Single is not combined: The role of Co and Ni bioavailability on toxicity mechanisms in liver and brain cells.

The two trace elements cobalt (Co) and nickel (Ni) are widely distributed in the environment due to the increasing industrial application, for example in lithium-ion batteries. Both metals are known to cause detrimental health impacts to humans when overexposed and both are supposed to be a risk factor for various diseases. The individual toxicity of Co and Ni has been partially investigated, however the underlying mechanisms, as well as the interactions of both remain unknown. In this study, we focused on the treatment of liver carcinoma (HepG2) and astrocytoma (CCF-STTG1) cells as a model for the target sites of these two metals. We investigated their effects in single and combined exposure on cell survival, cell death mechanisms, bioavailability, and the induction of oxidative stress. The combination of CoCl2 and NiCl2 resulted in higher Co levels with subsequent decreased amount of Ni compared to the individual treatment. Only CoCl2 and the combination of both metals led to RONS induction and increased GSSG formation, while apoptosis and necrosis seem to be involved in the cell death mechanisms of both CoCl2 and NiCl2. Collectively, this study demonstrates cell-type specific toxicity, with HepG2 representing the more sensitive cell line. Importantly, combined exposure to CoCl2 and NiCl2 is more toxic than single exposure, which may originate partly from the respective cellular Co and Ni content. Our data imply that the major mechanism of joint toxicity is associated with oxidative stress. More studies are needed to assess toxicity after combined exposure to elements such as Co and Ni to advance an improved hazard prediction for less artificial and more real-life exposure scenarios.

Whole genome sequencing of mouse lines divergently selected for fatness (FLI) and leanness (FHI) revealed several genetic variants as candidates for novel obesity genes.

BACKGROUND: Analysing genomes of animal model organisms is widely used for understanding the genetic basis of complex traits and diseases, such as obesity, for which only a few mouse models exist, however, without their lean counterparts. OBJECTIVE: To analyse genetic differences in the unique mouse models of polygenic obesity (Fat line) and leanness (Lean line) originating from the same base population and established by divergent selection over more than 60 generations. METHODS: Genetic variability was analysed using WGS. Variants were identified with GATK and annotated with Ensembl VEP. g.Profiler, WebGestalt, and KEGG were used for GO and pathway enrichment analysis. miRNA seed regions were obtained with miRPathDB 2.0, LncRRIsearch was used to predict targets of identified lncRNAs, and genes influencing adipose tissue amount were searched using the IMPC database. RESULTS: WGS analysis revealed 6.3 million SNPs, 1.3 million were new. Thousands of potentially impactful SNPs were identified, including within 24 genes related to adipose tissue amount. SNP density was highest in pseudogenes and regulatory RNAs. The Lean line carries SNP rs248726381 in the seed region of mmu-miR-3086-3p, which may affect fatty acid metabolism. KEGG analysis showed deleterious missense variants in immune response and diabetes genes, with food perception pathways being most enriched. Gene prioritisation considering SNP GERP scores, variant consequences, and allele comparison with other mouse lines identified seven novel obesity candidate genes: 4930441H08Rik, Aff3, Fam237b, Gm36633, Pced1a, Tecrl, and Zfp536. CONCLUSION: WGS revealed many genetic differences between the lines that accumulated over the selection period, including variants with potential negative impacts on gene function. Given the increasing availability of mouse strains and genetic polymorphism catalogues, the study is a valuable resource for researchers to study obesity.

Microbial impact to environmental toxicants Ni(II) and Co(II): Joint toxicity and cellular response in Paramecium.

Cobalt (Co) and Nickel (Ni) are increasingly found in our environment. We analysed their combined toxicity and uptake mechanisms in the early food chain by studying bacteria and the bacterivorous ciliate Paramecium as a primary consumer. We exposed both species to these metals to measure the toxicity, uptake and transfer of metals from bacteria to Paramecium. We found that Ni is more toxic than Co, and that toxicity increases for both metals when (i) food bacteria are absent and (ii) both metals are applied in combination. The cellular content in bacteria after exposure shows a concentration dependent bias for either Ni or Co. Comparing single treatment and joint exposure, bacteria show increased levels of both metals when these are both exposed. To imitate the basic level of the food chain, we fed these bacteria to paramecia. The cellular content shows a similar ratio of Nickel and Cobalt as in food bacteria. This is different to the direct application of both metals to paramecia, where Cobalt is enriched over Nickel. This indicates that bacteria can selectively pre-accumulate metals for introduction into the food chain. We also analysed the transcriptomic response of Paramecium to sublethal doses of Nickel and Cobalt to gain insight into their toxicity mechanisms. Gene ontology (GO) analysis indicates common deregulated pathways, such as ammonium transmembrane transport and ubiquitine-associated protein degradation. Many redox-related genes also show deregulation of gene expression, indicating cellular adaptation to increased RONS stress. This suggests that both metals may also target the same cellular pathways and this is consistent with the increased toxicity of both metals when used together. Our data reveal complex ecotoxicological pathways for these metals and highlights the different parameters for their fate in the ecosystem, in the food chain and their ecotoxicological risk after environmental contamination.

Endogenous Galectin-1 Modulates Cell Biological Properties of Immortalized Retinal Pigment Epithelial Cells In Vitro.

In the eye, an increase in galectin-1 is associated with various chorioretinal diseases, in which retinal pigment epithelium (RPE) cells play a crucial role in disease development and progression. Since little is known about the function of endogenous galectin-1 in these cells, we developed a galectin-1-deficient immortalized RPE cell line (ARPE-19-LGALS1-/-) using a sgRNA/Cas9 all-in-one expression vector and investigated its cell biological properties. Galectin-1 deficiency was confirmed by Western blot analysis and immunocytochemistry. Cell viability and proliferation were significantly decreased in ARPE-19-LGALS1-/- cells when compared to wild-type controls. Further on, an increased attachment of galectin-1-deficient RPE cells was observed by cell adhesion assay when compared to control cells. The diminished viability and proliferation, as well as the enhanced adhesion of galectin-1-deficient ARPE-19 cells, could be blocked, at least in part, by the additional treatment with human recombinant galectin-1. In addition, a significantly reduced migration was detected in ARPE-19-LGALS1-/- cells. In comparison to control cells, galectin-1-deficient RPE cells had enhanced expression of sm-α-actin and N-cadherin, whereas expression of E-cadherin showed no significant alteration. Finally, a compensatory expression of galectin-8 mRNA was observed in ARPE-19-LGALS1-/- cells. In conclusion, in RPE cells, endogenous galectin-1 has crucial functions for various cell biological processes, including viability, proliferation, migration, adherence, and retaining the epithelial phenotype.

Follow-up of CRT-D patients downgraded to CRT-P at the time of generator exchange.

Background: Some patients with cardiac resynchronisation therapy (CRT) experience super-response (LVEF improvements to ≥50%). At generator exchange (GE), downgrading (DG) from CRT-defibrillator (CRT-D) to CRT-pacemaker (CRT-P) could be an option for these patients on primary prevention ICD indication and no required ICD therapies. Long-term data on arrhythmic events in super-responders is scarce. Methods: CRT-D patients with LVEF improvement to ≥50% at GE were identified in four large centres for retrospective analysis. Mortality, significant ventricular tachyarrhythmia and appropriate ICD-therapy were determined, and patient analysis was split into two groups (downgraded to CRT-P or not). Results: Sixty-six patients (53% male, 26% coronary artery disease) on primary prevention were followed for a median of 129 months [IQR: 101-155] after implantation. 27 (41%) patients were downgraded to CRT-P at GE after a median of 68 [IQR: 58-98] months (LVEF 54% ± 4%). The other 39 (59%) continued with CRT-D therapy (LVEF 52% ± 6%). No cardiac death or significant arrhythmia occurred in the CRT-P group (median follow-up (FU) 38 months [IQR: 29-53]). Three appropriate ICD-therapies occurred in the CRT-D group [median FU 70 months (IQR: 39-97)]. Annualized event-rates after DG/GE were 1.5%/year and 1.0%/year in the CRT-D group and the whole cohort, respectively. Conclusions: No significant tachyarrhythmia were detected in the patients downgraded to CRT-P during follow-up. However, three events were observed in the CRT-D group. Whilst downgrading CRT-D patients is an option, a small residual risk for arrhythmic events remains and decisions regarding downgrade should be made on a case-by-case basis.

Pentafluorocyclopropanation of (Hetero)arenes Using Sulfonium Salts: Applications in Late-Stage Functionalization.

The evaluation of the pentafluorocyclopropyl group as a chemotype in crop protection and medicinal chemistry has been hampered in the past by the lack of suitable methodologies that enable the practical incorporation of this moiety into advanced synthetic intermediates. Herein, we report the gram-scale synthesis of an unprecedented sulfonium salt, 5-(pentafluorocyclopropyl)dibenzothiophenium triflate, and its use as a versatile reagent for the photoinduced C-H pentafluorocyclopropylation of a broad series of non-previously functionalized (hetero)arenes through a radical mediated mechanism. The scope and potential benefits of the protocol developed are further demonstrated by the late-stage introduction of the pentafluorocyclopropyl unit into biologically relevant molecules and widely used pharmaceuticals.

Ageing-associated small RNA cargo of extracellular vesicles.

Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.

GRASIAN: towards the first demonstration of gravitational quantum states of atoms with a cryogenic hydrogen beam.

At very low energies, a light neutral particle above a horizontal surface can experience quantum reflection. The quantum reflection holds the particle against gravity and leads to gravitational quantum states (gqs). So far, gqs were only observed with neutrons as pioneered by Nesvizhevsky and his collaborators at ill. However, the existence of gqs is predicted also for atoms. The Grasian collaboration pursues the first observation and studies of gqs of atomic hydrogen. We propose to use atoms in order to exploit the fact that orders of magnitude larger fluxes compared to those of neutrons are available. Moreover, recently the q-Bounce collaboration, performing gqs spectroscopy with neutrons, reported a discrepancy between theoretical calculations and experiment which deserves further investigations. For this purpose, we set up a cryogenic hydrogen beam at 6  K . We report on our preliminary results, characterizing the hydrogen beam with pulsed laser ionization diagnostics at 243  nm .

The Internet of Things for the Intelligent Management of the Heating of a Swimming Pool by Means of Smart Sensors.

By using various smart sensors integrated in a global domotic system, a proper solar thermal management is executed. The goal is to properly manage solar energy for heating swimming pool using various devices installed at home. Swimming pools are a necessity in many communities. In summer, they are a source of refreshment. However, maintaining a swimming pool at an optimal temperature can be a challenge even in the summer months. The use of the Internet of Things in homes has enabled proper management of solar thermal energy, thus significantly improving the quality of life by making homes more comfortable and safer without using additional resources. The houses built today have several smart devices that manage to optimize the energy consumption of the house. The solutions proposed in this study to improve energy efficiency in swimming pool facilities include the installation of solar collectors to heat swimming pool water more efficiently. The installation of smart actuation devices (to efficiently control energy consumption of a pool facility via different processes) together with sensors that provide valuable information on energy consumption in the different processes of a pool facility, can optimize energy consumption thus reducing overall consumption (by 90%) and economic cost (by more than 40%). Together, these solutions can help to significantly reduce energy consumption and economic costs and extrapolate it to different processes of similar characteristics in the rest of the society.

Enantioselective Au-Catalyzed Synthesis of Thia[5]- and Thia[6]helicenes and Their Transformation into Bowl-shaped Pleiadenes.

A series of helically shaped benzo[b]chryseno[4,3-d]thiophenes, naphtho[1,2-b]phenanthro[4,3-d]thiophenes, and chryseno[3,4-b]naphtho[1,2-d]thiophenes is synthesized via a highly enantioselective Au-catalyzed intramolecular alkyne hydroarylation reaction. The inversion barriers of the structures obtained are determined both theoretically and experimentally, and their chiroptical properties are reported. Preliminary studies on the post-synthetic functionalization of these thiahelicenes and their transformation into azahelicenes are also presented. In addition, a straightforward one-step protocol is developed, which wraps the initially obtained chryseno[3,4-b]naphtho[1,2-d]thiophenes into bowl-shaped pleiadene derivatives without erosion of the enantiopurity. The number of structurally related products that are obtained with high enantioselectivity enables the establishment of comprehensive correlations between the structure and conformational stability or (chir)optical properties.

Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness.

Alternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition.

5-(Trifluorovinyl)dibenzothiophenium Triflate: Introducing the 1,1,2-Trifluoroethylene Tether in Drug-Like Structures.

This manuscript reports the synthesis and structure of an unprecedented sulfonium salt, 5-(trifluorovinyl)dibenzothiophenium triflate, and its use as a versatile reagent for the introduction of the bioisosteric 1,1,2-trifluoroethylene linker in drug-like structures. The protocol developed consists of the reaction of this compound with alcohols and phenols to deliver a complete set of 1,2,2-trifluoro-2-(alkoxy-/aryloxy)ethyl sulfonium salts, which have been purified by column chromatography and fully characterized. Subsequent single electron reduction under mild photochemical conditions efficiently affords the corresponding fluoroalkyl radicals that are trapped either intra- or intermolecularly through their reaction with (hetero)arenes. Theoretical calculations are used to evaluate the conformational consequences derived from the presence of the CF2 -CHF tether.

Species-Specific Duplication of Surface Antigen Genes in Paramecium.

Paramecium is a free-living ciliate that undergoes antigenic variation and still the functions of these variable surface antigen coats in this non-pathogenic ciliate remain elusive. Only a few surface antigen genes have been described, mainly in the two model species P. tetraurelia strain 51 and P. primaurelia strain 156. Given the lack of suitable sequence data to allow for phylogenetics and deeper sequence comparisons, we screened the genomes of six different Paramecium species for serotype genes and isolated 548 candidates. Our approach identified the subfamilies of the isogenes of individual serotypes that were mostly represented by intrachromosomal gene duplicates. These showed different duplication levels, and chromosome synteny suggested rather young duplication events after the emergence of the P. aurelia species complex, indicating a rapid evolution of surface antigen genes. We were able to identify the different subfamilies of the surface antigen genes with internal tandem repeats, which showed consensus motifs across species. The individual isogene families showed additional consensus motifs, indicating that the selection pressure holds individual amino acids constant in these repeats. This may be a hint of the receptor function of these antigens rather than a presentation of random epitopes, generating the variability of these surface molecules.

Machine learning techniques to characterize functional traits of plankton from image data.

Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.

Manganese-Induced Toxicity in C. elegans: What Can We Learn from the Transcriptome?

Manganese (Mn) is an essential ubiquitous transition metal and, when occupationally or environmentally overexposed, a well-known risk factor for several neurological pathologies. However, the molecular mechanisms underlying Mn-induced neurotoxicity are largely unknown. In this study, addressing RNA-Seq analysis, bioavailability and survival assays, key pathways of transcriptional responses to Mn overexposure were investigated in the model organism Caenorhabditis elegans (C. elegans), providing insights into the Mn-induced cellular stress and damage response. Comparative transcriptome analyses identified a large number of differentially expressed genes (DEGs) in nematodes exposed to MnCl2, and functional annotation suggested oxidative nucleotide damage, unfolded protein response and innate immunity as major damage response pathways. Additionally, a time-dependent increase in the transcriptional response after MnCl2 exposure was identified by means of increased numbers of DEGs, indicating a time-dependent response and activation of the stress responses in Mn neurotoxicity. The data provided here represent a powerful transcriptomic resource in the field of Mn toxicity, and therefore, this study provides a useful basis for further planning of targeted mechanistic studies of Mn-induced neurotoxicity that are urgently needed in the face of increasing industrially caused environmental pollution with Mn.

Assessment of Alkali-Silica Reaction Potential in Aggregates from Iran and Australia Using Thin-Section Petrography and Expansion Testing.

The alkali-silica reaction can shorten concrete life due to expansive pressure build-up caused by reaction by-products, resulting in cracking. Understanding the role of the aggregate, as the main reactive component, is essential for understanding the underlying mechanisms of the alkali-silica reaction and thereby reducing, or even preventing, any potential damage. The present study aims to investigate the role of petrographic studies along with accelerated tests in predicting and determining the potential reactivity of aggregates, including granite, rhyodacite, limestone, and dolomite, with different geological characteristics in concrete. This study was performed under accelerated conditions in accordance with the ASTM C1260 and ASTM C1293 test methods. The extent of the alkali-silica reaction was assessed using a range of microanalysis techniques including optical microscopy, scanning electron microscopy, energy-dispersive X-ray analysis, and X-ray powder diffraction. The results showed that a calcium-rich aggregate with only a small quantity of siliceous component but with a higher porosity and water adsorption rate can lead to degradation due to the alkali-silica reaction, while dolomite aggregate, which is commonly considered a reactive aggregate, showed no considerable expansion during the conducted tests. The results also showed that rhyodacite samples, due to their glassy texture, the existence of strained quartz and quartz with undulatory extinction, as well as the presence of weathering minerals, have a higher alkali-reactivity potential than granite samples.

Paramecium epigenetics in development and proliferation.

The term epigenetics is used for any layer of genetic information aside from the DNA base-sequence information. Mammalian epigenetic research increased our understanding of chromatin dynamics in terms of cytosine methylation and histone modification during differentiation, aging, and disease. Instead, ciliate epigenetics focused more on small RNA-mediated effects. On the one hand, these do concern the transport of RNA from parental to daughter nuclei, representing a regulated transfer of epigenetic information across generations. On the other hand, studies of Paramecium, Tetrahymena, Oxytricha, and Stylonychia revealed an almost unique function of transgenerational RNA. Rather than solely controlling chromatin dynamics, they control sexual progeny's DNA content quantitatively and qualitatively. Thus epigenetics seems to control genetics, at least genetics of the vegetative macronucleus. This combination offers ciliates, in particular, an epigenetically controlled genetic variability. This review summarizes the epigenetic mechanisms that contribute to macronuclear heterogeneity and relates these to nuclear dimorphism. This system's adaptive and evolutionary possibilities raise the critical question of whether such a system is limited to unicellular organisms or binuclear cells. We discuss here the relevance of ciliate genetics and epigenetics to multicellular organisms.

Assessing Representation Learning and Clustering Algorithms for Computer-Assisted Image Annotation-Simulating and Benchmarking MorphoCluster.

Image annotation is a time-consuming and costly task. Previously, we published MorphoCluster as a novel image annotation tool to address problems of conventional, classifier-based image annotation approaches: their limited efficiency, training set bias and lack of novelty detection. MorphoCluster uses clustering and similarity search to enable efficient, computer-assisted image annotation. In this work, we provide a deeper analysis of this approach. We simulate the actions of a MorphoCluster user to avoid extensive manual annotation runs. This simulation is used to test supervised, unsupervised and transfer representation learning approaches. Furthermore, shrunken k-means and partially labeled k-means, two new clustering algorithms that are tailored specifically for the MorphoCluster approach, are compared to the previously used HDBSCAN*. We find that labeled training data improve the image representations, that unsupervised learning beats transfer learning and that all three clustering algorithms are viable options, depending on whether completeness, efficiency or runtime is the priority. The simulation results support our earlier finding that MorphoCluster is very efficient and precise. Within the simulation, more than five objects per simulated click are being annotated with 95% precision.

Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines.

BACKGROUND: Adipose tissue hypoxia and members of the hypoxia-inducible factor alpha (HIFA) are involved in development of obesity. However, the mechanism and functions of HIF3A, one of three HIFA paralogs, in fat deposition have not been sufficiently studied. METHODS AND RESULTS: In the present study, we investigated whether Hif3a sequence variants are associated with divergent fat deposition in mouse selection lines for fatness and leanness. Sequencing and RFLP were used to analyse sequence variants within Hif3a. To identify candidate regulatory variants, we performed literature screening and used databases and bioinformatics tools like Ensembl, MethPrimer, TargetScanMouse, miRDB, PolyAsite, RISE, LncRRIsearch, RNAfold, PredictProtein, CAIcal, and switches.ELM Resource. There are 90 sequence variants in Hif3a between the two mouse lines. While most Fat line variants locate within intronic regions, Lean line variants are mainly in 3' UTR. We constructed a map of Hif3a potential regulatory regions and identified 39 regulatory variants by integrating data on constrained and regulatory elements, CpGs, and miRNAs and lncRNAs binding sites. Moreover, 3' UTR and two exonic variants may influence mRNA stability, translation rate and protein functionality. We propose as priority candidates for further functional studies a missense (rs37398126) and synonymous (rs37739792) variants, and intronic (rs47471302) variant that overlap conserved element in promoter region and predicted lncRNAs binding site. CONCLUSION: The results indicate a potential involvement of Hif3a in fat deposition. Additionally, approach used in the present study may serve as a general guideline for constructing an integrative gene map for prioritizing candidate gene variants with phenotypic effects.