Catabolic Activity Research Articles

SEMA6D, Negatively Regulated by miR-7, Contributes to C28/I2 chondrocyte's Catabolic and Anabolic Activities via p38 Signaling Pathway.

MiR-7 has been recognized as an osteoarthritis (OA-)-promoting factor, but the specific downstream pathway of miR-7 still remains unknown. Further investigation of the molecular regulatory mechanism of miR-7 might help develop a novel therapeutic method for OA. In this study, we revealed that Semaphorin 6D (SEMA6D) was a direct target gene of miR-7 and presented a negative regulatory relation with SEMA6D in vitro and in vivo. SEMA6D could improve OA in rat OA models, as indicated by H&E and Safranin O-Fast green staining, and also μCT analysis. Further evaluation of SEMA6D suggested that SEMA6D promotes the anabolism and reduces the catabolism of C28/I2 chondrocytes via inhibiting the activation of the p38 pathway. The present research illustrated that SEMA6D is a negatively regulatory factor of miR-7 and a pivotal mediator of catabolism and anabolism in C28/I2 chondrocytes. SEMA6D exerts its function via inhibiting the activation of the p38 pathway.

Seasonal Enzyme Activities of Sympatric Calanus glacialis and C. finmarchicus in the High-Arctic

In the Arctic shelf seas, the mesozooplankton biomass is dominated by the arctic copepod Calanus glacialis, but its boreal congeneric C. finmarchicus is expanding northwards. Even though it is already there, C. finmarchicus may not be able to truly establish itself in the Arctic seas and potentially replace C. glacialis. We compared metabolic and digestive enzyme activities of sympatric C. glacialis and C. finmarchicus from Isfjorden, Svalbard and off-shelf north of Svalbard. The seasonal regulation of anabolic and catabolic enzyme activities was generally similar for the two species, but with some interspecific differences corresponding to their ontogeny. Wake-up from overwintering started earlier in adults of C. glacialis than in C. finmarchicus, while the onset of dormancy started early in the overwintering stages of both species. Furthermore, C. glacialis showed an earlier and higher mobilization of lipase enzyme activities, indicating higher efficiency in assimilating dietary lipids compared to C. finmarchicus. Similar population sizes and population structures for C. finmarchicus off-shelf north of Svalbard and in Isfjorden support a similar origin. Still, C. finmarchicus was able to match regulation of enzyme activities to the bloom even though the bloom peaked approximately a month later off-shelf north of Svalbard, indicating that food availability is an important signal for the final step of termination of diapause. Even though the two species largely follow the same patterns of metabolic enzyme activities, the more efficient lipid anabolism of C. glacialis may give it an advantage over C. finmarchicus in high-Arctic unpredictable environments with short-pulsed primary production regimes.

Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil.

Municipal landfills are known for methane production and a source of nitrate pollution leading to various environmental issues. Therefore, this niche was selected for the isolation of one-carbon (C1) utilizing bacteria with denitrifying capacities using anaerobic enrichment on nitrate mineral salt medium supplemented with methanol as carbon source. Eight axenic cultures were isolated of which, isolate AAK/M5 demonstrated thehighest methanol removal (73.28%) in terms of solublechemical oxygen demand and methane removal (41.27%) at the expense of total nitrate removal of 100% and 33% respectively. The whole genome characterization with phylogenomic approach suggested that the strain AAK/M5 could be assigned to Pseudomonas aeruginosa with close neighbours as type strains DVT779, AES1M, W60856, and LES400. The circular genome annotation showed the presence of complete set of genes essential for methanol utilization and complete denitrification process. The study demonstrates the potential of P. aeruginosa strain AAK/M5 in catalysing methane oxidation thus serving as a methane sink vis-à-vis utilization of nitrate. Considering the existence of such bacteria at landfill site, the study highlights the need to develop strategies for their enrichment and designing of efficient catabolic activity for such environments.

Flattening of circadian glucocorticoid oscillations drives acute hyperinsulinemia and adipocyte hypertrophy.

Disruption of circadian glucocorticoid oscillations in Cushing's disease and chronic stress results in obesity and adipocyte hypertrophy, which is believed to be a main source of the harmful effects of obesity. Here, we recapitulate stress due to jet lag or work-life imbalances by flattening glucocorticoid oscillations in mice. Within 3days, mice achieve a metabolic state with persistently high insulin, but surprisingly low glucose and fatty acids in the bloodstream, that precedes a more than 2-fold increase in brown and white adipose tissue mass within 3weeks. Transcriptomic and Cd36-knockout mouse analyses show that hyperinsulinemia-mediated de novo fatty acid synthesis and Cd36-mediated fatty acid uptake drive fat mass increases. Intriguingly, this mechanism by which glucocorticoid flattening causes acute hyperinsulinemia and adipocyte hypertrophy is unexpectedly beneficial in preventing high levels of circulating fatty acids and glucose for weeks, thus serving as a protective response to preserve metabolic health during chronic stress.

A2M inhibits inflammatory mediators of chondrocytes by blocking IL-1β/NF-κB pathway.

A hallmark of osteoarthritis (OA) is cartilage degeneration, which has been previously correlated with dramatic increases in inflammatory enzymes. Specifically, interleukin-1β (IL-1β) and subsequent upregulation of nuclear factor kappa B (NF-κB) is implicated as an important player in the development of posttraumatic osteoarthritis (PTOA). Alpha 2-macroglobulin (A2M) can inhibit this inflammatory pathway, making it a promising therapy for PTOA. Herein, we demonstrate that A2M binds and neutralizes IL-1β, blocking downstream NF-κB-induced catabolism seen in in vitro. Human chondrocytes (cell line C28) were incubated with A2M protein and then treated with IL-1β. A2M was labeled with VivoTag™ 680 to localize the protein postincubation. The degree of binding between A2M and IL-1β was evaluated through immunoprecipitation (IP). Catabolic proteins, including IL-1β and NF-kB, were detected by Western blot. Pro-inflammatory and chondrocyte-related gene expression was examined by qRT-PCR. VivoTag™ 680-labeled A2M was observed in the cytoplasm of C28 human chondrocytes by fluorescence microscopy. IP experiments demonstrated that A2M could bind IL-1β. Additionally, western blot analysis revealed that A2M neutralized IL-1β and NF-κB in a dose-dependent manner. Moreover, A2M decreased levels of MMPs and TNF-α and increased the expression of cartilage protective genes Col2, Type2, Smad4, and aggrecan. Mostly importantly, A2M was shown to directly neutralize IL-1β to downregulate the pro-inflammatory responses mediated by the NF-kB pathway. These results demonstrate a mechanism by which A2M reduces inflammatory catabolic activity and protects cartilage after joint injury. Further in vivo studies are needed to fully understand the potential of A2M as a novel PTOA therapy.

Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile.

Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou’s evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3– was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.

Catabolic Ornithine Carbamoyltransferase Activity Facilitates Growth of Staphylococcus aureus in Defined Medium Lacking Glucose and Arginine.

ABSTRACTPrevious studies have found that arginine biosynthesis in Staphylococcus aureus is repressed via carbon catabolite repression (CcpA), and proline is used as a precursor. Unexpectedly, however, robust growth of S. aureus is not observed in complete defined medium lacking both glucose and arginine (CDM-R). Mutants able to grow on agar-containing defined medium lacking arginine (CDM-R) were selected and found to contain mutations within ahrC, encoding the canonical arginine biosynthesis pathway repressor (AhrC), or single nucleotide polymorphisms (SNPs) upstream of the native arginine deiminase (ADI) operon arcA1B1D1C1. Reverse transcription-PCR (RT-PCR) studies found that mutations within ccpA or ahrC or SNPs identified upstream of arcA1B1D1C1 increased the transcription of both arcB1 and argGH, encoding ornithine carbamoyltransferase and argininosuccinate synthase/lyase, respectively, facilitating arginine biosynthesis. Furthermore, mutations within the AhrC homologue argR2 facilitated robust growth within CDM-R. Complementation with arcB1 or arcA1B1D1C1, but not argGH, rescued growth in CDM-R. Finally, supplementation of CDM-R with ornithine stimulated growth, as did mutations in genes (proC and rocA) that presumably increased the pyrroline-5-carboxylate and ornithine pools. Collectively, these data suggest that the transcriptional regulation of ornithine carbamoyltransferase and, in addition, the availability of intracellular ornithine pools regulate arginine biosynthesis in S. aureus in the absence of glucose. Surprisingly, ~50% of clinical S. aureus isolates were able to grow in CDM-R. These data suggest that S. aureus is selected to repress arginine biosynthesis in environments with or without glucose; however, mutants may be readily selected that facilitate arginine biosynthesis and growth in specific environments lacking arginine.

Differences in bacterial functional profiles from loamy sand and clay loam textured soils under fungicide QuadrisR impact

The non-target effect of the fungicide QuadrisR on the bacterial community from grassland loamy sand (LS) and cropland clay loam (CL) soils with unknown history of fungicide usage was investigated. QuadrisR was applied to soil mesocosms at 0.0 mg kg-1 (Az0), 2.90 mg kg-1 (Az1), 14.65 mg kg-1 (Az2) and 35.0 mg kg-1 (Az3) calculated towards the active ingredient azoxystrobin (Az). Response of bacterial communities to QuadrisR was investigated during a 120-day incubation experiment, evaluating the shifts in bacterial catabolic profiles by the community-level physiological profiling (CLPP) technique and Biolog EcoPlatesTM method. QuadrisR decreased the overall catabolic activity (AWCD) of soil bacterial communities and the rate of decrease was independent of soil type and fungicide concentration. Fungicide affected negatively the utilisation of amines and positively that of amino acids in both soil types, whereas the effects on other carbon guilds (carbohydrates, carboxylic acids and polymers) corresponded closely to the respective soil type and fungicide concentration. Results indicated the presence of non-target effects of QuadrisR on bacterial functioning; hence, it is important to address the fungicide side-effects on soil health.

Exogenous Putrescine Increases Heat Tolerance in Tomato Seedlings by Regulating Chlorophyll Metabolism and Enhancing Antioxidant Defense Efficiency

Crops around the world are facing a diversity of environmental problems, of which high temperatures are proving to be the most serious threat to crops. Polyamine putrescine (Put) acts as a master growth regulator that contributes to optimal plant growth and development and increased stress tolerance. Here, the current study aimed to elucidate how Put functions in regulating chlorophyll (Chl) metabolism, oxidative stress, and antioxidant defense, as well as to characterize the expression of genes related to heat stress in tomato seedlings under such stress. The results revealed that Put treatment significantly attenuates heat-induced damage by promoting biomass production, increasing photosynthetic efficiency, and inhibiting excessive production of oxidative stress markers. Heat stress markedly decreased the Chl content in the tomato leaf and accelerated the leaf yellowing process. However, Put-treated tomato seedlings showed a higher Chl content, which could be associated with the functions of Put in elevating PBGD activity (Chl biosynthesis enzyme) and suppressing the activity of the Chl catabolic enzyme (Chlase and MDCase). Under high-temperature stress, the expression levels of the gene encoding factors involved in Chl biosynthesis and Chl catabolism were significantly down- and upregulated, respectively, and this trend was reversed in Put-treated heat-stressed seedlings. In addition, exogenous application of Put boosted the activity of antioxidant enzymes, along with the levels of expression of their encoding genes, only in plants that were heat stressed. Furthermore, the expression levels of heat-shock-related genes (HSP90, HSP70, and HsfA1) were elevated in Put-treated, high-temperature-stressed tomato seedlings. Taken together, our results indicate that Put treatment significantly increases the heat tolerance of tomato seedlings, by elevating Chl concentrations and suppressing Chl catabolic enzyme activity, modulating endogenous free PA content, increasing antioxidant defense efficiency, and upregulating the expression of heat-shock-related genes.

Organic amendment regulates soil microbial biomass and activity in wheat-maize and wheat-soybean rotation systems

Long-term heavy application of inorganic fertilizers is associated with a decrease in soil quality and biodiversity. Organic amendments have been reported to positively affect soil quality; however, relatively little is known regarding soil carbon (C) cycle enzyme kinetic parameters (Vmax and Km), community-level physiological profiles (CLPP), and the interactions between these factors and soil microbes and physicochemical properties under sustained organic amendment. Therefore, this study aimed to evaluate the effect of organic amendments on crop yield, soil chemical properties, microbial activity, enzyme kinetic parameters of five extracellular C cycle-related hydrolase enzymes, and soil microbial functional diversity in wheat-maize (WM) and wheat-soybean (WS) rotation crop systems. The results of the study showed that combined application of organic and inorganic fertilizers increased crop yield (6.81–17.47%), soil total organic C (TOC, 29.44–39.54%), total nitrogen (TN, 24.22–50.79%), available potassium (AK, 39.47–59.62%), total dissolved nitrogen (TDN, 19.68–33.75%), dissolved organic C (DOC, 14.54–55.10%), available phosphorus (AP, 34.81–243.90%), and microbial biomass C and nitrogen (MBC, 17.65–40.86% and MBN, 18.63–50.76%) concentration. The combined application also enhanced microbial growth when compared with an inorganic amendments regime. Additionally, the combined application of organic and inorganic fertilizers increased soil microbial activity and catabolic diversity and maintained a high substrate-induced respiration (SIR) value. Furthermore, the conversion from a WM rotation to a WS rotation increased both soil pH and microbial biomass, and the resultant soil exhibited lower potential activity and higher enzyme-substrate affinity. Overall, the findings of this study showed that an increase in soil microbial biomass is a key determinant of microbial catabolic activity and functional diversity.

B. Pietrosimone, CHEMOKINE ENA-78/CXCL5 IS PRODUCED BY OA SYNOVIAL FIBROBLASTS IN RESPONSE TO A MATRIX DAMAGE STIMULUS AND IS FOUND IN SYNOVIAL FLUID COLLECTED FROM PATIENTS AFTER ACL INJURY

Purpose: Cartilage degradation in OA is due to the overproduction of secreted proteases by chondrocytes, including the matrix metalloproteinases (MMPs). Synoviocytes can also contribute to this activity by releasing mediators that exacerbate joint destruction. Cross-talk between synovial cells and chondrocytes mediated by proinflammatory factors could intensify catabolic signaling activity in both cell populations to contribute to joint tissue destruction. Protease cleavage of matrix proteins generates matrix fragments that include fibronectin fragments (FN-f) found in OA cartilage and synovial fluid.

Driving arginine catabolism to activate systemic autophagy.

Macroautophagy/autophagy is a conserved cellular self-digestive mechanism to catabolize superfluous or damaged cellular components to maintain cell homeostasis. Impaired autophagy underlies multiple pathophysiological states, including aging, neurodegenerative, inflammatory, and metabolic diseases. Intermittent fasting and caloric restriction are effective means by which to activate autophagy, yet relatively few people can sustain such intensive interventions in real-world settings. Moreover, current pharmacotherapies do not yet fully exploit autophagic flux as a target mechanism. Here, we discuss recent work, which demonstrates that arginine catabolism is a tractable process to activate autophagy with utility to treat obesity and its complications. Hepatocyte-specific transgenic activation of arginine catabolism, or systemic administration of an anti-tumor pharmacotherapy, pegylated arginine deiminase, each promote energy expenditure and insulin sensitivity, and reduce dyslipidemia and hepatic steatosis in obese mice. These effects depend upon hepatocyte Fgf21, and whole-body Becn1 expression. The data suggest that hepatocyte and systemic arginine catabolism drive autophagy, and identify an index pharmacological agent to leverage this process.

Interventions in Nicotinamide Adenine Dinucleotide Metabolism, the Intestinal Microbiota and Microcin Peptide Antimicrobials.

A proper NADH/NAD + balance allows for the flow of metabolic and catabolic activities determining cellular growth. In Escherichia coli, more than 80 NAD + dependent enzymes are involved in all major metabolic pathways, including the post-transcriptional build-up of thiazole and oxazole rings from small linear peptides, which is a critical step for the antibiotic activity of some microcins. In recent years, NAD metabolism boosting drugs have been explored, mostly precursors of NAD + synthesis in human cells, with beneficial effects on the aging process and in preventing oncological and neurological diseases. These compounds also enhance NAD + metabolism in the human microbiota, which contributes to these beneficial effects. On the other hand, inhibition of NAD + metabolism has been proposed as a therapeutic approach to reduce the growth and propagation of tumor cells and mitigating inflammatory bowel diseases; in this case, the activity of the microbiota might mitigate therapeutic efficacy. Antibiotics, which reduce the effect of microbiota, should synergize with NAD + metabolism inhibitors, but these drugs might increase the proportion of antibiotic persistent populations. Conversely, antibiotics might have a stronger killing effect on bacteria with active NAD + production and reduce the cooperation of NAD + producing bacteria with tumoral cells. The use of NADH/NAD + modulators should take into consideration the use of antibiotics and the population structure of the microbiota.

Regulatory network-based model to simulate the biochemical regulation of chondrocytes in healthy and osteoarthritic environments

In osteoarthritis (OA), chondrocyte metabolism dysregulation increases relative catabolic activity, which leads to cartilage degradation. To enable the semiquantitative interpretation of the intricate mechanisms of OA progression, we propose a network-based model at the chondrocyte level that incorporates the complex ways in which inflammatory factors affect structural protein and protease expression and nociceptive signals. Understanding such interactions will leverage the identification of new potential therapeutic targets that could improve current pharmacological treatments. Our computational model arises from a combination of knowledge-based and data-driven approaches that includes in-depth analyses of evidence reported in the specialized literature and targeted network enrichment. We achieved a mechanistic network of molecular interactions that represent both biosynthetic, inflammatory and degradative chondrocyte activity. The network is calibrated against experimental data through a genetic algorithm, and 81% of the responses tested have a normalized root squared error lower than 0.15. The model captures chondrocyte-reported behaviors with 95% accuracy, and it correctly predicts the main outcomes of OA treatment based on blood-derived biologics. The proposed methodology allows us to model an optimal regulatory network that controls chondrocyte metabolism based on measurable soluble molecules. Further research should target the incorporation of mechanical signals.

Identification of thrombin as a key regulator of chondrocyte catabolic activity through RNA-Seq and experimental verification

The present study was designed to explore the relationship between thrombin and catabolic activity in chondrocytes. Primary rat chondrocytes were cultured for 24 h with rat serum (RS), rat plasma (RP), or rat plasma supplemented with thrombin (RPT). RNA-sequencing was then performed. Cell proliferation was analyzed by EdU uptake, CCK-8 assays and protein–protein interaction (PPI) network of proliferation-related genes. Heatmaps were used to visualize differences in gene expression. Gene Ontology (GO) enrichment analyses of up- and down-regulated differentially expressed genes were conducted. Molecular probes were used to label the endoplasmic reticulum in chondrocytes from three treatment groups. Immunofluorescence and Safranin O staining were used to assess type II collagen (Col2a1) expression and proteoglycan synthesis, whereas Lox expression was assessed by immunocytochemistry. The expression of enzymes involved in the synthesis and maturation of extracellular matrix (ECM) components and chemokines were measured by qPCR while matrix metalloproteinases (MMPs) levels were evaluated by Western blotting. Relevant nodules were selected through further PPI network analyses. A total of 727 and 1162 genes were up- and down-regulated based on the Venn diagrams comparison among groups. Thrombin was thus able to promote chondrocyte proliferation and a shift towards fibrotic morphology, while upregulating MMPs and chemokines linked to ECM degradation. In addition, thrombin decreased the enzyme expression involved in the synthesis and maturation of ECM.

Gamma-Aminobutyrate Transaminase Protects against Lipid Overload-Triggered Cardiac Injury in Mice.

Lipid overload contributes to cardiac complications of diabetes and obesity. However, the underlying mechanisms remain obscure. This study investigates the role of gamma-aminobutyrate transaminase (ABAT), the key enzyme involved in the catabolism of γ-aminobutyric acid (GABA), in lipid overload-induced cardiac injury. Microarray revealed a down-regulation of ABAT mRNA expression in high fat diet (HFD)-fed mouse hearts, which correlated with a reduction in ABAT protein level and its GABA catabolic activity. Transgenic mice with cardiomyocyte-specific ABAT over-expression (Tg-ABAT/tTA) were generated to determine the role of ABAT in lipid overload-induced cardiac injury. Feeding with a HFD to control mice for 4 months reduced ATP production and the mitochondrial DNA copy number, and induced myocardial oxidative stress, hypertrophy, fibrosis and dysfunction. Such pathological effects of HFD were mitigated by ABAT over-expression in Tg-ABAT/tTA mice. In cultured cardiomyocytes, palmitate increased mitochondrial ROS production, depleted ATP production and promoted apoptosis, all of which were attenuated by ABAT over-expression. With the inhibition of ABAT’s GABA catabolic activity, the protective effects of ABAT remained unchanged in palmitate-induced cardiomyocytes. Thus, ABAT protects the mitochondrial function in defending the heart against lipid overload-induced injury through mechanisms independent of its GABA catabolic activity, and may represent a new therapeutic target for lipid overload-induced cardiac injury.

Short-Term Resilience of Soil Microbial Communities and Functions Following Severe Environmental Changes

Soil microorganisms are key drivers of soil biochemical processes, but the resilience of microbial communities and their metabolic activity after an extreme environmental change is still largely unknown. We studied structural (bacterial and fungal communities) and functional responses (soil respiration, adenosine triphosphate (ATP) content, hydrolase activities involved in the mineralization of organic C, N, P and S, and microbial community-level physiological profiles (CLPPs)) during the microbial recolonization of three heat-sterilized forest soils followed by cross- or self-reinoculation and incubation for 1, 7 and 30 days. Soil ATP content, biochemical activities and CLPP were annihilated by autoclaving, whereas most of the hydrolase activities were reduced to varying extents depending on the soil and enzyme activity considered. During the incubation period, the combination of self- and cross-reinoculation of different sterilized soils produced rapid dynamic changes in enzymatic activity as well as in microbial structure and catabolic activity. Physicochemical properties of the original soils exerted a major influence in shaping soil functional diversity, while reinoculation of sterilized soils promoted faster and greater changes in bacterial community structure than in fungal communities, varying with incubation period and soil type. Our results also confirmed the importance of microbial richness in determining soil resilience under severe disturbances. In particular, the new microbial communities detected in the treated soils revealed the occurrence of taxa which were not detected in the original soils. This result confirmed that rare microbial taxa rather than the dominant ones may be the major drivers of soil functionality and resilience.

Shikonin, a promising therapeutic drug for osteoarthritis that acts via autophagy activation

Osteoarthritis (OA) is a chronic joint degenerative disease characterised by narrowed articular space, formation of surrounding osteophytes, and subchondral bone sclerosis. OA is caused by cartilage degeneration, which is closely correlated with the disequilibrium of anabolism and catabolism in chondrocytes. Previous studies have revealed that autophagy plays a significant role in maintaining the balance of anabolic and catabolic activities. Thus, targeting autophagy may be a promising therapeutic strategy for OA. Shikonin, a traditional Chinese herbal medicine isolated from flavonoid glucuronide, has drawn focus for its role in activating autophagy. In this study, the mRNA and protein level of a disintegrin and metalloproteinase with thrombospondin motifs-5 and matrix metalloproteinases-1 decreased with shikonin treatment, in the IL-1β-induced OA cell model. On the contrary, IL-1β-induced downregulation of Aggrecan and Collagen II was ameliorated following shikonin treatment. In addition, the upregulation of autophagy-related marker genes Beclin-1 and LC3II/LC3I in chondrocytes indicated that autophagy could be activated upon shikonin treatment. Moreover, shikonin’s promotion of anabolism in chondrocytes through autophagy activation corresponded with the results from the examination using chloroquine, an autophagy inhibitor. OA mouse cartilage tissues were stained with safranin O and fast green dyes. Results were analysed using the Osteoarthritis Research Society International (OARSI) score, and suggested that mice cartilage degeneration was alleviated after shikonin treatment. Altogether, we identified that shikonin might be a novel promising drug for OA treatment.

Assessment of the Carbon and Nitrogen Mineralisation of Digestates Elaborated from Distinct Feedstock Profiles

The carbon (C) and nitrogen (N) mineralisation rates of five digestates were studied and compared with pig slurry, compost, and a solid fraction of digestate in aerobic incubation experiments. The objective was to identify the most relevant drivers of C and N mineralisation based on the physicochemical properties of the products. Net organic nitrogen mineralisation of digestates (Nmin,net) was on average 30%, although the range was relatively wide, with digestate from pig manure (39%) reaching double the value of digestate from sewage sludge (21%). The total carbon to total nitrogen (TC:TN) (r = −0.83, p < 0.05) and ammonium nitrogen to total nitrogen (NH4+-N:TN) (r = 0.83, p < 0.05) ratios of the products were strongly correlated with Nmin,net, adequately mirroring the expected fertilising potential of the products. The digestates had C sequestration values between 50 and 81% of applied total organic carbon (TOC), showcasing their potential to contribute to C build-up in agricultural soils. The carbon use efficiency of the amended soils was negatively correlated with dissolved organic carbon (DOC) (r = −0.75, p < 0.05) suggesting that catabolic activities were promoted proportionately to the DOC present in these products. Ratios of DOC:TOC (r = −0.88, p < 0.01) and TC:TN (r = 0.92, p < 0.01) were reliable predictors of the fraction of C that would remain one year after its incorporation and thus could be used as simple quality parameters to denote the C sequestration potential of digestates prior to their use in the field.

Biodegradation dynamics disparity between n‐alkanes and polycyclic aromatic hydrocarbons in the vadose zone: A critical review

AbstractIn the shallow terrestrial subsurface, bioavailability often controls biodegradation rates of various hydrophobic organic pollutants, such as hydrocarbons. Microorganism‐mediated depletion of n‐alkanes and polycyclic aromatic hydrocarbons (PAHs) in the vadose zone proceeds with distinctively different rates and kinetics. The observed disparity in biodegradation dynamics between these two classes of hydrocarbons are described here in terms of the Best equation, which allows for a complex process of hydrocarbon contaminant depletion to be explained in terms of the physically relevant processes. This equation combines terms describing contributions of two key elements of hydrocarbon biodegradation—the intrinsic catabolic activity of microorganisms and the mass transfer process delivering substrate to active microorganisms. If substrate supply is slow, biodegradation process is availability‐limited because microorganisms consume the substrate faster than it can be delivered. Conversely, when the mass transfer of substrate is faster than the microbial consumption, biodegradation rate tends to be controlled by metabolic kinetics.The evaluation conducted in this study ascertains that the critical factor limiting the rate and extent of PAH biodegradation is the mass transfer rather than the intrinsic microbial activity that appears to govern the rate of n‐alkane biodegradation. The specifics of mass transfer are determined by the magnitude of the substrate–soil interactions. Whereas sorption of n‐alkanes is controlled by weak hydrophobic and van der Waals forces, PAHs tend to bind to the soil matrix by much stronger electron‐donor–acceptor interactions. Stronger interactions between aromatic compounds and soil components translate into the higher activation energies for desorption of PAHs and therefore a slower mass transfer process. This aspect of the substrate–soil interaction explains a more prominent effect of mass transfer limitation on biodegradation dynamics of PAHs compared to that of the corresponding n‐alkanes.