermal and photolytic degradation. Ranitidine was found to degrade significantly at acidic, basic and oxidative stress conditions but was stable at heat and humidity. The developed method was validated as per International Conference on Harmonization (ICH) guidelines. The method was validated over this range for (i) system suitability (ii) specificity, (iii) precision, (iv) limit of detection and limit of quantification, (v) linearity, (vi) accuracy, (vii) robustness. The method was found to be precise, accurate, linear and robust. The proposed method was successfully employed for estimation of Ranitidine impurities in pharmaceutical preparations.

Development and validation of a stability-indicating RP-HPLC method for duloxetine hydrochloride in its bulk and tablet dosage form

The objective of the present work was to develop a stability-indicating RP-HPLC method for duloxetine hydrochloride (DUL) in the presence of its degradation products generated from forced decomposition studies. The drug substance was found to be susceptible to stress conditions of acid hydrolysis. The drug was found to be stable to dry heat, photodegradation, oxidation and basic condition attempted. Successful separation of the drug from the degradation products formed under acidic stress conditions was achieved on a Hypersil C-18 column (250 mm × 4.6 mm id, 5μm particle size) using acetonitrile: 0.01 M potassium dihydrogen phosphate buffer (pH 5.4 adjusted with orthophosphoric acid) (50:50, v/v) as the mobile phase at a flow rate of 1.0 ml/min. Quantification was achieved with photodiode array detection at 229 nm over the concentration range 1–25 μg/ml with range of recovery 99.8–101.3 % for DUL by the RP-HPLC method. Statistical analysis proved the method to be repeatable, specific, and accurate for estimation of DUL. It can be used as a stability-indicating method due to its effective separation of the drug from its degradation products,