scholarly journals Molecular Profiling and Optimization Studies for Growth and PHB Production Conditions in Rhodobacter sphaeroides

Energies ◽  
2020 ◽  
Vol 13 (23) ◽  
pp. 6471
Author(s):  
Yu Rim Lee ◽  
Hana Nur Fitriana ◽  
Soo Youn Lee ◽  
Min-Sik Kim ◽  
Myounghoon Moon ◽  
...  
Keyword(s):  
Time Course ◽  
Growth Conditions ◽  
Effect Of Temperature ◽  
Ros Scavenging ◽  
Renewable Materials ◽  
Experimental Conditions ◽  
Expression Levels ◽  
Recent Climate ◽  
Phb Production ◽  
In Cells

In the recent climate change regime, industrial demand for renewable materials to replace petroleum-derived polymers continues to rise. Of particular interest is polyhydroxybutyrate (PHB) as a substitute for polypropylene. Accumulating evidence indicates that PHB is highly produced as a carbon storage material in various microorganisms. The effects of growth conditions on PHB production have been widely studied in chemolithotrophs, particularly in Rhodobacter. However, the results on PHB production in Rhodobacter have been somewhat inconsistent due to different strains and experimental conditions, and it is currently unclear how diverse environmental factors are linked with PHB production. Here, we report optimized growth conditions for PHB production and show that the growth conditions are closely related to reactive oxygen species (ROS) regulation. PHB accumulates in cells up to approximately 50% at the highest level under dark-aerobic conditions as opposed to light aerobic/anaerobic conditions. According to the time-course, PHB contents increased at 48 h and then gradually decreased. When observing the effect of temperature and medium composition on PHB production, 30 °C and a carbon/nitrogen ratio of 9:1 or more were found to be most effective. Among PHB biosynthetic genes, PhaA and PhaB are highly correlated with PHB production, whereas PhaC and PhaZ showed little change in overall expression levels. We found that, while the amount of hydrogen peroxide in cells under dark conditions was relatively low compared to the light conditions, peroxidase activities and expression levels of antioxidant-related genes were high. These observations suggest optimal culture conditions for growth and PHB production and the importance of ROS-scavenging signaling with regard to PHB production.

A Simple Method for Estimation of Lipoxygenase and Cyclo-Oxygenase Pathways in Human Platelets - the Use of Thiobarbituric Acid Reaction

1980 ◽  
Vol 44 (02) ◽  
pp. 111-114 ◽  
Author(s):  
Hiroshi Takayama ◽  
Minoru Okuma ◽  
Haruto Uchino
Keyword(s):  
Time Course ◽  
Normal Values ◽  
Human Platelet ◽  
Thiobarbituric Acid ◽  
Human Platelets ◽  
Optimal Conditions ◽  
Experimental Conditions ◽  
Simple Method ◽  
Acid Reaction ◽  
Optimal Ph

SummaryTo develop a simple method for estimation of platelet lipoxygenase (PLO) and cyclo-oxygenase (PCO) pathways, the arachidonic acid (AA) metabolism of human platelet was investigated under various experimental conditions by the use of the thiobarbituric acid (TBA) reaction and a radioisotope technique. A TBA-reactive substance different from malondialdehyde (MDA) via PCO pathway was detected and shown to be derived from the PLO pathway. Since the optimal pH and time course of its formation were different from those of MDA formation via PCO pathway, PLO and PCO pathways were estimated by quantitating the TBA-reactive substances produced by the incubation of AA either with aspirin-treated platelets or with untreated ones, respectively, each under optimal conditions. Normal values expressed in terms of nmol MDA/108 platelets were 1.17±0.34 (M±SD, n = 31) and 0.79±0.15 (n = 31) for PLO and PCO pathways, respectively.

Applicability of Instability Index for In vitro Protein Stability Prediction

2019 ◽  
Vol 26 (5) ◽  
pp. 339-347 ◽  
Author(s):  
Dilani G. Gamage ◽  
Ajith Gunaratne ◽  
Gopal R. Periyannan ◽  
Timothy G. Russell
Keyword(s):  
Protein Stability ◽  
Caulobacter Crescentus ◽  
Effect Of Temperature ◽  
Instability Index ◽  
Dipeptide Composition ◽  
Experimental Conditions ◽  
The Stability ◽  
Vitro Protein

Background: The dipeptide composition-based Instability Index (II) is one of the protein primary structure-dependent methods available for in vivo protein stability predictions. As per this method, proteins with II value below 40 are stable proteins. Intracellular protein stability principles guided the original development of the II method. However, the use of the II method for in vitro protein stability predictions raises questions about the validity of applying the II method under experimental conditions that are different from the in vivo setting. Objective: The aim of this study is to experimentally test the validity of the use of II as an in vitro protein stability predictor. Methods: A representative protein CCM (CCM - Caulobacter crescentus metalloprotein) that rapidly degrades under in vitro conditions was used to probe the dipeptide sequence-dependent degradation properties of CCM by generating CCM mutants to represent stable and unstable II values. A comparative degradation analysis was carried out under in vitro conditions using wildtype CCM, CCM mutants and two other candidate proteins: metallo-β-lactamase L1 and α -S1- casein representing stable, borderline stable/unstable, and unstable proteins as per the II predictions. The effect of temperature and a protein stabilizing agent on CCM degradation was also tested. Results: Data support the dipeptide composition-dependent protein stability/instability in wt-CCM and mutants as predicted by the II method under in vitro conditions. However, the II failed to accurately represent the stability of other tested proteins. Data indicate the influence of protein environmental factors on the autoproteolysis of proteins. Conclusion: Broader application of the II method for the prediction of protein stability under in vitro conditions is questionable as the stability of the protein may be dependent not only on the intrinsic nature of the protein but also on the conditions of the protein milieu.

scholarly journals Naturally Occurring Ecdysteroids in Triticum aestivum L. and Evaluation of Fenarimol as a Potential Inhibitor of Their Biosynthesis in Plants

2021 ◽  
Vol 22 (6) ◽  
pp. 2855
Author(s):  
Anna Janeczko ◽  
Jana Oklestkova ◽  
Danuše Tarkowská ◽  
Barbara Drygaś
Keyword(s):  
Triticum Aestivum ◽  
Winter Wheat ◽  
Triticum Aestivum L ◽  
Growth Conditions ◽  
Animal Kingdom ◽  
Experimental Conditions ◽  
P450 Monooxygenase ◽  
Naturally Occurring ◽  
Regulatory Effects ◽  
Potential Use

Ecdysteroids (ECs) are steroid hormones originally found in the animal kingdom where they function as insect molting hormones. Interestingly, a relatively high number of these substances can also be formed in plant cells. Moreover, ECs have certain regulatory effects on plant physiology, but their role in plants still requires further study. One of the main aims of the present study was to verify a hypothesis that fenarimol, an inhibitor of the biosynthesis of ECs in the animal kingdom, also affects the content of endogenous ECs in plants using winter wheat Triticum aestivum L. as a model plant. The levels of endogenous ECs in winter wheat, including the estimation of their changes during a course of different temperature treatments, have been determined using a sensitive analytical method based on UHPLC-MS/MS. Under our experimental conditions, four substances of EC character were detected in the tissue of interest in amounts ranging from less than 1 to over 200 pg·g−1 FW: 20-hydroxyecdysone, polypodine B, turkesterone, and isovitexirone. Among them, turkesterone was observed to be the most abundant EC and accumulated mainly in the crowns and leaves of wheat. Importantly, the level of ECs was observed to be dependent on the age of the plants, as well as on growth conditions (especially temperature). Fenarimol, an inhibitor of a cytochrome P450 monooxygenase, was shown to significantly decrease the level of naturally occurring ECs in experimental plants, which may indicate its potential use in studies related to the biosynthesis and physiological function of these substances in plants.

Carbon Nanotubes Grown on Metallic Wires by Cold Plasma Technique

2002 ◽  
Vol 737 ◽  
Author(s):  
D. Sarangi ◽  
A. Karimi
Keyword(s):  
Electron Microscopy ◽  
Carbon Nanotubes ◽  
Growth Conditions ◽  
Effect Of Temperature ◽  
Rutherford Back Scattering ◽  
Novel Approach ◽  
Transmission Electron ◽  
Back Scattering ◽  
Metallic Wires ◽  
Metal Wires

ABSTRACTCarbon nanotubes on metallic wires may be act as electrode for the field emission (FE) luminescent devices. Growing nanotubes on metallic wires with controlled density, length and alignment are challenging issues for this kind of devices. We, in the present investigation grow carbon nanotubes directly on the metal wires by a powerful but simple technique. A novel approach has been proposed to align nanotubes during growth. Methane, acetylene and dimethylamine have been used as source gases. With the same growth conditions (viz. pressure, growth temperature and plasma) methane does not produce any nanotube but nanotubes grown with dimethylamine show shorter length and radius than acetylene. The effect of temperature to control the radius, time to control the density, plasma conditions to align the nanotubes has been focused. Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM) and Rutherford Back Scattering (RBS) are used to characterize the nanotubes.

Transcriptome response to different carbon sources in Acetobacter aceti

Microbiology ◽  
2011 ◽  
Vol 157 (3) ◽  
pp. 899-910 ◽  
Author(s):  
Kenta Sakurai ◽  
Hiroyuki Arai ◽  
Masaharu Ishii ◽  
Yasuo Igarashi
Keyword(s):  
Draft Genome ◽  
Coupling Efficiency ◽  
Tca Cycle ◽  
Energy Coupling ◽  
Proton Pumping ◽  
Type I ◽  
Acetobacter Aceti ◽  
Expression Levels ◽  
Glyoxylate Pathway ◽  
In Cells

The draft genome sequence of Acetobacter aceti NBRC 14818 was determined by whole-genome shotgun sequencing and the transcriptome profile in cells exponentially grown on ethanol, acetate or glucose was analysed by using a DNA microarray. The genes for all enzymes that constitute the complete tricarboxylic acid (TCA) cycle and glyoxylate pathway were identified in the genome. The TCA cycle genes showed higher expression levels in A. aceti cells grown on acetate or glucose and the glyoxylate pathway genes were significantly induced by ethanol or acetate. Many SOS-response genes were upregulated in cells grown on ethanol, indicating that ethanol provoked damage of DNA and proteins. The superoxide dismutase and catalase genes showed high expression levels in culture on glucose, indicating that oxidation of glucose induced oxidative stress. A. aceti NBRC 14818 was found to have a highly branched respiratory chain. The genes for two type I and one type II NADH dehydrogenase were identified. The genes for one of the type I enzymes were highly expressed when cells were grown on acetate or glucose, but were significantly downregulated in culture on ethanol, probably because ubiquinones were directly reduced by pyrroloquinoline quinone-dependent alcohol dehydrogenase. Four sets of the genes for quinol oxidases, one bo 3-type (BO3), one bd-type and two cyanide-insensitive-types (CIOs), were identified in the genome. The genes for BO3, which might have proton-pumping activity, were highly expressed under the conditions tested, but were downregulated in the glucose culture. In contrast, the genes for one of the CIOs were significantly upregulated in cells grown on glucose. The two CIOs, which are expected to have lower energy-coupling efficiency, seemed to have a higher contribution in glucose-grown cells. These results indicate that energy conservation efficiency is fine-tuned by changing the respiratory components according to the growth conditions in A. aceti cells.

Apical control of band elongation in Antithamnion defectum (Ceramiaceae, Rhodophyta)

1988 ◽  
Vol 66 (7) ◽  
pp. 1308-1315 ◽  
Author(s):  
David Garbary ◽  
Daniel Belliveau ◽  
Robert Irwin
Keyword(s):  
Cell Elongation ◽  
Experimental Conditions ◽  
Axial Cell ◽  
Wall Deposition ◽  
Apical Control ◽  
Band Position ◽  
Apical Cells ◽  
In Cells

Cell elongation in the Ceramiaceae typically occurs by means of one or two bands located apically and (or) basally in each cell. In axial cells of Antithamnion defectum two bands are present; however, most cell elongation occurs as a result of new wall deposition in bands at the base of each axial cell. In cells of determinate branches, only the basal band is present. In experimental conditions in which apical cells of indeterminate branches are differentially excised, location of the primary elongation band can be reestablished in relation to remaining indeterminate axes. Thus, the primary elongation band in axial cells is always basal with respect to indeterminate apical cells. When all indeterminate apices are removed, band growth becomes highly disrupted, and diffuse, irregularly located bands are formed. These results suggest that regulation of band position and elongation is through apical control.

scholarly journals Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Hitoshi Iuchi ◽  
Michiaki Hamada
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Course ◽  
Time Series Data ◽  
Expression Patterns ◽  
Detection Methods ◽  
Series Data ◽  
Expression Levels ◽  
Over Time ◽  
Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

scholarly journals Role of Mammalian Auditory Cortex in the Perception of Elementary Sound Properties

2001 ◽  
Vol 85 (6) ◽  
pp. 2350-2358 ◽  
Author(s):  
Sanjiv K. Talwar ◽  
Pawel G. Musial ◽  
George L. Gerstein
Keyword(s):  
Auditory Cortex ◽  
Time Course ◽  
Auditory Evoked Potentials ◽  
Mammalian Species ◽  
Sound Intensity ◽  
Primary Auditory Cortex ◽  
Normal Hearing ◽  
Auditory Task ◽  
Experimental Conditions

Studies in several mammalian species have demonstrated that bilateral ablations of the auditory cortex have little effect on simple sound intensity and frequency-based behaviors. In the rat, for example, early experiments have shown that auditory ablations result in virtually no effect on the rat's ability to either detect tones or discriminate frequencies. Such lesion experiments, however, typically examine an animal's performance some time after recovery from ablation surgery. As such, they demonstrate that the cortex is not essential for simple auditory behaviors in the long run. Our study further explores the role of cortex in basic auditory perception by examining whether the cortex is normally involved in these behaviors. In these experiments we reversibly inactivated the rat primary auditory cortex (AI) using the GABA agonist muscimol, while the animals performed a simple auditory task. At the same time we monitored the rat's auditory activity by recording auditory evoked potentials (AEP) from the cortical surface. In contrast to lesion studies, the rapid time course of these experimental conditions preclude reorganization of the auditory system that might otherwise compensate for the loss of cortical processing. Soon after bilateral muscimol application to their AI region, our rats exhibited an acute and profound inability to detect tones. After a few hours this state was followed by a gradual recovery of normal hearing, first of tone detection and, much later, of the ability to discriminate frequencies. Surface muscimol application, at the same time, drastically altered the normal rat AEP. Some of the normal AEP components vanished nearly instantaneously to unveil an underlying waveform, whose size was related to the severity of accompanying behavioral deficits. These results strongly suggest that the cortex is directly involved in basic acoustic processing. Along with observations from accompanying multiunit experiments that related the AEP to AI neuronal activity, our results suggest that a critical amount of activity in the auditory cortex is necessary for normal hearing. It is likely that the involvement of the cortex in simple auditory perceptions has hitherto not been clearly understood because of underlying recovery processes that, in the long-term, safeguard fundamental auditory abilities after cortical injury.

scholarly journals Agonist-induced Ca2+ influx in human neutrophils is secondary to the emptying of intracellular calcium stores

1991 ◽  
Vol 277 (1) ◽  
pp. 73-79 ◽  
Author(s):  
M Montero ◽  
J Alvarez ◽  
J Garcia-Sancho
Keyword(s):  
Plasma Membrane ◽  
Intracellular Calcium ◽  
Time Course ◽  
Human Neutrophils ◽  
Calcium Stores ◽  
Free Medium ◽  
Prolonged Incubation ◽  
Intracellular Calcium Stores ◽  
Cytochrome P 450 ◽  
In Cells

Emptying of the intracellular calcium stores of human neutrophils, by prolonged incubation in Ca(2+)-free medium, by treatment with low concentrations of the Ca2+ inophore ionomycin, or by activation with cell agonists, increased the plasma-membrane permeability to Ca2+ and Mn2+. The chemotactic peptide formylmethionyl-leucyl-phenylalanine and the natural agonists platelet-activating factor and leukotriene B4 released different amounts of calcium from the stores and induced Ca2+ (Mn2+) uptake, the rate of which correlated inversely with the amount of calcium left in the stores. The increased Mn2+ uptake induced by these agonists was persistent in cells incubated in Ca(2+)-free medium, but returned to basal levels in cells incubated in Ca(2+)-containing medium, with the same time course as the refilling of the calcium stores. The calcium-stores-regulated Mn2+ influx, including that induced by agonists, was prevented by cytochrome P-450 inhibitors. We propose that agonist-induced Ca2+ (Mn2+) influx in human neutrophils is secondary to the emptying of the intracellular stores which, in turn, activates plasma-membrane Ca2+ channels by a mechanism involving microsomal cytochrome P-450, similar to that described previously in thymocytes [Alvarez, Montero & Garcia-Sancho (1991) Biochem. J. 274, 193-197].

scholarly journals Effect of temperature on acid hydrolysis of Jerusalem artichoke as raw material for ethanol production

2013 ◽  
pp. 279-287 ◽  
Author(s):  
Radojka Razmovski ◽  
Vesna Vucurovic ◽  
Uros Miljic ◽  
Vladimir Puskas
Keyword(s):  
Hold Time ◽  
Jerusalem Artichoke ◽  
Raw Material ◽  
Effect Of Temperature ◽  
Industrial Biotechnology ◽  
Microbial Conversion ◽  
Experimental Conditions ◽  
Theoretical Yield ◽  
Renewable Raw Material ◽  
Layer Chromatography

Jerusalem artichoke (JA) is a low-requirement crop, which does not interfere with food chain, and is a promising carbon source for industrial fermentation. Microbial conversion of such a renewable raw material to useful products, such as ethanol, is an important objective in industrial biotechnology. In this study, ethanol was efficiently produced from the hydrolyzates of JA obtained at different pH values (pH 2.5, pH 3.0 and pH 3.5), temperature (120, 130, 132 and 134?C) and hold time (30 and 60 min) by Saccharomyces cerevisiae. The efficient degradation of JA by HCl under certain experimental conditions was confirmed by thin-layer chromatography. Ethanol concentration of 7.52% (w/w), which corresponds to 93.89 % of the theoretical yield is achieved by ethanol fermentation of JA hydrolyzate obtained at pH 2.5.

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