Selection for novel, acid-tolerant Desulfovibrio spp. from a closed Transbaikal mine site in a temporal pH- gradient bioreactor

Almost all the known isolates of acidophilic or acid-tolerant sulphate-reducing bacteria (SRB) belong to the spore-forming genus Desulfosporosinus in the Firmicutes. The objective of this study was to isolate acidophilic/acid-tolerant members of the genus Desulfovibrio belonging to deltaproteobacterial SRB. The sample material originated from microbial mat biomass submerged in mine water and was enriched for sulphate reducers by cultivation in anaerobic medium with lactate as an electron donor. A stirred tank bioreactor with the same medium composition was inoculated with the sulphidogenic enrichment. The bioreactor was operated with a temporal pH gradient, changing daily, from an initial pH of 7.3 to a final pH of 3.7. Among the bacteria in the bioreactor culture, Desulfovibrio was the only SRB group retrieved from the bioreactor consortium as observed by 16S rRNA-targeted denaturing gradient gel electrophoresis. Moderately acidophilic/acid-tolerant isolates belonged to Desulfovibrio aerotolerans - Desulfovibrio carbinophilus - Desulfovibrio magneticus and Desulfovibrio idahonensis - Desulfovibrio mexicanus clades within the genus Desulfovibrio. A moderately acidophilic strain, Desulfovibrio sp. VK (pH optimum 5.7) and acid-tolerant Desulfovibrio sp. ED (pH optimum 6.6) dominated in the bioreactor consortium at different time points and were isolated in pure cultur

Interaction of microplastics and terrestrial and aquatic insects (bioaccumulation, degradation, ecotoxicological effects)

World production of convenient and durable materials made of synthetic plastics during the last 70 years caused the dispersal of microplastic particles in the environment. Microplastic pollution is the focus of interest worldwide due to its global distribution and adverse effects on living organisms. The largest number of studies addressing this issue explored the aquatic environment, yet terrestrial ecosystems also suffer from microplastic pollution. Insects are crucial for most terrestrial ecosystems. Few can compete with them in biomass productivity and species diversity, which makes them targets for studying the toxic bioaccumulation. This review article presents a systematic analysis of data on bioaccumulation, degradation of microplastics by aquatic and terrestrial entomofauna, and its ecotoxicological effects

Потребление микропластика рыбами с различным пищевым поведением в реках Обь и Енисей

Microplastic particles in the size range 0.15 to 5.00 mm were quantified and characterised in the gastrointestinal tracts of three wild freshwater fish (n = 141) from the Ob and Yenisei rivers, including common ruffe (Gymnocephalus cernua L.), Siberian dace (Leuciscus baicalensis Dybowski) and European perch (Perca fluviatilis L.). Microplastics were found in the gastrointestinal tract of 62% of the fish examined, ranging from 18.5% in the Yenisei perch sample to 92.6% in the Ob ruffe sample. The vast majority of microplastics in all fish species were fibres (up to 99.7% of all particles detected in perch), followed by irregularly shaped fragments (up to 22.7% in ruffe), with no preference between the three species. Spheres and films were found exclusively in dace and ruffe, with proportions of 3.7% and 1.2% respectively. Particles consisted of polyethylene terephthalate, polypropylene, polyamide and other synthetic polymers with a significant proportion of highly degraded polymers. The mean MP content in fish GITs ranged from 0.44 ± 0.25 items per individual in Yenisei perch to 3.81 ± 0.55 items per individual in Ob ruffe. Particle burdens in fish were significantly higher in the Ob than in the Yenisei (p dace (omnivorous) > perch (hunter) in both rivers (p < 0.01). This study was the first to quantify MP consumption by freshwater fish of different species in the Ob and Yenisei rivers and to identify patterns associated with different feeding habits

Isolation, characterization, and metal response of novel, acid-tolerant Penicillium spp. from extremely metal-rich waters at a mining site in Transbaikal (Siberia, Russia)

The role of fungi in metal cycling in acidic environments has been little explored to date. In this study, two acid-tolerant and metal-resistant Penicillium isolates, strains ShG4B and ShG4C, were isolated from a mine site in the Transbaikal area of Siberia (Russia). Waters at the mine site were characterized by extremely high metal concentrations: up to 18 g l−1 Fe and &gt;2 g l−1 each of Cu, Zn, Al, and As. Both isolates were identified as Penicillium spp. by phylogenetic analyses and they grew well in Czapek medium acidified to pH 2.5. Resistance to Cu, Cd, Ni, Co, and arsenate was in the range of 1–10 g l−1. Further experiments with Penicillium strain ShG4C demonstrated that growth in Cu-containing media was accompanied by the precipitation of Cu-oxalate (moolooite) and the formation of extracellular vesicles enriched in Cu on the mycelia. Vesicles were greatly reduced in size in Cd-containing media and were not formed in the presence of Ni or Co. Cd-oxalate was detected as a crystalline solid phase in Cd-exposed mycelia. Hydrated Nisulfate (retgersite) and Co-sulfate (bieberite) were detected in mycelia grown in the presence of Ni and Co, respectively. The results demonstrated that acid-tolerant and metal-resistant Penicillium constitute a component in extremophilic microbiomes, contributing to organic matter breakdown and formation of secondary solid phases at pH ranges found in acid rock drainage

Effect of different types of microplastics on the vital activity of bloodsucking mosquitoes Aedes aegypti L. (Diptera: Culicidae)

We have experimentally investigated the effect of three different types of microplastics (high-density polyethylene, polypropylene and polystyrene) on body weight, metamorphosis rate and mortality of bloodsucking mosquitoes Aedes aegypti (Linnaeus 1762), vectors of protozoal and helminthic diseases of humans and animals. Supplementation of the diet with polypropylene was found to have no effect on mosquito weight at all life stages, while the addition of high-density polyethylene and polystyrene promoted a decrease in larval weight and an increase in adult weight (p < 0.05). Ingestion of high-density polyethylene by larvae increased pupal weight and decreased adult weight compared to the control, whereas no such effect was found for polypropylene and polystyrene. High-density polyethylene and polystyrene did not affect mosquito mortality at all stages, but there was a tendency for polypropylene to have an adverse effect on pupal and adult survival. The survival rate of mosquitoes at all life stages in both the control and experimental groups was generally quite high. Supplementation of the diet with different types of plastics did not affect the metamorphosis rate at all stages of mosquito development and was comparable in both the control and experimental groups. The experiments revealed no significant effect of different types of plastics on the vital activity of Ae. aegypti. Only high-density polyethylene microparticles were found to significantly affect mosquito body weight, yet this was opposite at the pupal and adult stages

Microplastic size matters for absorption and excretion by Artemia salina and Acipenser ruthenus larvae in models of water pollution and food chain transfer

Microplastics pervade the hydrosphere and inevitably come into contact with aquatic organisms. The study reports quantitative data on absorption and excretion of polystyrene microspheres 2 and 10 µm in diameter by zooplankton and fish larvae on the example of Artemia salina L. and Acipenser rithenus L. At the initial concentration of 500 µg/L, A. salina accumulated 2 and 10 µm particles in amounts up to 0.103 and 0.151 ng/individual, respectively, at a similar rate. The mass content of large-sized particles in A. salina was significantly higher (p < 0.01) compared to small-sized particles throughout the experiment. Artemia salina and A. rithenus larvae did not accumulate microplastics in the gastrointestinal tract over a period of 96 and 72 h, respectively. Consumption of microplastics by A. ruthenus larvae with A. salina through the food chain was slower and less pronounced in mass than their direct absorption from water. The rates of absorption of 2 and 10 μm particles by fish attained 0.9 and 8.22 ng/individual/h from water, and 0.06 and 0.23 ng/individual/h with food, respectively. In the models of water pollution and food chain transfer, A. ruthenus larvae consumed more 10 µm particles in mass compared to 2 µm particles (p < 0.05) and at a higher rate. For 2 µm particles, the excretion time for 50% of particles from the gastrointestinal tract of fish (T50) was 32–33 h, whereas for 10 µm particles, the excretion of particles consumed with food was slower (T50=45 h) compared to that of particles absorbed directly from water (T50=25 h). The data obtained can be used to simulate transport and circulation of microplastics of different sizes in the environment

Differential Targeting of c-Maf, Bach-1, and Elmo-1 by microRNA-143 and microRNA-365 Promotes the Intracellular Growth of Mycobacterium tuberculosis in Alternatively IL-4/IL-13 Activated Macrophages

Mycobacterium tuberculosis (Mtb) can subvert the host defense by skewing macrophage activation toward a less microbicidal alternative activated state to avoid classical effector killing functions. Investigating the molecular basis of this evasion mechanism could uncover potential candidates for host directed therapy against tuberculosis (TB). A limited number of miRNAs have recently been shown to regulate host-mycobacterial interactions. Here, we performed time course kinetics experiments on bone marrow-derived macrophages (BMDMs) and human monocyte-derived macrophages (MDMs) alternatively activated with IL-4, IL-13, or a combination of IL-4/IL-13, followed by infection with Mtb clinical Beijing strain HN878. MiR-143 and miR-365 were highly induced in Mtb-infected M(IL-4/IL-13) BMDMs and MDMs. Knockdown of miR-143 and miR-365 using antagomiRs decreased the intracellular growth of Mtb HN878, reduced the production of IL-6 and CCL5 and promoted the apoptotic death of Mtb HN878-infected M(IL-4/IL-13) BMDMs. Computational target prediction identified c-Maf, Bach-1 and Elmo-1 as potential targets for both miR-143 and miR-365. Functional validation using luciferase assay, RNA-pulldown assay and Western blotting revealed that c-Maf and Bach-1 are directly targeted by miR-143 while c-Maf, Bach-1, and Elmo-1 are direct targets of miR-365. Knockdown of c-Maf using GapmeRs promoted intracellular Mtb growth when compared to control treated M(IL-4/IL-13) macrophages. Meanwhile, the blocking of Bach-1 had no effect and blocking Elmo-1 resulted in decreased Mtb growth. Combination treatment of M(IL-4/IL-13) macrophages with miR-143 mimics or miR-365 mimics and c-Maf, Bach-1, or Elmo-1 gene-specific GapmeRs restored Mtb growth in miR-143 mimic-treated groups and enhanced Mtb growth in miR-365 mimics-treated groups, thus suggesting the Mtb growth-promoting activities of miR-143 and miR-365 are mediated at least partially through interaction with c-Maf, Bach-1, and Elmo-1. We further show that knockdown of miR-143 and miR-365 in M(IL-4/IL-13) BMDMs decreased the expression of HO-1 and IL-10 which are known targets of Bach-1 and c-Maf, respectively, with Mtb growth-promoting activities in macrophages. Altogether, our work reports a host detrimental role of miR-143 and miR-365 during Mtb infection and highlights for the first time the role and miRNA-mediated regulation of c-Maf, Bach-1, and Elmo-1 in Mtb-infected M(IL-4/IL-13) macrophages

Recent Advances in Practical Methods for Liver Cell Biology: A Short Overview

Molecular and cellular research modalities for the study of liver pathologies have been tremendously improved over the recent decades. Advanced technologies offer novel opportunities to establish cell isolation techniques with excellent purity, paving the path for 2D and 3D microscopy and high-throughput assays (e.g., bulk or single-cell RNA sequencing). The use of stem cell and organoid research will help to decipher the pathophysiology of liver diseases and the interaction between various parenchymal and non-parenchymal liver cells. Furthermore, sophisticated animal models of liver disease allow for the in vivo assessment of fibrogenesis, portal hypertension and hepatocellular carcinoma (HCC) and for the preclinical testing of therapeutic strategies. The purpose of this review is to portray in detail novel in vitro and in vivo methods for the study of liver cell biology that had been presented at the workshop of the 8th meeting of the European Club for Liver Cell Biology (ECLCB-8) in October of 2018 in Bonn, Germany

Differential Targeting of c-Maf, Bach-1, and Elmo-1 by microRNA-143 and microRNA-365 Promotes the Intracellular Growth of Mycobacterium tuberculosis in Alternatively IL-4/IL-13 Activated Macrophages.

Mycobacterium tuberculosis (Mtb) can subvert the host defense by skewing macrophage activation toward a less microbicidal alternative activated state to avoid classical effector killing functions. Investigating the molecular basis of this evasion mechanism could uncover potential candidates for host directed therapy against tuberculosis (TB). A limited number of miRNAs have recently been shown to regulate host-mycobacterial interactions. Here, we performed time course kinetics experiments on bone marrow-derived macrophages (BMDMs) and human monocyte-derived macrophages (MDMs) alternatively activated with IL-4, IL-13, or a combination of IL-4/IL-13, followed by infection with Mtb clinical Beijing strain HN878. MiR-143 and miR-365 were highly induced in Mtb-infected M(IL-4/IL-13) BMDMs and MDMs. Knockdown of miR-143 and miR-365 using antagomiRs decreased the intracellular growth of Mtb HN878, reduced the production of IL-6 and CCL5 and promoted the apoptotic death of Mtb HN878-infected M(IL-4/IL-13) BMDMs. Computational target prediction identified c-Maf, Bach-1 and Elmo-1 as potential targets for both miR-143 and miR-365. Functional validation using luciferase assay, RNA-pulldown assay and Western blotting revealed that c-Maf and Bach-1 are directly targeted by miR-143 while c-Maf, Bach-1, and Elmo-1 are direct targets of miR-365. Knockdown of c-Maf using GapmeRs promoted intracellular Mtb growth when compared to control treated M(IL-4/IL-13) macrophages. Meanwhile, the blocking of Bach-1 had no effect and blocking Elmo-1 resulted in decreased Mtb growth. Combination treatment of M(IL-4/IL-13) macrophages with miR-143 mimics or miR-365 mimics and c-Maf, Bach-1, or Elmo-1 gene-specific GapmeRs restored Mtb growth in miR-143 mimic-treated groups and enhanced Mtb growth in miR-365 mimics-treated groups, thus suggesting the Mtb growth-promoting activities of miR-143 and miR-365 are mediated at least partially through interaction with c-Maf, Bach-1, and Elmo-1. We further show that knockdown of miR-143 and miR-365 in M(IL-4/IL-13) BMDMs decreased the expression of HO-1 and IL-10 which are known targets of Bach-1 and c-Maf, respectively, with Mtb growth-promoting activities in macrophages. Altogether, our work reports a host detrimental role of miR-143 and miR-365 during Mtb infection and highlights for the first time the role and miRNA-mediated regulation of c-Maf, Bach-1, and Elmo-1 in Mtb-infected M(IL-4/IL-13) macrophages

NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR

Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform