Determination of trichloroacetic acid in environmental studies using carbon 14 and chlorine 36.

Radioisotopes carbon 14 and chlorine 36 were used to elucidate the environmental role of trichloroacetic acid (TCA) formerly taken to be a herbicide and a secondary air pollutant with phytotoxic effects. However, use of 14C-labeling posed again known analytical problems, especially in TCA extraction from the sample matrix. Therefore--after evaluation of available methods--a new procedure using decarboxylation of [1,2-14C]TCA combined with extraction of the resultant 14C-chloroform with a non-polar solvent and its subsequent radiometric measurement was developed. The method solves previous difficulties and permits an easy determination of amounts between 0.4 and 20 kBq (10 - 500 ng g(-1)) of carrier-less [1,2-14C]TCA in samples from environmental investigations. The procedure is, however, not suitable for direct [36Cl]TCA determination in chlorination studies with 36Cl. Because TCA might be microbially degraded in soil during extraction and sample storage and its extraction from soil or needles is never complete, the decarboxylation method--i.e. 2 h TCA decomposition to chloroform and CO2 in aqueous solution or suspension in closed vial at 90 degrees C and pH 4.6 with subsequent CHCl3 extraction-is recommended here, estimated V < 7%. Moreover, the influence of pH and temperature on the decarboxylation of TCA in aqueous solution was studied in a broad range and its environmental relevance is shown in the case of TCA decarboxylation in spruce needles which takes place also at ambient temperatures and might amount more than 10-20% after a growing season. A study of TCA distribution in spruce needles after below-ground uptake shows the highest uptake rate into current needles which have, however, a lower TCA content than older needle-year classes, TCA biodegradation in forest soil leads predominatingly to CO2

The formation and fate of chlorinated organic substances in temperate and boreal forest soils.

BACKGROUND, AIM AND SCOPE: Chlorine is an abundant element, commonly occurring in nature either as chloride ions or as chlorinated organic compounds (OCls). Chlorinated organic substances were long considered purely anthropogenic products; however, they are, in addition, a commonly occurring and important part of natural ecosystems. Formation of OCls may affect the degradation of soil organic matter (SOM) and thus the carbon cycle with implications for the ability of forest soils to sequester carbon, whilst the occurrence of potentially toxic OCls in groundwater aquifers is of concern with regard to water quality. It is thus important to understand the biogeochemical cycle of chlorine, both inorganic and organic, to get information about the relevant processes in the forest ecosystem and the effects on these from human activities, including forestry practices. A survey is given of processes in the soil of temperate and boreal forests, predominantly in Europe, including the participation of chlorine, and gaps in knowledge and the need for further work are discussed. RESULTS: Chlorine is present as chloride ion and/or OCls in all compartments of temperate and boreal forest ecosystems. It contributes to the degradation of SOM, thus also affecting carbon sequestration in the forest soil. The most important source of chloride to coastal forest ecosystems is sea salt deposition, and volcanoes and coal burning can also be important sources. Locally, de-icing salt can be an important chloride input near major roads. In addition, anthropogenic sources of OCls are manifold. However, results also indicate the formation of chlorinated organics by microorganisms as an important source, together with natural abiotic formation. In fact, the soil pool of OCls seems to be a result of the balance between chlorination and degradation processes. Ecologically, organochlorines may function as antibiotics, signal substances and energy equivalents, in descending order of significance. Forest management practices can affect the chlorine cycle, although little is at present known about how. DISCUSSION: The present data on the apparently considerable size of the pool of OCls indicate its importance for the functioning of the forest soil system and its stability, but factors controlling their formation, degradation and transport are not clearly understood. It would be useful to estimate the significance and rates of key processes to be able to judge the importance of OCls in SOM and litter degradation. Effects of forest management processes affecting SOM and chloride deposition are likely to affect OCls as well. Further standardisation and harmonisation of sampling and analytical procedures is necessary. CONCLUSIONS AND PERSPECTIVES: More work is necessary in order to understand and, if necessary, develop strategies for mitigating the environmental impact of OCls in temperate and boreal forest soils. This includes both intensified research, especially to understand the key processes of formation and degradation of chlorinated compounds, and monitoring of the substances in question in forest ecosystems. It is also important to understand the effect of various forest management techniques on OCls, as management can be used to produce desired effects

Antioxidant defense in quiescent cells determines selectivity of electron transport chain inhibition-induced cell death.

Mitochondrial electron transport chain (ETC) targeting shows a great promise in cancer therapy. It is particularly effective in tumors with high ETC activity where ETC-derived reactive oxygen species (ROS) are efficiently induced. Why modern ETC-targeted compounds are tolerated on the organismal level remains unclear. As most somatic cells are in non-proliferative state, the features associated with the ETC in quiescence could account for some of the specificity observed. Here we report that quiescent cells, despite increased utilization of the ETC and enhanced supercomplex assembly, are less susceptible to cell death induced by ETC disruption when glucose is not limiting. Mechanistically, this is mediated by the increased detoxification of ETC-derived ROS by mitochondrial antioxidant defense, principally by the superoxide dismutase 2 - thioredoxin axis. In contrast, under conditions of glucose limitation, cell death is induced preferentially in quiescent cells and is correlated with intracellular ATP depletion but not with ROS. This is related to the inability of quiescent cells to compensate for the lost mitochondrial ATP production by the upregulation of glucose uptake. Hence, elevated ROS, not the loss of mitochondrially-generated ATP, are responsible for cell death induction by ETC disruption in ample nutrients condition, e.g. in well perfused healthy tissues, where antioxidant defense imparts specificity. However, in conditions of limited glucose, e.g.in poorly perfused tumors, ETC disruption causes rapid depletion of cellular ATP, optimizing impact towards tumor-associated dormant cells. In summary, we propose that antioxidant defense in quiescent cells is aided by local glucose limitations to ensure selectivity of ETC inhibition-induced cell death

Oxidative biodegradation of tetrachloroethene in needles of Norway spruce (Picea abies L.).

Through employing [14C]-PER exposure experiments it was shown for the first time that PER taken up by drought-stressed spruce needles via the air/needle pathway is preferably degraded to trichloroacetic acid (TCA) in the chloroplasts.TCA formed by oxidative biotransformation is mineralised to CO2 and HCl via various degradation routes. HCl contributes to increased proton concentration in the chloroplast, inducing a pH shift leading to a pathophysiological effect on H+ transport from the thylakoid interior into the stroma. As a result of their high degree of dissociation and related protonation, the PER metabolites, TCA and HCl, cause a change in protein structures. In addition to this, the TCA anions created in the process may lead to destabilisation of the thylakoid membrane potential. The damage to the chloroplasts inflicted by protons and trichloroacetate ions subsequently leads to an impairment of photosynthesis, most particularly to uncoupling of photosynthetic electron transport. Since progressive aridity as consequence of the climate change observed throughout the world is predicted, a regionally variable marked enhancement of the phytotoxic risk caused by PER emission is anticipated

BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization

The amount of biological data, generated with (single cell) omics technologies, is rapidly increasing, thereby exacerbating bottlenecks in the data analysis and interpretation of omics experiments. Data mining platforms that facilitate non-bioinformatician experimental scientists to analyze a wide range of experimental designs and data types can alleviate such bottlenecks, aiding in the exploration of (newly generated or publicly available) omics datasets. Here, we present BIOMEX, a browser-based software, designed to facilitate the Biological Interpretation Of Multi-omics EXperiments by bench scientists. BIOMEX integrates state-of-the-art statistical tools and field-tested algorithms into a flexible but well-defined workflow that accommodates metabolomics, transcriptomics, proteomics, mass cytometry and single cell data from different platforms and organisms. The BIOMEX workflow is accompanied by a manual and video tutorials that provide the necessary background to navigate the interface and get acquainted with the employed methods. BIOMEX guides the user through omics-tailored analyses, such as data pretreatment and normalization, dimensionality reduction, differential and enrichment analysis, pathway mapping, clustering, marker analysis, trajectory inference, meta-analysis and others. BIOMEX is fully interactive, allowing users to easily change parameters and generate customized plots exportable as high-quality publication-ready figures. BIOMEX is open source and freely available at https://www.vibcancer.be/software-tools/biomex.status: publishe

Measuring Glycolytic and Mitochondrial Fluxes in Endothelial Cells Using Radioactive Tracers

Endothelial cells (ECs) form the inner lining of the vascular network. Although they can remain quiescent for years, ECs exhibit high plasticity in both physiological and pathological conditions, when they need to rapidly form new blood vessels in a process called angiogenesis. EC metabolism recently emerged as an important driver of this angiogenic switch. The use of radioactive tracer substrates to assess metabolic flux rates in ECs has been essential for the discovery that fatty acid, glucose, and glutamine metabolism critically contribute to vessel sprouting. In the future, these assays will be useful as a tool for the characterization of pathological conditions in which deregulation of EC metabolism underlies and/or precedes the disease, but also for the identification of anti-angiogenic metabolic targets. This chapter describes in detail the radioactive tracer substrate assays that have been used for the determination of EC metabolic flux in vitro.status: Published onlin

Single-Cell RNA Sequencing Reveals Renal Endothelium Heterogeneity and Metabolic Adaptation to Water Deprivation

Background Renal endothelial cells from glomerular, cortical, and medullary kidney compartments are exposed to different microenvironmental conditions and support specific kidney processes. However, the heterogeneous phenotypes of these cells remain incompletely inventoried. Osmotic homeostasis is vitally important for regulating cell volume and function, and in mammals, osmotic equilibrium is regulated through the countercurrent system in the renal medulla, where water exchange through endothelium occurs against an osmotic pressure gradient. Dehydration exposes medullary renal endothelial cells to extreme hyperosmolarity, and how these cells adapt to and survive in this hypertonic milieu is unknown.Methods We inventoried renal endothelial cell heterogeneity by single-cell RNA sequencing >40,000 mouse renal endothelial cells, and studied transcriptome changes during osmotic adaptation upon water deprivation. We validated our findings by immunostaining and functionally by targeting oxidative phosphorylation in a hyperosmolarity model in vitro and in dehydrated mice in vivo.Results We identified 24 renal endothelial cell phenotypes (of which eight were novel), highlighting extensive heterogeneity of these cells between and within the cortex, glomeruli, and medulla. In response to dehydration and hypertonicity, medullary renal endothelial cells upregulated the expression of genes involved in the hypoxia response, glycolysis, and-surprisingly-oxidative phosphorylation. Endothelial cells increased oxygen consumption when exposed to hyperosmolarity, whereas blocking oxidative phosphorylation compromised endothelial cell viability during hyperosmotic stress and impaired urine concentration during dehydration.Conclusions This study provides a high-resolution atlas of the renal endothelium and highlights extensive renal endothelial cell phenotypic heterogeneity, as well as a previously unrecognized role of oxidative phosphorylation in the metabolic adaptation of medullary renal endothelial cells to water deprivation.Nephrolog