Catabolic Functions Research Articles

Microbial catabolism of lindane in distinct layers of acidic paddy soils combinedly affected by different water managements and bioremediation strategies

The environmental fate of the recalcitrant organic chlorine insecticide lindane and its removal from contaminated soils are still of great concern. However, the key factors influencing microbial removal of lindane from paddy soils with intermittent flooding and draining remain largely unknown. Here, we conducted laboratory experiments to investigated lindane biodegradation in different layers of typical acidic paddy soils under different water managements and bioremediation strategies, together with the changes of functional bacterial consortium, key genes and metabolic pathways. It was found that under flooded conditions, lindane spiking significantly stimulated the growth of some bacterial genera with potential anaerobic catabolic functions in both top- (0–20 cm depth) and subsoil (20–40 cm depth), leading to the shortest half-life of lindane with 7.6–9.0 d in the topsoil. In contrary, lindane spiking dramatically stimulated the growth of bacterial members with aerobic catabolic functions under drained conditions, exhibiting half-lives of lindane with 85–131 d and 18–23 d in the top- and subsoil, respectively. Overall, biostimulation coupled with flooding management would be the better combination for increased lindane bioremediation. Functional genes involved in lindane degradation and retrieved from metagenomic data further supported the anaerobic and aerobic biodegradation of lindane under flooded and drained conditions, respectively. Moreover, the integrated network analysis suggested water management and organic matter were the primary factors shaped the assembly of functional bacteria in lindane degradation, among which Clostridium and Rhodanobacter were the key anaerobic and aerobic functional genera, respectively. Taken together, our study provides a comprehensive understanding of lindane biodegradation in distinct layers of acidic paddy soils that were combinedly affected by different water managements and bioremediation strategies.

Ubiquitin Carboxyl-Terminal Hydrolases (UCHs): Potential Mediators for Cancer and Neurodegeneration.

Emerging evidence suggests an inverse association between cancer and neurodegenerative diseases (NDD). Although phenotypically different, both diseases display a significant imbalance in the ubiquitination/deubiquitination processes. Therefore, we particularly investigated the expression of ubiquitin C-terminal hydrolases (UCHs: UCH-L1, UCH-L3, UCH-L5 and BAP1), a subfamily of deubiquitinating enzymes (DUBs), using publically available datasets (GTEx, TCGA) and observed altered expression of UCH-L1, UCH-L3, UCH-L5 in 17 cancer types. Interestingly, UCH-L1 (known to be enriched in neurons and interacting with the Parkinson’s disease-associated protein α-synuclein) appeared to be a prognostic indicator of unfavorable outcome in endometrial and urothelial cancer, while increased expression of UCH-L3 and UCH-L5 was associated with poor survival in liver and thyroid cancer, respectively. In normal tissues, UCH-L1 was found to be strongly expressed in the cerebral cortex and hypothalamus, while UCH-L3 expression was somewhat higher in the testis. The occurrence of mutation rates in UCHs also suggests that BAP1 and UCH-L5 may play a more dominant role in cancers than UCH-L1 and UCH-L3. We also characterized the functional context and configuration of the repeat elements in the promoter of DUBs genes and found that UCHs are highly discriminatory for catabolic function and are mainly enriched with LINE/CR1 repeats. Regarding the thesis of an inverse association between cancer and NDD, we observed that among all DUBs, UCHs are the one most involved in both entities. Considering a putative therapeutic potential based on presumed common mechanisms, it will be useful to determine whether other DUBs can compensate for the loss of UCH activity under physiological conditions. However, experimental evidence is required to substantiate this argument.

TFEB Modulates p21/WAF1/CIP1 during the DNA Damage Response.

The MiT/TFE family of transcription factors (MITF, TFE3, and TFEB), which control transcriptional programs for autophagy and lysosome biogenesis have emerged as regulators of energy metabolism in cancer. Thus, their activation increases lysosomal catabolic function to sustain cancer cell growth and survival in stress conditions. Here, we found that TFEB depletion dramatically reduces basal expression levels of the cyclin-dependent kinase (CDK) inhibitor p21/WAF1 in various cell types. Conversely, TFEB overexpression increases p21 in a p53-dependent manner. Furthermore, induction of DNA damage using doxorubicin induces TFEB-mediated activation of p21, delays G2/M phase arrest, and promotes cell survival. Pharmacological inhibition of p21, instead, abrogates TFEB-mediated protection during the DNA damage response. Together, our findings uncover a novel and direct role of TFEB in the regulation of p21 expression in both steady-state conditions and during the induction of DNA-damage response (DDR). Our observations might open novel therapeutic strategies to promote cancer cell death by targeting the TFEB-p21 pathway in the presence of genotoxic agents.

Alpha-Synuclein and LRRK2 in Synaptic Autophagy: Linking Early Dysfunction to Late-Stage Pathology in Parkinson's Disease.

The lack of effective disease-modifying strategies is the major unmet clinical need in Parkinson’s disease. Several experimental approaches have attempted to validate cellular targets and processes. Of these, autophagy has received considerable attention in the last 20 years due to its involvement in the clearance of pathologic protein aggregates and maintenance of neuronal homeostasis. However, this strategy mainly addresses a very late stage of the disease, when neuropathology and neurodegeneration have likely “tipped over the edge” and disease modification is extremely difficult. Very recently, autophagy has been demonstrated to modulate synaptic activity, a process distinct from its catabolic function. Abnormalities in synaptic transmission are an early event in neurodegeneration with Leucine-Rich Repeat Kinase 2 (LRRK2) and alpha-synuclein strongly implicated. In this review, we analyzed these processes separately and then discussed the unification of these biomolecular fields with the aim of reconstructing a potential “molecular timeline” of disease onset and progression. We postulate that the elucidation of these pathogenic mechanisms will form a critical basis for the design of novel, effective disease-modifying therapies that could be applied early in the disease process.

Glucose Involvement in Articular Cartilage Remodeling

Currently, the interest in studying glucose as a signaling molecule and a regulator of chondrocyte metabolism is increasing significantly. There is little available data on chondrocytes’ ability to respond to extracellular glucose concentration changes that help them to avoid harmful effects resulting from the lack or accumulation of intracellular glucose. We have collected and analyzed the information about the mechanism of glucose influence on articular cartilage chondrocyte in this study. We have learned that chondrocytes adapt to both high and low glucose concentrations by modulating the synthesis and degradation of GluT1. Consequently, glucose in different concentrations affects many fundamental cellular functions such as the cartilage matrix synthesis and disruption, proliferation, differentiation, and apoptosis. To build a functional model of glucose participation in articular cartilage remodeling the exhaustive search and analysis of literature has been performed using open access resources. The scheme reflects key processes that have direct or indirect effects on the catabolic or anabolic function of chondrocytes. As a result, we have created a functional model that shows the effect of glucose on the suppression or expression of compounds that are actively involved in cartilage tissue remodeling. For example, these are compounds such as nitric oxide, aggrecans and type II collagen and others. Despite the role of glucose in energy metabolism in all cell types, including chondrocytes, high concentrations of glucose can also have a harmful effect. The advantage of this model is systematic data, which facilitates the perception of the results and their relevance.

Zwitterionic HILIC tandem mass spectrometry with isotope dilution for rapid, sensitive and robust quantification of pyridine nucleotides in biological extracts

The pyridine nucleotides nicotineamide adenine dinucleotide (NAD) and nicotineamide adenine dinucleotide phosphate (NADP) are conserved coenzymes across all domains of life, and are involved in more than 200 different hydride transfer reactions supporting essential catabolic and anabolic functions. The intracellular levels of these metabolites, and the ratio of their oxidized to reduced forms regulate an extensive network of reactions ranging beyond metabolism. Hence, monitoring their intracellular levels provides information about, but not limited to, the metabolic state of a cell or tissue. Interconversion between oxidized and reduced forms, varying pH liability and varying intracellular concentrations of the different species leaves absolute quantification of the pyridine nucleotides analytically challenging. These polar metabolites are poorly retained on conventional reverseed-phase stationary phases without ion-pair reagents that contaminates the LC-system. Herein we demonstrate that zwitterionic HILIC-tandem mass spectroemtry can be applied to successfully resolve the pyridine nucleotides in biological extracts in a fast, robust and highly sensitive way. The presented method applies isotope dilution to compensate potential loss of these labile metabolites and is validated for low, medium and high biomass samples of two popular biological model systems; Escherichia coli and the human cell line JJN-3. High stability and rapid sample preparation without solvent removal allows for long sequence runs, making this method ideal for high-throughput analysis of biological extracts.

Salinization effects on stream biofilm functioning

Secondary salinization threatens fresh waters worldwide leading to deleterious ecological and economic consequences. The goal of the present study was to assess the potential response of catabolic functions (respiration rate, activities of acid phosphatase and β-glucosidase) of stream biofilms to salinization. Biofilm assemblages from five streams were incubated under controlled conditions in microcosms in spring water under four different treatments: no salt addition (0) and adding 0.25, 1, and 4 g NaCl l−1. Respiration rate at 0.25 g NaCl l−1 was higher than that at 1 and 4 g l−1, the latter concentration presenting the lowest value. Acid phosphatase activity was highest in the treatment without salt addition. The activity of β-glucosidase was highest in the non-salted treatment and at 1 g NaCl l−1. Results reveal salinization as an important threat for catabolism-related functions of stream biofilms, which can compromise nutrient cycling in small shaded streams and consequently the ecosystem services that they provide.

Lactate: Fueling the fire starter.

It is becoming increasingly appreciated that intermediates of metabolic pathways, besides their anabolic and catabolic functions, can act as signaling molecules and influence the outcome of immune responses. Although lactate was previously considered as a waste product of glucose metabolism, accumulating evidence has highlighted its pivotal role in regulating diverse biological processes, including immune cell polarization, differentiation and effector functions. In addition, lactate is a key player in modulating tumor immune surveillance. Hence, targeting lactate‐induced signaling pathways is a promising tool to reduce inflammation, to prevent autoimmunity and to restore anti‐tumor immune response.This article is characterized under:Biological Mechanisms > Metabolism

Human Synovia Contains Trefoil Factor Family (TFF) Peptides 1-3 Although Synovial Membrane Only Produces TFF3: Implications in Osteoarthritis and Rheumatoid Arthritis.

Objective: Trefoil factor family peptide 3 (TFF3) has been shown to support catabolic functions in cases of osteoarthritis (OA). As in joint physiology and diseases such as OA, the synovial membrane (SM) of the joint capsule also plays a central role. We analyze the ability of SM to produce TFF compare healthy SM and its secretion product synovial fluid (SF) with SM and SF from patients suffering from OA or rheumatoid arthritis (RA). Methods: Real-time PCR and ELISA were used to measure the expression of TFFs in healthy SM and SM from patients suffering from OA or RA. For tissue localization, we investigated TFF1-3 in differently aged human SM of healthy donors by means of immunohistochemistry, real-time PCR and Western blot. Results: Only TFF3 but not TFF1 and -2 was expressed in SM from healthy donors as well as cases of OA or RA on protein and mRNA level. In contrast, all three TFFs were detected in all samples of SF on the protein level. No significant changes were observed for TFF1 at all. TFF2 was significantly upregulated in RA samples in comparison to OA samples. TFF3 protein was significantly downregulated in OA samples in comparison to healthy samples and cases of RA significantly upregulated compared to OA. In contrast, in SM TFF3 protein was not significantly regulated. Conclusion: The data demonstrate the production of TFF3 in SM. Unexpectedly, SF contains all three known TFF peptides. As neither articular cartilage nor SM produce TFF1 and TFF2, we speculate that these originate with high probability from blood serum.

Understanding organelle biogenesis during the autophagy process in the RPE

AbstractThe retinal pigmented epithelium (RPE) is critically important to retinal homeostasis, in part due to it's very active processes of phagocytosis and autophagy. Both of these processes depend upon the normal functioning of lysosomes, organelles which must fuse with (auto)phagosomes to deliver the hydrolases that effect degradation of cargo. It has become clear that signaling through mTOR complex 1 (mTORC1), is very important in the regulation of lysosomal function. Lysosomes are cellular organelles that modulate various processes such as autophagy and heterophagy, plasma membrane repair, cholesterol homeostasis, and cell death. The number, size, and content of lysosomes vary in different cell types. The distribution of lysosomes within the cell is determined by the nutrient sensing machinery at the lysosomal membrane, and is an important factor in lysosomal catabolic function. In this course, we will focus on the effector molecules present in RPE cells that impact the lysosomal‐autophagic pathway in retinal health and disease.

Plant cover of Ammopiptanthus mongolicus and soil factors shape soil microbial community and catabolic functional diversity in the arid desert in Northwest China

Although the spatial patterns of soil microbial community composition are well studied, little is known about the main factors driving microbial distributions in desert ecosystems. Therefore, the objective of this study was to examine the comprehensive effect of spatial scale, plant cover and environmental properties on soil microorganisms under Ammopiptanthus mongolicus canopies at 5 desert locations in Northwest China. Sampling site significantly influenced the soil microbial community structure and metabolic functions under A. mongolicus canopies. Variation of soil microbial communities was mostly attributed to the simultaneous effects of plant cover and soil factors, while purely plant cover explained more variation in catabolic function than did the principle coordinates of neighbour matrices (PCNM) and soil factors. Soil microbial structure and catabolic metabolism were both significantly affected by phosphatase, glomalin and soil organic carbon. Bacterial and actinomycete phospholipid fatty acids (PLFAs) were positively correlated with ammonium nitrogen (N), and the utilization of carbohydrates, carboxylic acids and amino acids was positively correlated with Olsen phosphorus (P). Bacteria (1.43–4.79 nmol∙g−1) were most common in the microbial community, followed by actinomycetes (0.54–1.89 nmol∙g−1) and fungi (0.29–0.48 nmol∙g−1). Carbohydrates (12%–85%) and amino acids (5%–59%) were the main carbon sources for soil microbes. Soil microbial community abundance and catabolic utilization were significantly higher in the rhizosphere of A. mongolicus than in the bulk soils, and principal component analyses (PCAs) significantly separated the rhizospheric soil microbes from those of infertile bulk soils. The results of this study support the conclusion that soil microbial composition and catabolic functional diversity in desert soils are spatially predictable and determined more by specific soil properties and plant cover than by large-scale distance. This research provides a basis for evaluating the management of soil resources and microbial function in desert environments.

Regulation of Hepatic Metabolism, Recent Advances, and Future Perspectives.

The purpose of this review is to provide a brief summary of recent advances in our understanding of liver metabolism. The critical role of the liver in controlling whole-body energy homeostasis makes such understanding crucial to efficiently design new treatments for metabolic syndrome diseases, including type 2 diabetes (T2D). Significant advances have been made regarding our understanding of the direct and indirect effects of insulin on hepatic metabolism and the communication between the liver and other tissues. Moreover, the catabolic functions of glucagon, as well as the importance of hepatic redox status for the regulation of glucose production, are emerging as potential targets to reduce hyperglycemia. A resolution to the long-standing question "insulin suppression of hepatic glucose production, direct or indirect effect?" is starting to emerge. New advances in our understanding of important fasting-induced hepatic metabolic fluxes may help design better therapies for T2D.

Abstract 632: MTOR-Proteasome Imbalance Upon Deletion of Pras40 Inhibits Cardiac Growth but Results in Cardiac Failure

Background: The mammalian target of Rapamycin complex 1 (mTORC1) increases cell size by initiating translation as well as by inhibiting catabolic functions such as proteolysis or autophagy. We have previously proposed Proline-rich Akt substrate 1 (Pras40) as a cardioprotective endogenous inhibitor of mTOR-dependent protein synthesis during pathologic growth. Pras40 is released from mTORC1 during growth, but other interactions are largely unknown. In a proteomic screen we have now found a novel interaction of Pras40 with the 26S proteasome during hypertrophy. We hypothesize that Pras40 directly links the mTOR-dependent protein synthesis network and the proteasomal degradation machinery to balance both processes. Methods and Results: To determine the growth-dependent Pras40-interactome, we identified binding partners by proximity-dependent biotin labeling using APEX2 and subsequent mass-spec. Interestingly, aside from interactions with the mTOR-dependent translation machinery, we find Pras40 binding to subunits of the 26S proteasome only during growth. To test consequences of Pras40 deletion on cardiac function in vivo , we generated cardiomycyte-specific knock-out mice, that we subjected to pathologic hypertrophy (TAC). Conversely to Pras40 overexpression, we find growth significantly blunted in KO animals, function reduced and fibrosis elevated. mTORC1 signaling as well as autophagy and proteasomal function are severely disturbed in KO animals. Mechanistically, chymotrypsin-like 26S proteasome activity is blunted in KO hearts as well as isolated cardiomyocytes from KO animals, whereas overexpression shows reciprocal effects in myocytes. Disturbed proteasomal function in KO mice leads to severe alterations in metabolic functions highlighting the importance of both intact mTORC1 signaling and proper proteasomal maintenance during cardiac stress. Conclusion: In this study we find a novel mechanism how mTOR and proteasomal function are linked in the diseased heart. We provide evidence that Pras40 links anabolic protein synthesis and catabolic proteolysis in the heart: At rest, Pras40 binds and inhibits mTOR, but when released during pathologic growth, Pras40 directly interacts with the 26S proteasome and modulates its activity.

Bisphenol A increases intestinal permeability through disrupting intestinal barrier function in mice

That an alteration of the intestinal permeability is associated with gut barrier function has been increasingly evident, which plays an important role in human and animal health. Bisphenol A (BPA), an industrial compound used worldwide, has recently been classified as an environmental pollutant. One of our earlier studies has demonstrated that BPA disrupts the intestinal barrier function by inducing apoptosis and inhibiting cell proliferation in the human colonic epithelial cells line. In this study, we investigated the effects of dietary BPA uptake on the colonic barrier function in mice, as well as the intestinal permeability. Dietary BPA uptake was observed to destroy the morphology of the colonic epithelium and increase the pathology score. The levels of endotoxin, diamine peroxidase, D-lactate, and zonulin were found to have been significantly elevated in both plasma and colonic mucosa. A decline in the number of intestinal goblet cells and in mucin 2 gene expression was observed in the mice belonging to the BPA group. The results of immunohistochemistry revealed that the expression of tight junction proteins (ZO-1, occludin, and claudin-1) in colonic epithelium of BPA mice decreased significantly, and their gene abundance was also inhibited. Moreover, dietary BPA uptake was also found to have significantly reduced colonic microbial diversity and altered microbial structural composition. The functional profiles of colonic bacterial community exhibited adverse effects of dietary BPA intake on the endocrine and digestive systems, as well as the transport and catabolism functions. Collectively, our study highlighted that dietary BPA increased the colonic permeability, and this effect was closely related to the disruption of intestinal chemistry and physical and biological barrier functions.

Heterologous Microcompartment Assembly in Bacillaceae: Establishing the Components Necessary for Scaffold Formation

Bacterial microcompartments (BMCs) are organelles that host specific biochemical reactions for both anabolic and catabolic functions. Engineered morphologically diverse BMCs bearing heterologous enzymatic pathways have shown enhanced productivity for commodity chemicals, which makes BMCs an important focus for metabolic engineering. Gaining control of BMC assembly and incorporation of a heterologous enzymatic cargo has yet to be achieved in thermophiles. Herein, we address this by first conducting a detailed bioinformatic analysis of the propanediol utilization (pdu) operon in the thermophile Parageobacillus thermoglucosidasius. We then demonstrated, in vivo, the ability to assemble the native BMCs at an elevated temperature of 60 °C. Heterologous expression of Pdu shell proteins from P. thermoglucosidasius in Bacillus subtilis resulted in the assembly of a single tubular BMC with an average length of 1.4 μm; BMCs assembled after a 20 min induction of expression of the shell operons. Moreover, we show that it is possible to target the monomeric superfolder GFP (msfGFP) to the interior of the compartment by fusion of an N-terminal sequence of the propanediol utilization protein (PduP) of at least 24 amino acids. This study establishes the feasibility of constructing cell factories for small molecules in industrially important Bacillus and Geobacillus spp. by heterologous cargo-carrying BMC production and assembly. Additionally, the study provides experimental confirmation that BMCs are produced in thermophilic bacteria, which opens a path for future research on repurposing the native organelles to provide new functionality at elevated temperatures.

Quantitative Variation in m.3243A\u2009>\u2009G Mutation Produce Discrete Changes in Energy Metabolism

Mitochondrial DNA (mtDNA) 3243A > G tRNALeu(UUR) heteroplasmic mutation (m.3243A > G) exhibits clinically heterogeneous phenotypes. While the high mtDNA heteroplasmy exceeding a critical threshold causes mitochondrial encephalomyopathy, lactic acidosis with stroke-like episodes (MELAS) syndrome, the low mtDNA heteroplasmy causes maternally inherited diabetes with or without deafness (MIDD) syndrome. How quantitative differences in mtDNA heteroplasmy produces distinct pathological states has remained elusive. Here we show that despite striking similarities in the energy metabolic gene expression signature, the mitochondrial bioenergetics, biogenesis and fuel catabolic functions are distinct in cells harboring low or high levels of the m.3243 A > G mutation compared to wild type cells. We further demonstrate that the low heteroplasmic mutant cells exhibit a coordinate induction of transcriptional regulators of the mitochondrial biogenesis, glucose and fatty acid metabolism pathways that lack in near homoplasmic mutant cells compared to wild type cells. Altogether, these results shed new biological insights on the potential mechanisms by which low mtDNA heteroplasmy may progressively cause diabetes mellitus.

Embryonic and postnatal tendon cells respond differently to interleukin-1β.

Adult tendons heal as scar tissue, whereas embryonic tendons heal scarlessly via unknown mechanisms. Scarred tendon healing results from inflammation-driven imbalances in anabolic and catabolic functions. To test scarless versus scarring age tendon cell responses to inflammatory conditions, we treated embryonic and postnatal tendon cells with interleukin (IL)-1β and characterized expression of collagens, matrix metalloproteinases (MMPs), inflammatory mediators, and phosphorylation of signaling molecules. At baseline, postnatal cells expressed significantly higher levels of inflammatory mediators. When treated with IL-1β, both postnatal and embryonic cells upregulated inflammatory mediators and MMPs. Notably, postnatal cells secreted inflammatory factors up to 12.5 times the concentration in embryonic cultures. IL-1β activated NF-κB p65 and p38 mitogen-activated protein kinase(MAPK) pathways in both cell types, but phosphorylated p38 MAPK levels were two times higher in postnatal than embryonic cells. Our results suggest that scarred healing tendon cells respond to proinflammatory cytokines by promoting an imbalance in anabolic and catabolic functions, and that the heightened response involves p38 MAPK signaling activity. In contrast, embryonic cell responses are smaller in magnitude. These intriguing findings support a potential role for tendon cells in determining scarless versus scarred healing outcomes by regulating the balance between anabolic and catabolic functions during tendon healing.

Knee Osteoarthritis Molecular Subgroups Revealed by Pathogenic Joint Gene Expression

Background: Osteoarthritis (OA) is a complex and heterogeneous condition, and one of the most common degenerative joint diseases. A standardized OA classification based on molecular criteria has yet to be defined. We performed transcriptomic profiling to determine the different molecular signatures associated with knee OA phenotypes. Methods: Five centres clinical research with next-generation sequencing was carried out using 201 samples from patients with knee osteoarthritis. Transcriptomic analysis and unsupervised clustering methods were performed on 131 cartilage samples. To investigate tissue crosstalk of the whole knee microenvironment, transcriptomic analysis was performed in 60 synovia and 65 subchondral bone samples. Findings: We identified four OA subgroups with distinct biological signatures: 1) the glycosaminoglycan metabolic disorder subgroup highly expressed ACAN, lowly expressed VCAN, and was enriched with glycosaminoglycan metabolic functions; 2) the collagen metabolic disorder subgroup presented with osteophyte formation, highly expressed COL1A1 and COL6A1, and was enriched with collagen catabolic functions; 3) the sensory neurons activated subgroup highly expressed GRIK2 and GRM7, and was enriched with synapse assembly functions; and 4) the immunogenic subgroup presented with high inflammation and narrow joint space, highly expressed IL1AŸ and CD34, and was enriched with immune responses. We also explored immune cell composition and tissue crosstalk for three identified metabolic disorder subgroups. Interpretation: These findings challenge the classical diagnosis model based on medical imaging, revealing distinct molecular subgroups in knee OA patients, and opening the door to precision diagnosis and treatment of OA. Funding Statement: This work was financially supported by the National Key R&D Program of China (2017YFA0104902), the National Natural Science Foundation of China (81630065, 31830029, 81802195) grants and China Postdoctoral Science Foundation (2017M621913). Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: Informed consent was obtained from all the participants. The study was approved by the local clinical ethics committees of Zhejiang University School of Medicine and the affiliated hospital of Wenzhou Medical University (2017KYLL11).

Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies.

Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant-catabolic consortia remain largely unknown. In this study, an original enrichment (AT) capable of degrading atrazine was obtained. And two enrichments – with a better/worse atrazine-degrading efficiency (ATB/ATW) – were derived from the original enrichment AT by continuous sub-enrichment with or without atrazine. Subsequently, an Arthrobacter sp. strain, AT5, that was capable of degrading atrazine was isolated from enrichment AT. The bacterial community structures of these three enrichments were investigated using high-throughput sequencing analysis of the 16S rRNA gene. The atrazine-degrading efficiency improved as the abundance of Arthrobacter species increased in enrichment ATB. The relative abundance of Arthrobacter was positively correlated with those of Hyphomicrobium and Methylophilus, which enhanced atrazine degradation via promoting the growth of Arthrobacter. Furthermore, six genera/families such as Azospirillum and Halomonas showed a significantly negative correlation with atrazine-degrading efficiency, as they suppressed atrazine degradation directly. These results suggested that atrazine-degrading efficiency was affected by not only the degrader but also some non-degraders in the community. The promotion and suppression of atrazine degradation by Methylophilus and Azospirillum/Halomonas, respectively, were experimentally validated in vitro, showing that shifts in both the composition and abundance in consortia can drive the change in the efficiency of catabolic function. This study provides valuable information for designing enhanced bioremediation strategies.

Molecular and histological characteristics of bovine caudal nucleus pulposus by combined changes in hydrostatic and osmotic pressures in vitro.

ABSTRACTIntervertebral disc degeneration is ubiquitous among aging patients, and altered matrix homeostasis is one of the key features of this condition. Physicochemical stresses have a significant impact on matrix homeostasis as they lead to progressive degeneration and may be associated with spinal pain and dysfunction. Thus, it is important to understand the cellular and matrix characteristics of nucleus pulposus in response to these stresses, which include hydrostatic and osmotic pressures during alternate loading conditions. We hypothesized that a combination of changes in hydrostatic pressure and in osmotic pressure that mimic normal, daily spinal stress would stimulate anabolic function, whereas a non‐realistic combination of those stresses would stimulate catabolic function in nucleus pulposus cells. We examined the effects of these combined stresses, represented by 12 systematic conditions, on the metabolic activities of enzymatically isolated bovine caudal nucleus pulposus in vitro. We measured the gene expression of extracellular matrix (ECM) molecules and proliferating cell nuclear antigen (PCNA) and evaluated the quality of the matrix and the capability of cell proliferation immunohistologically. Combined cyclic hydrostatic pressure at 0.5 MPa, 0.5 Hz, and high osmotic pressure at 450 mOsm upregulated the aggrecan core protein and collagen type‐II gene expression significantly (p < 0.05), and showed trends of upregulation of chondroitin sulfate N‐acetylgalactosaminyltransferase 1, matrix metalloproteinase‐13, and PCNA. ECM, however, contained empty spaces at a high osmotic pressure with and without hydrostatic pressure. Since ECM has highly specialized physicochemical properties, homeostasis should involve not only phenotypic cellular behavior but also turnover of ECM. © 2018 The Authors. Journal of Orthopaedic Research® Published by Wiley Periodicals, Inc. on behalf of Orthopaedic Research Society. J Orthop Res 37:466–476, 2019.