Relative Rates Of Degradation Research Articles

Color recycling: metabolization of apocarotenoid degradation products suggests carbon regeneration via primary metabolic pathways

Key messageAnalysis of carotenoid-accumulating roots revealed that oxidative carotenoid degradation yields glyoxal and methylglyoxal. Our data suggest that these compounds are detoxified via the glyoxalase system and re-enter primary metabolic pathways.Carotenoid levels in plant tissues depend on the relative rates of synthesis and degradation. We recently identified redox enzymes previously known to be involved in the detoxification of fatty acid-derived reactive carbonyl species which were able to convert apocarotenoids into corresponding alcohols and carboxylic acids. However, their subsequent metabolization pathways remain unresolved. Interestingly, we found that carotenoid-accumulating roots have increased levels of glutathione, suggesting apocarotenoid glutathionylation to occur. In vitro and in planta investigations did not, however, support the occurrence of non-enzymatic or enzymatic glutathionylation of β-apocarotenoids. An alternative breakdown pathway is the continued oxidative degradation of primary apocarotenoids or their derivatives into the shortest possible oxidation products, namely glyoxal and methylglyoxal, which also accumulated in carotenoid-accumulating roots. In fact, combined transcriptome and metabolome analysis suggest that the high levels of glutathione are most probably required for detoxifying apocarotenoid-derived glyoxal and methylglyoxal via the glyoxalase pathway, yielding glycolate and d-lactate, respectively. Further transcriptome analysis suggested subsequent reactions involving activities associated with photorespiration and the peroxisome-specific glycolate/glyoxylate transporter. Finally, detoxified primary apocarotenoid degradation products might be converted into pyruvate which is possibly re-used for the synthesis of carotenoid biosynthesis precursors. Our findings allow to envision carbon recycling during carotenoid biosynthesis, degradation and re-synthesis which consumes energy, but partially maintains initially fixed carbon via re-introducing reactive carotenoid degradation products into primary metabolic pathways.

Protein turnover in the developing Triticum aestivum grain.

Summary Protein abundance in cereal grains is determined by the relative rates of protein synthesis and protein degradation during grain development but quantitation of these rates is lacking.Through combining in vivo stable isotope labelling and in‐depth quantitative proteomics, we have measured the turnover of 1400 different types of proteins during wheat grain development.We demonstrate that there is a spatiotemporal pattern to protein turnover rates which explain part of the variation in protein abundances that is not attributable to differences in wheat gene expression. We show that c. 20% of total grain adenosine triphosphate (ATP) production is used for grain proteome biogenesis and maintenance, and nearly half of this budget is invested exclusively in storage protein synthesis. We calculate that 25% of newly synthesized storage proteins are turned over during grain development rather than stored.This approach to measure protein turnover rates at proteome scale reveals how different functional categories of grain proteins accumulate, calculates the costs of protein turnover during wheat grain development and identifies the most and the least stable proteins in the developing wheat grain.

Plant apocarotenoid metabolism utilizes defense mechanisms against reactive carbonyl species and xenobiotics.

Carotenoid levels in plant tissues depend on the relative rates of synthesis and degradation of the molecules in the pathway. While plant carotenoid biosynthesis has been extensively characterized, research on carotenoid degradation and catabolism into apocarotenoids is a relatively novel field. To identify apocarotenoid metabolic processes, we characterized the transcriptome of transgenic Arabidopsis (Arabidopsis thaliana) roots accumulating high levels of β-carotene and, consequently, β-apocarotenoids. Transcriptome analysis revealed feedback regulation on carotenogenic gene transcripts suitable for reducing β-carotene levels, suggesting involvement of specific apocarotenoid signaling molecules originating directly from β-carotene degradation or after secondary enzymatic derivatizations. Enzymes implicated in apocarotenoid modification reactions overlapped with detoxification enzymes of xenobiotics and reactive carbonyl species (RCS), while metabolite analysis excluded lipid stress response, a potential secondary effect of carotenoid accumulation. In agreement with structural similarities between RCS and β-apocarotenoids, RCS detoxification enzymes also converted apocarotenoids derived from β-carotene and from xanthophylls into apocarotenols and apocarotenoic acids in vitro. Moreover, glycosylation and glutathionylation-related processes and translocators were induced. In view of similarities to mechanisms found in crocin biosynthesis and cellular deposition in saffron (Crocus sativus), our data suggest apocarotenoid metabolization, derivatization and compartmentalization as key processes in (apo)carotenoid metabolism in plants.

Quantifying the forces that maintain prophages in bacterial genomes

Genome sequencing has revealed that prophages, viral sequences integrated in a bacterial chromosome, are abundant, accounting for as much as 20% of the bacterial genome. These sequences can confer fitness benefits to the bacterial host, but may also instigate cell death through induction. Several recent investigations have revealed that the distribution of prophage lengths is bimodal, with a clear distinction between small and large prophages. Here we develop a mathematical model of the evolutionary forces affecting the prophage size distribution, and fit this model to three recent data sets. This approach offers quantitative estimates for the relative rates of lysogeny, induction, mutational degradation and selection acting on a wide class of prophage sequences. The model predicts that large prophages are predominantly maintained by the introduction of new prophage sequences through lysogeny, whereas shorter prophages can be enriched when they no longer encode the genes necessary for induction, but still offer selective benefits to their hosts.

Understanding the complexity of the matrix metalloproteinase system and its relevance to age-related diseases: Age-related macular degeneration and Alzheimer's disease.

Extracellular matrices (ECMs) are maintained by tightly coupled processes of continuous synthesis and degradation. The degradative arm is mediated by a family of proteolytic enzymes called the matrix metalloproteinases (MMPs). These enzymes are released as latent proteins (pro-MMPs) and on activation are capable of degrading most components of an ECM. Activity of these enzymes is checked by the presence of tissue inhibitors of MMPs (TIMPs) and current opinion holds that the ratio of TIMPs/MMPs determines the relative rate of degradation. Thus, elevated ratios are thought to compromise degradation leading to the accumulation of abnormal ECM material, whilst diminished ratios are thought to lead to excessive ECM degradation (facilitating angiogenesis and the spread of cancer cells). Our recent work has shown this system to be far more complex. MMP species tend to undergo covalent modification leading to homo- and hetero-dimerization and aggregation resulting in the formation of very large macromolecular weight MMP complexes (LMMCs). In addition, the various MMP species also show a bound-free compartmentalisation. The net result of these changes is to reduce the availability of the latent forms of MMPs for the activation process. An assessment of the degradation potential of the MMP system in any tissue must therefore take into account the degree of sequestration of the latent MMP species, a protocol that has not previously been addressed. Taking into consideration the complexities already described, we will present an analysis of the MMP system in two common neurodegenerative disorders, namely age-related macular degeneration (AMD) and Alzheimer's disease (AD).

Kinetic study of gold nanoparticle mediated photocatalytic degradation of Victoria blue.

In the study, biogenic gold nanoparticles (AuNPs) were used for the photocatalytic degradation of triphenylmethane dyes Victoria blue B (VBB) and R (VBR). The process was found to result in an approximate degradation of 65 and 52%, respectively, for VBB and VBR within a period of 8h. The relative rate of photocatalytic degradation of VBB and VBR was identified to be 0.0195±0.0031/min and 0.0295±0.0025/min, respectively, byusing the Langmuir-Hinshelwood model. By using the Vigna unguiculata model system, the degradation products were demonstrated to have non-toxic effect. Moreover, the less toxic nature of AuNPs used for dye removal highlights its feasibility for large-scale application. Hence, the AuNPs-based photocatalytic dye degradation as described in the study is cost-effective, rapid and environment-friendly.

Methylene blue as a lignin surrogate in manganese peroxidase reaction systems

Manganese peroxidase (MnP) is associated with lignin degradation and is thus relevant to lignocellulosic-utilization technologies. Technological applications require reaction mixture optimization. A surrogate substrate can facilitate this if its susceptibility to degradation is easily monitored and mirrors that of lignin. The dye methylene blue (MB) was evaluated in these respects as a surrogate substrate by testing its reactivity in reaction mixtures containing relevant redox mediators (dicarboxylic acids, fatty acids). Relative rates of MB degradation were compared to available literature reports of lignin degradation under similar conditions, and suggest that MB can be a useful lignin surrogate in MnP systems.

Skeletal Muscle Loss is Associated with TNF Mediated Insufficient Skeletal Myogenic Activation After Burn.

Muscle loss accompanies severe burn; in this hyper-catabolic state, muscle undergoes atrophy through protein degradation and disuse. Muscle volume is related to the relative rates of cellular degradation and myogenesis. We hypothesize that muscle atrophy after injury is in part because of insufficient myogenesis associated with the hyper-inflammatory response. The aim of this study was to investigate the role of skeletal myogenesis and muscle cell homeostasis in response to severe burn. Twenty-eight male C57BL6 mice received 25% TBSA scald. Gluteus muscle from these animals was analyzed at days 1, 3, 7, and 14 after injury. Six additional animals without burn served as controls. We showed muscle wet weight and protein content decreased at days 3 and 7 after burn, with elevated tumor necrosis factor (TNF) mRNA expression (P < 0.05). Increased cell death was observed through TUNEL staining, and cleaved caspase-3 levels reached a peak in muscle lysate at day 3 (P < 0.05). The cell proliferation marker proliferating cell nuclear antigen (PCNA) significantly increased after burn, associated with increased gene and protein expression of myogenesis markers Pax7 and myogenin. Desmin mRNA expression and the ratio of desmin to PCNA protein expression, however, significantly decreased at day 7 (P < 0.05). In vitro, the ratio of desmin to PCNA protein expression significantly decreased in C2C12 murine myoblasts after TNF-α stimulation for 24 h. We showed that severe burn induces both increased cell death and proliferation. Myogenesis, however, does not counterbalance increased cell death after burn. Data suggest insufficient myogenesis might be associated with pro-inflammatory mediator TNF activity.

Kinetic studies of the reaction between pesticides and hydroxyl radical generated by laser flash photolysis.

Due to contamination of the environment by pesticides and their mishandling, there is the need for treatment of contaminated sites and correct disposal of materials containing them. Thus, studies with advanced oxidation processes are expanding and can determine the rate constant of the hydroxyl radical with organic compounds of great importance in environmental contamination. In this context, the use of laser flash photolysis has been shown to be viable for the determination of these constants. The reaction rate constants of different pesticides with HO(•) in degassed acetonitrile have been determined. They were 1.6 × 10(9) M(-1) s(-1), 0.6 × 10(9) M(-1) s(-1), 1.2 × 10(9) M(-1) s(-1), 2.4 × 10(9) M(-1) s(-1) and 2.2 × 10(9) M(-1) s(-1) for the pesticides carbaryl, propoxur, fenoxycarb, ethoxysulfuron and chlorimuron-ethyl, respectively. These values are about an order of magnitude smaller than the diffusion controlled rate and correlate with the relative rates of disappearance of the pesticides in the photo-Fenton reaction in water. The correlation of the relative rate constants determined by laser flash photolysis with the relative rates of photo-Fenton degradation of the pesticides is compelling evidence for the participation of the hydroxyl radical in the degradation of these pesticides in the latter system.

Assays to monitor autophagy in Drosophila

The term autophagy refers to the engulfment and degradation of cytoplasmic components within the lysosome. This process can benefit cells and organisms by removing damaged, superfluous, or harmful cellular components, and by generating a supply of recycled macromolecules that can support biosynthesis or energy production. Recent interest in autophagy has been driven by its potential role in several disease-related phenomena including neurodegeneration, cancer, immunity and aging. Drosophila provides a valuable animal model context for these studies, and work in this system has also begun to identify novel developmental and physiological roles of autophagy. Here, we provide an overview of methods for monitoring autophagy in Drosophila, with a special emphasis on the larval fat body. These methods can be used to investigate whether observed vesicles are of autophagic origin, to determine a relative rate of autophagic degradation, and to identify specific step(s) in the autophagic process in which a given gene functions.

Relative reactivity of different monovalent alkalis on poly(ethylene terephthalate) geotextiles: Aqueous and alcoholic systems

The relative rate of degradation of poly(ethylene terephthalate) geotextiles in various monovalent alkali hydroxides was studied in both aqueous and alcoholic systems. In an aqueous system, the reaction of all three alkalis on poly(ethylene terephthalate) geotextiles is restricted to the surface since tenacity loss was insignificant and no surface cracks was noticed, whereas in an alcoholic system, significant loss in tenacity occurred due to the formation of surface crack. Furthermore, the relative rate of reactivity of metal hydroxides in aqueous and alkaline media was temperature dependent. However, in equimolar concentration, at 80℃, the relative rate in an aqueous system is of the following order: LiOH &gt; NaOH &gt; KOH in the ratio of 1.65:1.1:1.0. Above 80℃, the reaction is reversed, as aqueous KOH reacts faster than aqueous NaOH. Two different activation energies were found for aqueous KOH at a threshold temperature of 80℃. Furthermore, in heterogeneous systems using dimethyl terephthalate, aqueous KOH was slightly faster than aqueous NaOH in the temperature range of 70–80℃. In an alcoholic system, KOH is almost 1.5 times faster than NaOH at 20℃ and at 60℃.

Enzymatic degradation of polylactide/layered silicate nanocomposites: Effect of organic modifiers

AbstractBiodegradable polylactide (PLA)/layered silicate nanocomposites have been prepared via solution route using two different kinds of organically modified nanoclays. The nanostructure as observed from wide‐angle X‐ray diffraction indicates intercalated hybrids and the extent of intercalation depends on the type of organic modifiers used. Melt‐quenched PLA and its nanocomposites are predominantly amorphous but, after annealing, they are fairly crystalline. The nanohybrids show significant improvement in thermal properties as compared to neat polymer. The nature of interaction between nanoclays and matrix polymer depends on the organic modifiers used, as evident from varying heat of fusion and shifting of Fourier transform infrared peaks. The nanoclays act as nucleating agent, and thereby, control the spherulite dimension of the matrix. The comparison of biodegradation of PLA and its nanocomposites has been studied in enzyme, compost, and buffer solution. Biodegradability of PLA has significantly been enhanced in the presence of nanoclays and the rate varies on organic modifications. The surface morphology, before and after enzymatic degradation, confirms the relative rate of degradation through laser scanning confocal images, scanning electron microscope, and atomic force microscope. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013

Dynamics of post‐translational modifications and protein stability in the stroma of Chlamydomonas reinhardtii chloroplasts

The proteome of any system is a dynamic entity dependent on the intracellular concentration of the entire set of expressed proteins. In turn, this whole protein concentration will be reliant on the stability/turnover of each protein as dictated by their relative rates of synthesis and degradation. In this study, we have investigated the dynamics of the stromal proteome in the model organism Chlamydomonas reinhardtii by characterizing the half-life of the whole set of proteins. 2-DE stromal proteins profiling was set up and coupled with MS analyses. These identifications featuring an average of 26% sequence coverage and eight non-redundant peptides per protein have been obtained for 600 independent samples related to 253 distinct spots. An interactive map of the global stromal proteome, of 274 distinct protein variants is now available on-line at http://www.isv.cnrs-gif.fr/gel2dv2/. N-α-terminal-Acetylation (NTA) was noticed to be the most frequently detectable post-translational modification, and new experimental data related to the chloroplastic transit peptide cleavage site was obtained. Using this data set supplemented with series of pulse-chase experiments, elements directing the relationship between half-life and N-termini were analyzed. Positive correlation between NTA and protein half-life suggests that NTA could contribute to protein stabilization in the stroma.

Hydroxyl radical involvement in the decomposition of hydrogen peroxide by ferrous and ferric-nitrilotriacetate complexes at neutral pH

The relative rates of degradation of three hydroxyl radical probe compounds (atrazine, fenuron and parachlorobenzoic acid (pCBA)) by Fe III/H 2O 2 (pH = 2.85), Fe IIINTA/H 2O 2 (neutral pH), Fe II/O 2, Fe IINTA/O 2, Fe II/H 2O 2 and Fe IINTA/H 2O 2 (neutral pH) have been investigated using the competitive kinetic method. Experiments were carried out in batch and in semi-batch reactors, in the dark, at 25 °C. The data showed that the three probe compounds could be degraded by all the systems studied, and in particular by Fe IINTA/H 2O 2 and Fe IIINTA/H 2O 2 at neutral pH. The relative rate constants of degradation of the three probe compounds obtained for all the systems tested were identical and equal to 1.45 ± 0.03 and 0.47 ± 0.02 for k Atrazine/ k pCBA and k Fenuron/ k pCBA, respectively. These values as well as the decrease of the rates of degradation of the probe compounds upon the addition of hydroxyl radical scavengers ( tert-butanol, bicarbonate ions) suggest that the degradation of atrazine, fenuron and pCBA by Fe IINTA/O 2, Fe IINTA/H 2O 2 and Fe IIINTA/H 2O 2 is initiated by hydroxyl radicals.

Conserving Southeast Asia’s imperiled biodiversity: scientific, management, and policy challenges

Southeast Asia was almost entirely covered by rainforest 8,000 years ago. Today, this region is experiencing the highest relative rates of deforestation and forest degradation in the humid tropics. Every year, millions of hectares of tropical forests are destroyed and degraded. Given the rapid rate of deforestation and the high concentration of endemic species in the region, Southeast Asia could lose 13–42% of local populations by the turn of the next century, at least 50% of which could represent global species extinction. In this Special Issue, we discuss the uniqueness of Southeast Asian biodiversity, drivers of forest destruction, threats to the region’s unique ecosystems and taxa, and key conservation challenges to provide a broad-based review of the science, management and policy issues concerning biodiversity conservation. Overall, we highlight the need for an interdisciplinary and multi-pronged strategy requiring all major stakeholders to work together to achieve the ultimate goal of reconciling biodiversity conservation and human well-being in the region.

Major role for mRNA stability in shaping the kinetics of gene induction

BackgroundmRNA levels in cells are determined by the relative rates of RNA production and degradation. Yet, to date, most analyses of gene expression profiles were focused on mechanisms which regulate transcription, while the role of mRNA stability in modulating transcriptional networks was to a large extent overlooked. In particular, kinetic waves in transcriptional responses are usually interpreted as resulting from sequential activation of transcription factors.ResultsIn this study, we examined on a global scale the role of mRNA stability in shaping the kinetics of gene response. Analyzing numerous expression datasets we revealed a striking global anti-correlation between rapidity of induction and mRNA stability, fitting the prediction of a kinetic mathematical model. In contrast, the relationship between kinetics and stability was less significant when gene suppression was analyzed. Frequently, mRNAs that are stable under standard conditions were very rapidly down-regulated following stimulation. Such effect cannot be explained even by a complete shut-off of transcription, and therefore indicates intense modulation of RNA stability.ConclusionTaken together, our results demonstrate the key role of mRNA stability in determining induction kinetics in mammalian transcriptional networks.

Facile Pretreatment of Bacillus circulans β-Galactosidase Increases the Yield of Galactosyl Oligosaccharides in Milk and Lactose Reaction Systems

The commercially available preparation of beta-galactosidase from Bacillus circulans , known as Biolacta FN5, has been extensively used in the production of prebiotic galactooligosaccharides (GOS). This study focuses on characterizing the production of GOS in two reaction systems: 10% lactose (w/v) in buffer and skim milk. Analysis of the temperature dependence of the GOS yield along with the relative rates of GOS synthesis and degradation leads to the finding that GOS degradation activity was selectively decreased in Biolacta FN5 above 40 degrees C. Facile heat treatment of Biolacta FN5 solution prior to use allowed for GOS yields to be significantly increased in both reaction systems.

Physical properties of PLGA films during polymer degradation

AbstractThe rates of change of polymer properties (glass transition temperature, weight fraction sorbed water, and polymer molecular weight) were determined in poly (DL‐lactide‐co‐glycolide) films under accelerated storage conditions. Films were stored at 70°C and 95%, 75%, 60%, 45%, or 28% relative humidity. Weight fraction sorbed water was determined by thermogravimetric analysis, the glass transition temperature (Tgmix) of the polymer/water mixture by modulated temperature differential scanning calorimetry, and PLGA number‐average molecular weight (Mn) by size exclusion chromatography (SEC). Rates of moisture increase and Tgmix decrease were related to the decrease in PLGA Mn through a modification of the Gordon‐Taylor equation. Understanding the relative rates of polymer physical and chemical degradation will allow for improved design of PLGA formulations that control rates of drug delivery and preserve drug stability. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009

Turnover of the Human Proteome: Determination of Protein Intracellular Stability by Dynamic SILAC

The proteome of any system is a dynamic entity, such that the intracellular concentration of a protein is dictated by the relative rates of synthesis and degradation. In this work, we have analyzed time-dependent changes in the incorporation of a stable amino acid resolved precursor, a protocol we refer to as "dynamic SILAC", using 1-D gel separation followed by in-gel digestion and LC-MS/MS analyses to profile the intracellular stability of almost 600 proteins from human A549 adenocarcinoma cells, requiring multiple measures of the extent of labeling with stable isotope labeled amino acids in a classic label-chase experiment. As turnover rates are acquired, a profile can be built up that allows exploration of the 'dynamic proteome' and of putative features that predispose a protein to a high or a low rate of turnover. Moreover, measurement of the turnover rate of individual components of supramolecular complexes provides a unique insight in processes of protein complex assembly and turnover.

Impacts of land use change on South‐east Asian forest butterflies: a review

Summary South‐east Asia has the highest relative rate of habitat loss and degradation in the humid tropics. The responses of less ‘charismatic’ groups, including butterflies, to habitat disturbance remain relatively poorly understood. Many South‐east Asian butterflies are endemic to the region and face global extinction if current levels of deforestation were to continue. Here, I highlight South‐east Asia as a region urgently in need of butterfly conservation research and review empirical studies of the responses of South‐east Asian butterflies to land use change. Additionally, I discuss some methodological pitfalls for such studies. Furthermore, I argue for the importance of identifying the ecological correlates of sensitivity of butterfly species to forest modification and the potential biological mechanisms underlying their responses to land use change. There has been no consensus among previous studies on the effects of land use change on butterfly communities in South‐east Asia. Of the 20 studies I reviewed, seven reported higher species richness/diversity in undisturbed (or the least disturbed) forest than in disturbed habitats, nine reported the opposite trend, three reported no difference and one reported a strong influence of seasonality on the impacts of logging. Some of these studies may contain inherent methodological biases resulting from the failure to control for sampling effects, the lack of consideration for the spatial scale of analysis and incomplete sampling of the vertical strata in tropical rainforests. Synthesis and applications. Empirical studies of the effects of land use change on tropical forest insects are sorely lacking from South‐east Asia. Butterflies are an ideal taxonomic group for such investigations. Future studies should be designed carefully to avoid the methodological pitfalls highlighted here. Determining the ecological correlates of sensitivity of butterflies to forest modification is important for the pre‐emptive identification of species of conservation concern and for generating testable hypotheses on the differential responses of species to forest modification. Experimental studies are needed to determine the mechanisms underlying the responses of species to land use change in order to develop effective strategies for the conservation of butterflies in human disturbed landscapes.