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Brain research has in recent years indisputably entered a new epoch, driven bysubstantialmethodologicaladvances and digitallyenabled data integration and modeling at multiple scales –from molecules to the whole system. Major advances are emerging at theintersection of neurosciencewith technology and computing. This new science of the brain integrates high-quality basic research,systematic data integration across multiple scales, a new culture of large-scale collaboration andtranslation into applications. A systematic approach, as pioneered in Europe’s Human Brain Project(HBP), will be essential in meeting the pressing medical andtechnological challenges of the comingdecade. The aims of this paper are To develop a concept for the coming decade of digital brain research To discuss it with the research community at large, with the aim of identifying points of convergence and common goals To provide a scientific framework for current and future development of EBRAINS To inform and engage stakeholders, funding organizations and research institutions regarding future digital brain research To identify and address key ethical and societal issues While we do not claim that there is a ‘one size fits all’ approach to addressing these aspects, we areconvinced that discussions around the theme of digital brain research will help drive progress in thebroader field of neuroscience. You can submit your comments here and be considered for co-authorship Or become a supporter by clicking here More information below Comments on this manuscript are welcome This manuscriptis a living document that is being further developed in a participatory process. The work has been initiated by the Science and Infrastructure Board of the Human Brain Project (HBP). Now, the entire research community is invited to contribute to shaping the vision by submitting comments.Comments can be submitted via an online commentary form here. All submitted comments will be considered and discussed. The final decision on whether edits or additions will be made to the next version of the manuscript based on an individual comment will be made by the Science and Infrastructure Board (SIB) of the Human Brain Project (HBP) at regular intervals. The final version of the manuscript will be prepared and published in the next months. Comments may be submitted until the end of May, 2023. Every researcher is welcome to provide comment or indicate support for the contents of this paper and jointly shape the future of brain research. Supporters of the paper: Pietro Avanzini, Marc Beyer, Maria Del Vecchio, Jitka Annen, Maurizio Mattia, Steven Laureys, Rosanne Edelenbosch, Rafael Yuste, Jean-Pierre Changeux, Linda Richards, Hye Weon Jessica Kim, Chrysoula Samara, Luis Miguel González de la Garza, Nikoleta Petalidou, Vasudha Kulkarni, Cesar David Rincon, Isabella O'Shea, Munira Tamim Electricwala, Nicola Palomero-Gallagher, Bernd Carsten Stahl, Bahar Hazal Yalcinkaya, Meysam Hashemi, Carola Sales Carbonell, Marcel Carrère, Anthony Randal McIntosh, Hiba Sheheitli, Abolfazl Ziaeemehr, Martin Breyton, Giovanna Ramos Queda, Anirudh NIhalani Vattikonda, Gyorgy Buzsaki George Ogoh, William Knight Torbjørn V Ness, MIchiel van der Vlag, Mu-ming Poo.

Selenium (Se) is a vital micronutrient with widespread biological action but leads to toxicity when taken in excessive amounts. The biological benefits of Se are mainly derived from its presence in active sites of selenoproteins such as glutathione peroxidase (GPx). An enzyme whose role is to protect tissues against oxidative stress by catalysing the reduction of peroxidase responsible for various forms of cellular damage. The benefits of Se can be harvested when proper regulations of its intake are used. In South Africa, Se distribution in people's diets and animals are low with socio-economic factors and heterogeneous spread of Se in soil throughout the country playing a significant role. The possible causes of low Se in soils may be influenced by underlying geological material, climatic conditions, and anthropogenic activities. Sedimentary rock formations show higher Se concentrations compared to igneous and metamorphic rock formations. Higher Se concentrations in soils dominates in humid and sub-humid areas of South Africa. Furthermore, atmospheric acid deposition dramatically influences the availability of Se to plants. The studies reviewed in this article have shown that atomic absorption spectroscopy (AAS) is the most utilised analytical technique for total Se concentration determination in environmental samples and there is a lack of speciation data for Se concentrations. Shortcomings in Se studies have been identified, and the future research directions of Se in South Africa have been discussed.

Research in other species suggests that the source of embryonic calcium (Ca) and phosphorus (P) for Crocodylus niloticus is likely yolk and shell. Using inductively coupled plasma optical emission ...

Intensive Nile crocodile (Crocodylus niloticus) farming operates with considerable variation in housing and stocking density. In this study, current commercial stocking densities for crocodilians were investigated using 261 grower-phase crocodiles (15 months old, average total body length 94.5 cm, and average weight 2.7 kg). Low (2.60 m2 per crocodile), medium (1.24 m2 per crocodile), and high (0.41 m2 per crocodile) stocking densities were tested. Growth, morphometric measures, Fulton’s condition scores and skin qualities were assessed over a six-month (May - November 2017) period. High stocking density had no adverse effects on the growth of grower Nile crocodiles. Crocodiles stocked at medium and high densities outperformed those that were stocked at low density in Fulton’s body condition scores, change in body condition from the start to the end of the trial, and feed conversion efficiencies. However, the high and, to a lesser extent, the medium stocking densities resulted in lower skin quality scores compared with those in the low-density treatment because of teeth marks from more aggressive behaviour. The results indicated that the medium pen density treatment is closer to the ideal than either the high or low stocking density groups. Stocking densities that provide 0.41 m2 per crocodile or less should be avoided because of lower skin quality scores, which weigh more heavily than growth and feed efficiency responses in the financial viability of commercial crocodile farming in typical South African production systems.

Compartmentalized chemical reactions at the microscale are important in biotechnology, yet monitoring the molecular content at these small scales is challenging. To address this challenge, we integrate a compact, reconfigurable reaction cell featuring electrochemical functionality with high‐resolution NMR spectroscopy. We demonstrate the operation of this system by monitoring the activity of enzymes immobilized in chemically distinct layers within a multi‐layered chitosan hydrogel assembly. As a benchmark, we observed the parallel activities of urease (Urs), catalase (Cat), and glucose oxidase (GOx) by monitoring reagent and product concentrations in real‐time. Simultaneous monitoring of an independent enzymatic process (Urs) together with a cooperative process (GOx + Cat) was achieved, with chemical conversion modulation of the GOx + Cat process demonstrated by varying the order in which the hydrogel was assembled., We integrate a compact, reconfigurable reaction cell featuring electrochemical functionality with high‐resolution NMR spectroscopy. This system is used to monitor the activity of enzymes immobilized in chemically distinct layers within a multi‐layered chitosan hydrogel assembly. We observed the parallel activities of urease, catalase, and glucose oxidase by monitoring reagent and product concentrations in real‐time.

Pyrrolizidine alkaloids (PAs) are secondary plant metabolites synthesized by a wide range of plants as protection against herbivores. These toxins are found worldwide and pose a threat to human health. PAs induce acute effects like hepatic sinusoidal obstruction syndrome and pulmonary arterial hypertension. Moreover, chronic exposure to low doses can induce cancer and liver cirrhosis in laboratory animals. The mechanisms causing hepatotoxicity have been investigated previously. However, toxic effects in the lung are less well understood, and especially data on the correlation effects with individual chemical structures of different PAs are lacking. The present study focuses on the identification of gene expression changes in vivo in rat lungs after exposure to six structurally different PAs (echimidine, heliotrine, lasiocarpine, senecionine, senkirkine, and platyphylline). Rats were treated by gavage with daily doses of 3.3 mg PA/kg bodyweight for 28 days and transcriptional changes in the lung and kidney were investigated by whole-genome microarray analysis. The results were compared with recently published data on gene regulation in the liver. Using bioinformatics data mining, we identified inflammatory responses as a predominant feature in rat lungs. By comparison, in liver, early molecular consequences to PAs were characterized by alterations in cell-cycle regulation and DNA damage response. Our results provide, for the first time, information about early molecular effects in lung tissue after subacute exposure to PAs, and demonstrates tissue-specificity of PA-induced molecular effects. Supplementary Information The online version contains supplementary material available at 10.1007/s00204-021-03108-x.

Local accumulation of xenobiotics in human and animal tissues may cause adverse effects. Large differences in their concentrations may exist between individual cell types, often due to the expression of specific uptake and export carriers. Here we established a two-photon microscopy-based technique for spatio-temporal detection of the distribution of mycotoxins in intact kidneys and livers of anesthetized mice with subcellular resolution. The mycotoxins ochratoxin A (OTA, 10 mg/kg b.w.) and aflatoxin B1 (AFB1, 1.5 mg/kg b.w.), which both show blue auto-fluorescence, were analyzed after intravenous bolus injections. Within seconds after administration, OTA was filtered by glomeruli, and enriched in distal tubular epithelial cells (dTEC). A striking feature of AFB1 toxicokinetics was its very rapid uptake from sinusoidal blood into hepatocytes (t1/2 ~ 4 min) and excretion into bile canaliculi. Interestingly, AFB1 was enriched in the nuclei of hepatocytes with zonal differences in clearance. In the cytoplasm of pericentral hepatocytes, the half-life (t1/2~ 63 min) was much longer compared to periportal hepatocytes of the same lobules (t1/2 ~ 9 min). In addition, nuclear AFB1 from periportal hepatocytes cleared faster compared to the pericentral region. These local differences in AFB1 clearance may be due to the pericentral expression of cytochrome P450 enzymes that activate AFB1 to protein- and DNA-binding metabolites. In conclusion, the present study shows that large spatio-temporal concentration differences exist within the same tissues and its analysis may provide valuable additional information to conventional toxicokinetic studies.

Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in polyploid crops, which helps e.g. for introgression breeding. However, methods such as random mutation breeding are difficult to apply in polyploid crops because there are multiple homoeologous copies (alleles) of each gene. Genome editing technology has revolutionized mutagenesis as it enables precisely selecting targets. The genome editing tool CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as all alleles and/or copies of a gene can be targeted at once. Even multiple genes, each with multiple alleles, may be targeted simultaneously. In addition to targeted mutagenesis, targeted replacement of undesirable alleles by desired ones may become a promising application of genome editing for the improvement of polyploid crops, in the near future. Several examples of the application of genome editing for targeted mutagenesis are described here for a range of polyploid crops, and achievements and bottlenecks are highlighted.

Histatin-1 is a salivary antimicrobial peptide involved in the maintenance of enamel and oral mucosal homeostasis. Moreover, Histatin-1 has been shown to promote re-epithelialization in soft tissues, by stimulating cell adhesion and migration in oral and dermal keratinocytes, gingival and skin fibroblasts, endothelial cells and corneal epithelial cells. The broad-spectrum activity of Histatin-1 suggests that it behaves as a universal wound healing promoter, although this is far from being clear yet. Here, we report that Histatin-1 is a novel osteogenic factor that promotes bone cell adhesion, migration, and differentiation. Specifically, Histatin-1 promoted cell adhesion, spreading, and migration of SAOS-2 cells and MC3T3-E1 preosteoblasts in vitro, when placed on a fibronectin matrix. Besides, Histatin-1 induced the expression of osteogenic genes, including osteocalcin, osteopontin, and Runx2, and increased both activity and protein levels of alkaline phosphatase. Furthermore, Histatin-1 promoted mineralization in vitro, as it augmented the formation of calcium deposits in both SAOS-2 and MC3T3-E1 cells. Mechanistically, although Histatin-1 failed to activate ERK1/2, FAK, and Akt, which are signaling proteins associated with osteogenic differentiation or cell migration, it triggered nuclear relocalization of β-catenin. Strikingly, the effects of Histatin-1 were recapitulated in cells that are nonosteogenically committed, since it promoted surface adhesion, migration, and the acquisition of osteogenic markers in primary mesenchymal cells derived from the apical papilla and dental pulp. Collectively, these observations indicate that Histatin-1 is a novel osteogenic factor that promotes bone cell differentiation, surface adhesion and migration, as crucial events required for bone tissue regeneration.

Summary Most alpha‐gliadin genes of the Gli‐D2 locus on the D genome of hexaploid bread wheat (Triticum aestivum) encode for proteins with epitopes that can trigger coeliac disease (CD), and several contain a 33‐mer peptide with six partly overlapping copies of three epitopes, which is regarded as a remarkably potent T‐cell stimulator. To increase genetic diversity in the D genome, synthetic hexaploid wheat lines are being made by hybridising accessions of Triticum turgidum (AB genome) and Aegilops tauschii (the progenitor of the D genome). The diversity of alpha‐gliadins in A. tauschii has not been studied extensively. We analysed the alpha‐gliadin transcriptome of 51 A. tauschii accessions representative of the diversity in A. tauschii. We extracted RNA from developing seeds and performed 454 amplicon sequencing of the first part of the alpha‐gliadin genes. The expression profile of allelic variants of the alpha‐gliadins was different between accessions, and also between accessions of the Western and Eastern clades of A. tauschii. Generally, both clades expressed many allelic variants not found in bread wheat. In contrast to earlier studies, we detected the 33‐mer peptide in some A. tauschii accessions, indicating that it was introduced along with the D genome into bread wheat. In these accessions, transcripts with the 33‐mer peptide were present at lower frequencies than in bread wheat varieties. In most A. tauschii accessions, however, the alpha‐gliadins do not contain the epitope, and this may be exploited, through synthetic hexaploid wheats, to breed bread wheat varieties with fewer or no coeliac disease epitopes., Significance Statement We sequenced the expressed alpha‐gliadins in grains of Aegilops tauschii across its range. Some accessions contained the 33‐mer peptide with six overlapping coeliac disease epitopes, indicating that this was introduced into bread wheat from A. tauschii. We also found a large variation in the occurrence of coeliac disease epitopes, including accessions with small numbers of epitopes, suitable as basis for breeding bread wheat varieties with fewer or no coeliac disease epitopes.

Sleep strongly affects synaptic strength, making it critical for cognition, especially learning and memory formation. Whether and how sleep deprivation modulates human brain physiology and cognition is not well understood. Here we examined how overnight sleep deprivation vs overnight sufficient sleep affects (a) cortical excitability, measured by transcranial magnetic stimulation, (b) inducibility of long-term potentiation (LTP)- and long-term depression (LTD)-like plasticity via transcranial direct current stimulation (tDCS), and (c) learning, memory, and attention. The results suggest that sleep deprivation upscales cortical excitability due to enhanced glutamate-related cortical facilitation and decreases and/or reverses GABAergic cortical inhibition. Furthermore, tDCS-induced LTP-like plasticity (anodal) abolishes while the inhibitory LTD-like plasticity (cathodal) converts to excitatory LTP-like plasticity under sleep deprivation. This is associated with increased EEG theta oscillations due to sleep pressure. Finally, we show that learning and memory formation, behavioral counterparts of plasticity, and working memory and attention, which rely on cortical excitability, are impaired during sleep deprivation. Our data indicate that upscaled brain excitability and altered plasticity, due to sleep deprivation, are associated with impaired cognitive performance. Besides showing how brain physiology and cognition undergo changes (from neurophysiology to higher-order cognition) under sleep pressure, the findings have implications for variability and optimal application of noninvasive brain stimulation.

BACKGROUND Pancreatic panniculitis is an extremely rare condition associated with different underlying pancreatic disorders and characterized by subcutaneous fat necrosis induced by elevated serum lipase levels. These lesions usually affect the lower extremities and may precede abdominal symptoms of pancreatic disease. Acinar cell carcinoma (ACC) of the pancreas is a rare pancreatic neoplasm, accounting for only 1%-2% of pancreatic tumors in adults. CASE SUMMARY We present the case of a 72-year-old man with ACC of the pancreatic head and synchronous liver metastases. Both the primary tumor and liver metastases were resected. Serum lipase was elevated before surgery and decreased to normal postoperatively. Rising serum lipase levels at follow-up led to the diagnosis of hepatic recurrence. This disease progression was then accompanied by pancreatic panniculitis, with subcutaneous fat necrosis and acute arthritis. To the best of our knowledge, only 4 cases have been reported in the literature and each showed a similar association of serum lipase levels with pancreatic panniculitis and progression of ACC. CONCLUSION Clinical symptoms and progression of ACC may correlate with serum lipase levels, suggesting potential usefulness as a follow-up biomarker.

The Mediterranean Sea is characterized by a relatively strong west to east salinity gradient, which makes it an area suitable for testing the effect of salinity on foraminiferal shell geochemistry. We collected living specimens of the planktonic foraminifer Globigerinoides ruber albus to analyse the relation between element ∕ Ca ratios, stable oxygen isotopes of their shells, and surface seawater salinity, isotopic composition and temperature. The oxygen isotopes of sea surface water also correlate with salinity in the Mediterranean during winter, which is when sampling for this study took place. Seawater oxygen and hydrogen isotopes are positively correlated in both the eastern and western Mediterranean Sea, although the relationship differs from previously reported values, especially in the eastern region. The slope between salinity and seawater oxygen isotopes is lower than previously published results. Still, despite the rather modest slope, seawater and foraminiferal carbonate oxygen isotopes are correlated in our dataset, albeit with large residuals and high residual variability. This scatter could be due to either biological variability in vital effects or environmental variability. Numerical models backtracking particles show that ocean-current-driven mixing of particles of different origins might dampen sensitivity and could result in an offset caused by horizontal transport. Results show that Na ∕ Ca is positively correlated with salinity and independent of temperature. As expected, foraminiferal Mg ∕ Ca increases with temperature, which is in line with earlier calibrations, and in the high salinity environment. By using living foraminifera during winter, the previously established Mg ∕ Ca–temperature calibration is extended to temperatures below 18 ∘C, which is a fundamental prerequisite of using single foraminifera for reconstructing past seasonality.

We screened nonequine animals with unexplained neurologic signs or death in South Africa during 2010-2018 for Shuni virus (SHUV). SHUV was detected in 3.3% of wildlife, 1.1% of domestic, and 2.0% of avian species. Seropositivity was also demonstrated in wildlife. These results suggest a range of possible SHUV hosts in Africa.

Acyl carrier proteins (ACPs) are the scaffolds for fatty acid biosynthesis in living systems, rendering them essential to a comprehensive understanding of lipid metabolism. However, accurate quantitative methods to assess individual acyl-ACPs do not exist. We developed a robust method to quantify acyl-ACPs to the picogram level. We successfully identified acyl-ACP elongation intermediates (3-hydroxyacyl-ACPs and 2,3-trans-enoyl-ACPs) and unexpected medium-chain (C10:1, C14:1) and polyunsaturated long-chain (C16:3) acyl-ACPs, indicating both the sensitivity of the method and how current descriptions of lipid metabolism and ACP function are incomplete. Such ACPs are likely important to medium-chain lipid production for fuels and highlight poorly understood lipid remodeling events in the chloroplast. The approach is broadly applicable to type II fatty acid synthase systems found in plants and bacteria as well as mitochondria from mammals and fungi because it capitalizes on a highly conserved Asp-Ser-Leu-Asp amino acid sequence in ACPs to which acyl groups attach. Our method allows for sensitive quantification using liquid chromatography-tandem mass spectrometry with de novo-generated standards and an isotopic dilution strategy and will fill a gap in our understanding, providing insights through quantitative exploration of fatty acid biosynthesis processes for optimal biofuels, renewable feedstocks, and medical studies in health and disease.

Carbon origami enables the fabrication of lightweight and mechanically stiff 3D complex architectures of carbonaceous materials, which have a high potential to impact a wide range of applications positively. The precursor materials and their inherent microstructure play a crucial role in determining the properties of carbon origami structures. Here, non-porous polyaramid Nomex sheets and macroporous fibril cellulose sheets are explored as the precursor sheets for studying the effect of precursor nature and microstructure on the material and structural properties of the carbon origami structures. The fabrication process involves pre-creasing precursor sheets using a laser engraving process, followed by manual-folding and carbonization. The cellulose precursor experiences a severe structural shrinkage due to its macroporous fibril morphology, compared to the mostly non-porous morphology of Nomex-derived carbon. The morphological differences further yield a higher specific surface area for cellulose-derived carbon. However, Nomex results in more crystalline carbon than cellulose, featuring a turbostratic microstructure like glassy carbon. The combined effect of morphology and glass-like features leads to a high mechanical stiffness of 1.9 ± 0.2 MPa and specific modulus of 2.4 × 104 m2·s−2 for the Nomex-derived carbon Miura-ori structure, which are significantly higher than cellulose-derived carbon Miura-ori (elastic modulus = 504.7 ± 88.2 kPa; specific modulus = 1.2 × 104 m2·s−2) and other carbonaceous origami structures reported in the literature. The results presented here are promising to expand the material library for carbon origami, which will help in the choice of suitable precursor and carbon materials for specific applications.

Over the years, a wide variety of therapeutic antibodies has been successfully introduced in the autoimmunology clinic and many more are on the edge to follow. Many of these treatments address either a pathogenic circulating molecule or a cell-bound molecule. Whereas the former target results in neutralization of the soluble factor, the latter target either inhibits cellular function or induces selective cell death. If this targeted molecule or cell is part of the immune system, this therapy evokes a state of immunodeficiency. Knowing the exact function of the respective components enables the risk stratification for possible infectious complications in patients treated with biologics. Much of the understanding of the function of immune cells and their associated molecules, in relation to redundancy in the immune system, is derived from studies in knockout mice. However, as mice are not men in terms of their life-expectancy, their infection exposure, or the composition of their immune system, the most useful knowledge for estimating the consequence of therapeutic intervention on immune competence comes from monitoring patients. In the current chapter, we focus on patients with a primary immunodeficiency (PID) because they provide us with a unique perspective to estimate the redundancy of a certain genetic defect for overall immune competence. These patients have inborn errors of the immune system that, in general, are due to single gene defects. Depending on the immunological pathway that is defective, patients can present with different types of (opportunistic) infectious diseases, as well as other clinical manifestations. Based on selected examples, we focus in this chapter on finding parallels in the infectious risk of autoimmune patients treated with biologics and PID patients with a defect in the immunological pathway that is affected by the respective biologic. The goal is to learn from the (dis)similarities between both patient populations in terms of safety profiles of biologic treatments.

Holstein cows on a farm in the Humansdorp district, Eastern Cape province, South Africa, developed reddened, painful teat skin 3 days after grazing a mixed forage crop dominated by bulb turnip (Brassica rapa, Barkant cultivar). The crop was grazed 45 days after planting and 10% of the herd developed symptoms. More characteristic non-pigmented skin lesions started manifesting 1-2 days after the appearance of the teat lesions. Affected cows had elevated serum activities of gamma-glutamyl transferase, glutamate dehydrogenase and aspartate aminotransferase. These blood chemistry findings confirmed a secondary (hepatogenous) photosensitivity. As a result of the severity of the teat and skin lesions, seven cows were slaughtered and tissue samples from five of them were collected for histopathological examination. Liver lesions in cows that were culled 3 or more weeks after the onset of the outbreak showed oedematous concentric fibrosis around medium-sized bile ducts and inflammatory infiltrates in portal tracts. Characteristic lesions associated with other known hepatobiliary toxicities were not found. No new cases were reported 5 days after the cattle were removed from the turnips. The sudden introduction of the cows, without any period of transitioning or adaptation to grazing turnips, as well as the short latent period, clinical signs of photosensitisation, blood chemistry and histopathology, confirmed a diagnosis of Brassica-associated liver disease, a condition seen in New Zealand but not previously described in South Africa. Brassica forage crops are potentially toxic under certain conditions and farmers must be aware of these risks.

In vertebrates, the anterior pituitary plays a crucial role in regulating several essential physiological processes via the secretion of at least seven peptide hormones by different endocrine cell types. Comparative and comprehensive knowledge of the spatial distribution of those endocrine cell types is required to better understand their physiological functions. Using medaka as a model and several combinations of multi-color fluorescence in situ hybridization, we present the first 3D atlas revealing the gland-wide distribution of seven endocrine cell populations: lactotropes, thyrotropes, Lh and Fsh gonadotropes, somatotropes, and pomca-expressing cells (corticotropes and melanotropes) in the anterior pituitary of a teleost fish. By combining in situ hybridization and immunofluorescence techniques, we deciphered the location of corticotropes and melanotropes within the pomca-expressing cell population. The 3D localization approach reveals sexual dimorphism of tshba-, pomca-, and lhb-expressing cells in the adult medaka pituitary. Finally, we show the existence of bi-hormonal cells co-expressing lhb-fshb, fshb-tshba and lhb-sl using single-cell transcriptomics analysis and in situ hybridization. This study offers a solid basis for future comparative studies of the teleost pituitary and its functional plasticity.

Inflammation has been recognized as essential for restorative regeneration. Here, we analyzed the sequential processes during onset of liver injury and subsequent regeneration based on time-resolved transcriptional regulatory networks (TRNs) to understand the relationship between inflammation, mature organ function, and regeneration. Genome-wide expression and TRN analysis were performed time dependently in mouse liver after acute injury by CCl4 (2 h, 8 h, 1, 2, 4, 6, 8, 16 days), as well as lipopolysaccharide (LPS, 24 h) and compared to publicly available data after tunicamycin exposure (mouse, 6 h), hepatocellular carcinoma (HCC, mouse), and human chronic liver disease (non-alcoholic fatty liver, HBV infection and HCC). Spatiotemporal investigation differentiated lobular zones for signaling and transcription factor expression. Acute CCl4 intoxication induced expression of gene clusters enriched for inflammation and stress signaling that peaked between 2 and 24 h, accompanied by a decrease of mature liver functions, particularly metabolic genes. Metabolism decreased not only in pericentral hepatocytes that underwent CCl4-induced necrosis, but extended to the surviving periportal hepatocytes. Proliferation and tissue restorative TRNs occurred only later reaching a maximum at 48 h. The same upstream regulators (e.g. inhibited RXR function) were implicated in increased inflammation and suppressed metabolism. The concomitant inflammation/metabolism TRN occurred similarly after acute LPS and tunicamycin challenges, in chronic mouse models and also in human liver diseases. Downregulation of metabolic genes occurs concomitantly to induce inflammation-associated genes as an early response and appears to be initiated by similar upstream regulators in acute and chronic liver diseases in humans and mice. In the acute setting, proliferation and restorative regeneration associated TRNs peak only later when metabolism is already suppressed. ispartof: ARCHIVES OF TOXICOLOGY vol:94 issue:1 pages:205-217 ispartof: location:Germany status: published

Liver fibrosis interferes with normal liver function and facilitates hepatocellular carcinoma (HCC) development, representing a major threat to human health. Here, we present a comprehensive perspective of microRNA (miRNA) function on targeting the fibrotic microenvironment. Starting from a murine HCC model, we identify a miRNA network composed of 8 miRNA hubs and 54 target genes. We show that let-7, miR-30, miR-29c, miR-335, and miR-338 (collectively termed antifibrotic microRNAs [AF-miRNAs]) down-regulate key structural, signaling, and remodeling components of the extracellular matrix. During fibrogenic transition, these miRNAs are transcriptionally regulated by the transcription factor Ppar γ and thus we identify a role of Ppar γ as regulator of a functionally related class of AF-miRNAs. The miRNA network is active in human HCC, breast, and lung carcinomas, as well as in 2 independent mouse liver fibrosis models. Therefore, we identify a miRNA:mRNA network that contributes to formation of fibrosis in tumorous and nontumorous organs of mice and humans.

West Nile virus (WNV) lineage 2 is associated with neurologic disease in horses and humans in South Africa. Surveillance in wildlife and nonequine domestic species during 2010–2018 identified WNV in 11 (1.8%) of 608 animals with severe neurologic and fatal infections, highlighting susceptible hosts and risk for WNV epizootics in Africa.

Newly constructed wetlands are created to provide a range of ecosystem services, including carbon sequestration. Our understanding of the initial factors leading to successful peat formation in such environments is, however, limited. In a new 100-ha wetland that was created north of Amsterdam (the Netherlands), we conducted an experiment to determine the best combination of abiotic and biotic starting conditions for initial peat-forming processes. Sediment conditions were the main driver of vegetation development, biomass production and elemental composition during the 3-year study period. Overall, helophytes (Typhaspp.) dominated basins with nutrient-rich conditions, whereas nutrient-poor basins were covered by submerged vegetation, which produced about seven times less aboveground biomass than helophytes. The C/N ratios for all plant species and biomass components were generally lower under nutrient-rich conditions and were lower for submerged species than helophytes. Because total basin biomass showed five times higher shoot and ten times higher root and rhizome production for clay and organic than sand sediments, even with some differences in decomposition rates are the conditions in the nutrient-rich basins expected to produce higher levels of initial peat formation. The results suggest that addition of a nutrient-rich sediment layer creates the best conditions for initial peat formation by stimulating rapid development of helophytes.

Pyrrolizidine alkaloids (PAs) are widely occurring phytotoxins which can induce severe liver damage in humans and other mammalian species by mechanisms that are not fully understood. Therefore, we investigated the development of PA hepatotoxicity in vivo, using an acutely toxic dose of the PA senecionine in mice, in combination with intravital two-photon microscopy, histology, clinical chemistry, and in vitro experiments with primary mouse hepatocytes and liver sinusoidal endothelial cells (LSECs). We observed pericentral LSEC necrosis together with elevated sinusoidal marker proteins in the serum of senecionine-treated mice and increased sinusoidal platelet aggregation in the damaged tissue regions. In vitro experiments showed no cytotoxicity to freshly isolated LSECs up to 500 µM senecionine. However, metabolic activation of senecionine by preincubation with primary mouse hepatocytes increased the cytotoxicity to cultivated LSECs with an EC50 of approximately 22 µM. The cytochrome P450 (CYP)-dependency of senecionine bioactivation was confirmed in CYP reductase-deficient mice where no PA-induced hepatotoxicity was observed. Therefore, toxic metabolites of senecionine are generated by hepatic CYPs, and may be partially released from hepatocytes leading to destruction of LSECs in the pericentral region of the liver lobules. Analysis of hepatic bile salt transport by intravital two-photon imaging revealed a delayed uptake of a fluorescent bile salt analogue from the hepatic sinusoids into hepatocytes and delayed elimination. This was accompanied by transcriptional deregulation of hepatic bile salt transporters like Abcb11 or Abcc1. In conclusion, senecionine destroys LSECs although the toxic metabolite is formed in a CYP-dependent manner in the adjacent pericentral hepatocytes.

11 páginas, 7 figuras, The biorecovery of europium (Eu) from primary (mineral deposits) and secondary (mining wastes) resources is of interest due to its remarkable luminescence properties, important for modern technological applications. In this study, we explored the tolerance levels, reduction and intracellular bioaccumulation of Eu by a site-specific bacterium, Clostridium sp. 2611 isolated from Phalaborwa carbonatite complex. Clostridium sp. 2611 was able to grow in minimal medium containing 0.5 mM Eu3+. SEM-EDX analysis confirmed an association between Eu precipitates and the bacterium, while TEM-EDX analysis indicated intracellular accumulation of Eu. According to the HR-XPS analysis, the bacterium was able to reduce Eu3+ to Eu2+ under growth and non-growth conditions. Preliminary protein characterization seems to indicate that a cytoplasmic pyruvate oxidoreductase is responsible for Eu bioreduction. These findings suggest the bioreduction of Eu3+ by Clostridium sp. as a resistance mechanism, can be exploited for the biorecovery of this metal., This research was conducted with financial support from the Technology and Innovation Agency. The financial assistance of the National Research Foundation of South Africa (88833 and 106460) towards this research is hereby acknowledged.

The aim of this paper is twofold: The general aim is to shed light on the structure of species discoveries new to biology by bringing together a practice-oriented philosophy of science perspective with a philosophy of language perspective. The more specific aim is to argue that and to show how the overall structure of biological species discoveries comprises aspects of both institutional and non-institutional reality. The author proceeds as follows: (1) he shows that placing the focus on the topic of scientific discoveries enables us to circumvent two long-standing problems. (2) He analyzes three fictional cases of discoveries in order to bring about a greater sensitivity for the concept of discovery. (3) He takes a closer look at a real example – the discovery of a deep-sea anglerfish – and identifies the main structural features of species discovery processes in biology. (4) In order to connect these results with Searle’s account of institutional reality, he provides an overview of the conceptual apparatus needed here. (5) In bringing Searle’s account together with the structural features of species discoveries developed before, he shows to what extent declarative speech acts play a central role in species discovery processes in biology.

Die oorlewing en lewenskragtigheid van Nylkrokodil (Crocodylus niloticus) broeilinge is belangrik vir die sukses van kommersiële krokodilboerdery en die instandhouding van populasies in die natuur. In hierdie studie beskryf ons eers die verband tussen die massa van Nylkrokodilbroeilinge en die geskatte volume van die eier waaruit elkeen gebroei het. Daarna beskryf ons die variasie in die verhouding tussen die massa van individuele broeilinge en die volume van die eier waaruit elk gebroei het (die produktiwiteit van die eier) binne en tussen broeisels. Die volumes van 316 Nylkrokodileiers uit 51 broeisels is met ’n doelgemaakte algoritme geskat op grond van sleutelafmetings van die eiers wat op foto’s van die uitgebroeide eierdoppe gemaak is. Die broeiling wat uit elke eier gebroei het is direk na uitbroei geweeg. Nóg die duur van inkubering tot uitbroei (P = 0.88) nóg die jaar waarin broeisels gelê is (P = 0.35) nóg die aantal eiers in die broeisel (P = 0.57) het broeilingmassa beïnvloed. Daar bestaan ’n sterk, lineêre positiewe verband tussen die uitbroeimassa van Nylkrokodilbroeilinge en die geskatte volume van die eiers waaruit hulle gebroei het r = 0.88, P < 0.001, n =316). Sonder inagneming van geskatte eiervolume is 86.9% van die variasie in broeilingmassa die gevolg van variasie tussen broeisels en 13.1% die gevolg van variasie binne broeisels. Indien geskatte eiervolume in berekening gebring word is 59% van die variasie in broeilingmassa vir ’n bepaalde geskatte eiervolume die gevolg van variasie tussen broeisels en 41% die gevolg van variasie binne broeisels. Die produktiwiteit van eiers het van 0.57 g/ml tot 0.81 g/ml gevarieer, met 45.4% van die variasie wat tussen broeisels voorgekom het en 54.6% binne broeisels. Verdere navorsing is nodig om die verband tussen broeilingmassa en die groei van broeilinge, sowel as die verband tussen eierproduktiwiteit en die groei van broeilinge te ondersoek.

Supplemental Digital Content is available in the text, Tyrosine kinase receptor (Tie2) is mainly expressed by endothelial cells. In animal models mimicking critical illness, Tie2 levels in organs are temporarily reduced. Functional consequences of these reduced Tie2 levels on microvascular endothelial behavior are unknown. We investigated the effect of partial deletion of Tie2 on the inflammatory status of endothelial cells in different organs. Newly generated heterozygous Tie2 knockout mice (exon 9 deletion, ΔE9/Tie2+/−) exhibiting 50% reduction in Tie2 mRNA and protein, and wild-type littermate controls (Tie2+/+), were subjected to hemorrhagic shock and resuscitation (HS + R), or challenged with i.p. lipopolysaccharide (LPS). Kidney, liver, lung, heart, brain, and intestine were analyzed for mRNA levels of adhesion molecules E-selectin, vascular cell adhesion molecule 1 (VCAM-1), and intercellular cell adhesion molecule 1 (ICAM-1), and CD45. Exposure to HS + R did not result in different expression responses of these molecules between organs from Tie2+/− or Tie2+/+ mice and sham-operated mice. In contrast, the LPS-induced mRNA expression levels of E-selectin, VCAM-1, and ICAM-1, and CD45 in organs were attenuated in Tie2+/− mice when compared with Tie2+/+ mice in kidney and liver, but not in the other organs studied. Furthermore, reduced expression of E-selectin and VCAM-1 protein, and reduced influx of CD45+ cells upon LPS exposure, was visible in a microvascular bed-specific pattern in kidney and liver of Tie2+/− mice compared with controls. In contrast to the hypothesis that a disbalance in the Ang/Tie2 system leads to increased microvascular inflammation, heterozygous deletion of Tie2 is associated with an organ-restricted, microvascular bed-specific attenuation of endothelial inflammatory response to LPS.

Summary During mammalian development, liver differentiation is driven by signals that converge on multiple transcription factor networks. The hepatocyte nuclear factor signaling network is known to be essential for hepatocyte specification and maintenance. In this study, we have generated deletion and point mutants of hepatocyte nuclear factor-4alpha (HNF4α) to precisely evaluate the function of protein domains during hepatocyte specification from human pluripotent stem cells. We demonstrate that nuclear HNF4α is essential for hepatic progenitor specification, and the introduction of point mutations in HNF4α′s Small Ubiquitin-like Modifier (SUMO) consensus motif leads to disrupted hepatocyte differentiation. Taking a multiomics approach, we identified key deficiencies in cell biology, which included dysfunctional metabolism, substrate adhesion, tricarboxylic acid cycle flux, microRNA transport, and mRNA processing. In summary, the combination of genome editing and multiomics analyses has provided valuable insight into the diverse functions of HNF4α during pluripotent stem cell entry into the hepatic lineage and during hepatocellular differentiation., Graphical Abstract, Highlights • Deletion of HNF4α's DNA-binding domain blocks hepatic progenitor formation • HNF4α′s C-terminal SUMO consensus motif plays roles in hepatocyte specification • Multiomics analyses reveal various processes regulated by HNF4α during differentiation, Biological Sciences; Cell Biology; Developmental Biology; Stem Cells Research

Melioidosis is a severe disease caused by Burkholderia pseudomallei. The biofilm of B. pseudomallei acquires resistance to several antibiotics and may be related to relapse in melioidosis patients. Here, the killing activity of antimicrobial peptides (LL-37, LL-31) and the D-enantiomers (D-LL-37, D-LL-31) in combination with ceftazidime (CAZ) against B. pseudomallei 1026b, H777 and a biofilm mutant M10, derived from H777 grown under biofilm-stimulating conditions was observed. Using static conditions, D-LL-31 exhibited the strongest killing activity against the three isolates in a dose-dependent manner. IC50 values for D-LL-31 ranged from 1 to 6 µM, for isolates M10, H777, and 1026b, respectively. Moreover, D-LL-31 combined with CAZ synergistically decreased the IC50 values of the peptide and antibiotic and caused also disruption of biofilms of B. pseudomallei 1026b under flow conditions. Thus a combination of D-LL-31 and CAZ may enhance the efficacy of the currently used antibiotic treatments against B. pseudomallei.

Die waarde van hul leer stimuleer kommersiële boerdery met verskeie spesies van die Crocodilia. Oorlewings- en groeivermoë van krokodilbroeilinge hou verband met hul geboortemassa. Daar bestaan ’n positiewe verband tussen broeilinggrootte en eiergrootte van verskeie spesies van die Crocodilia. Krokodileiers se grootte word dikwels nie gemeet voordat hulle uitbroei nie. Die doel van hierdie studie was om ’n model te skep waarmee die volume van individuele Nylkrokodileiers geskat kan word nadat hulle uitgebroei het en die dop gebreek is, sodat die verband tussen eiervolume en broeilingmassa op ’n individuele basis bestudeer kan word sonder dat die grootte van eiers gemeet is voordat hulle uitbroei. Onvrugbare eiers is in sy-aansig gefotografeer, met een pool na onder en die ander na bo en ’n skaal op die vlak van fokus. Hul volume is met waterverplasing gemeet (verplasingsvolume). ’n Rekenaarprogram wat vir die doel geskryf is, is gebruik om die fotobeelde te meet. Die program het die eierbeeld regop gedraai en die posisie van die poolas bepaal sonder om die boonste pool se posisie in ag te neem. Die lengte van verskeie dwarsdeursnitte (loodreg op die poolas) is gemeet, en die volume van die eier bereken deur die funksie wat die horison van die eier op die poolas beskryf te integreer (berekende volume). Die beste modelle is bepaal om die berekende volume te skat deur gebruik te maak van inligting beperk tot verskillende afstande van die onderste pool in die rigting van die boonste te gebruik, en vir eiers met verskillende polariteit. Die modelle is daarna gebruik om die volumes van 138 eiers waarvan 15%, 20%, 25% en 30% van elke eierbeeld, van die boonste pool in die rigting van die onderste, gemaskeer is. Deur analise van die gemaskeerde fotobeelde kan die volume van eiers met volumes van 60 ml tot 135 ml met 95% vertroue binne 4.57 ml van die werklike voorspel word. Hierdie studie skep die moontlikheid om die volume van uitgebroeide Nylkrokodileiers te skat. Variasie in Nylkrokodille se geboortemassa van groter as 7.72% kan met 95% vertroue geïdentifi seer word vir broeilinge uit eiers met ’n geskatte volume van 60 ml, terwyl die presisie verbeter tot ’n variasie groter as 3.40% vir broeilinge uit eiers met ’n geskatte volume van 135 ml.

Crocodylus niloticus eggs are a useful starting point to study reproduction in this species. Using samples collected from a single farm during a single breeding season, the present research aimed to describe and compare the masses of unbanded and fertile eggs and their components. The clustering effect of clutch on egg and egg component mass was investigated, and the relationship between the mass of unbanded eggs and their components, together with the effect of possible confounding variables was explored. Estimated egg volume (ellipsoid volume) was strongly positively correlated with egg mass. A strong positive linear relationship existed between egg mass and the combined mass of the foetus and intra-abdominal yolk, as well as between egg mass and the isolated yolk-free foetal mass. If egg mass and incubation period were kept constant, foetal mass increased by 1.1 g for each gram that yolk decreased. The wet yolk and dried shell masses of fertile eggs were significantly lower than those of size-matched unbanded eggs. Clutch had a strong clustering effect on all component masses, particularly total egg mass and hatchling mass. Unbanded egg mass and its individual component masses tended to be similar within a clutch, however some variability existed which should not be discounted. The mass of an egg was strongly positively linearly correlated with the mass of each of its components. The period within the laying season an egg was laid had no effect on its mass nor the mass of any of its components, whereas the breeding pond in which the female resided did affect these measurements. The strong clustering effect of clutch on total egg mass and the masses of all egg components must be accounted for when selecting samples for future studies. The potential confounding effect of breeding pond of origin (which related to female size in the current study) should be considered, particularly where the age or size of females differ among ponds.

When one thinks about electrodes, especially ones meant for humans, one typically thinks of some kind of metal. Whether on the skin or in the brain, metal electrodes are characteristically expensive, stiff, non-efficient in electron-ion transduction, and prone to toxic metal ion by-products during stimulation. In order to circumvent these disadvantages, electrically-conductive laser-induced graphene (LIG) and mixed electron-ion conducting polymer (poly(3, 4‐ethylenedioxythiophene) polystyrene sulfonate – PEDOT:PSS) was leveraged to create a metal-free electrode combination that allows for an economical, soft, and organic electrode for applications on human skin. Compared to clinical-standard silver – silver chloride (Ag/AgCl) skin electrodes, the metal-free hydrogel electrodes show notable improvement in electrochemical stability and prolonged stable potentials during long-term DC stimulation (0.5–24 h). Recording and stimulation performance on human participants rivals that of Ag/AgCl, thus fortifying the notion that they are an appropriate progression to their noble metal counterparts.

Increased airway wall thickness and remodeling of bronchial mucosa are characteristic of asthma and may arise from altered integrin signaling on airway cells. Here, we analyzed the expression of β1-subfamily integrins on blood and airway cells (flow cytometry), inflammatory biomarkers in serum and bronchoalveolar lavage, reticular basement membrane (RBM) thickness and collagen deposits in the mucosa (histology), and airway geometry (CT-imaging) in 92 asthma patients (persistent airflow limitation subtype: n = 47) and 36 controls. Persistent airflow limitation was associated with type-2 inflammation, elevated soluble α2 integrin chain, and changes in the bronchial wall geometry. Both subtypes of asthma showed thicker RBM than control, but collagen deposition and epithelial α1 and α2 integrins staining were similar. Type-I collagen accumulation and RBM thickness were inversely related to the epithelial expression of the α2 integrin chain. Expression of α2β1 integrin on T-cells and eosinophils was not altered in asthma. Collagen I deposits were, however, more abundant in patients with lower α2β1 integrin on blood and airway CD8+ T-cells. Thicker airway walls in CT were associated with lower α2 integrin chain on blood CD4+ T-cells and airway eosinophils. Our data suggest that α2β1 integrin on inflammatory and epithelial cells may protect against airway remodeling advancement in asthma.

Axonal projections from layer V neurons of distinct neocortical areas are topographically organized into discrete clusters within the pontine nuclei during the establishment of voluntary movements. However, the molecular determinants controlling corticopontine connectivity are insufficiently understood. Here, we show that an intrinsic cortical genetic program driven by Nr2f1 graded expression is directly implicated in the organization of corticopontine topographic mapping. Transgenic mice lacking cortical expression of Nr2f1 and exhibiting areal organization defects were used as model systems to investigate the arrangement of corticopontine projections. Combining three-dimensional digital brain atlas tools, Cre-dependent mouse lines, and axonal tracing, we show that Nr2f1 expression in postmitotic neurons spatially and temporally controls somatosensory topographic projections, whereas expression in progenitor cells influences the ratio between corticopontine and corticospinal fibres passing the pontine nuclei. We conclude that cortical gradients of area patterning genes are directly implicated in the establishment of a topographic somatotopic mapping from the cortex onto pontine nuclei.Summary statementCortical gradient expression of the area patterning gene Nr2f1 spatially and temporally controls corticopontine topographic connectivity in layer V projection neurons.

International audience; Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown aetiology for which there are no approved therapeutic options. Patients with PSC display changes in gut microbiota and in bile acid (BA) composition; however, the contribution of these alterations to disease pathogenesis remains controversial. Here we identify a role for microbiota-dependent changes in BA synthesis that modulates PSC pathophysiology. In a genetic mouse model of PSC, we show that loss of microbiota-mediated negative feedback control of BA synthesis results in increased hepatic BA concentrations, disruption of bile duct barrier function and, consequently, fatal liver injury. We further show that these changes are dependent on decreased BA signalling to the farnesoid X receptor, which modulates the activity of the rate-limiting enzyme in BA synthesis, CYP7A1. Moreover, patients with advanced stages of PSC show suppressed BA synthesis as measured by serum C4 levels, which is associated with poor disease prognosis. Our preclinical data highlight the microbiota-dependent dynamics of BA metabolism in cholestatic liver disease, which could be important for future therapies targeting BA and gut microbiome interactions, and identify C4 as a potential biomarker to functionally stratify patients with PSC and predict disease outcomes.

Drug-induced liver injury (DILI) is the most prevalent adversity encountered in drug development and clinical settings leading to urgent needs to understand the underlying mechanisms. In this study, we have systematically investigated the dynamics of the activation of cellular stress response pathways and cell death outcomes upon exposure of a panel of liver toxicants using live cell imaging of fluorescent reporter cell lines. We established a comprehensive temporal dynamic response profile of a large set of BAC-GFP HepG2 cell lines representing the following components of stress signaling: i) unfolded protein response (UPR) [ATF4, XBP1, BIP and CHOP]; ii) oxidative stress [NRF2, SRXN1, HMOX1]; iii) DNA damage [P53, P21, BTG2, MDM2]; and iv) NF-κB pathway [A20, ICAM1]. We quantified the single cell GFP expression as a surrogate for endogenous protein expression using live cell imaging over > 60 h upon exposure to 14 DILI compounds at multiple concentrations. Using logic-based ordinary differential equation (Logic-ODE), we modelled the dynamic profiles of the different stress responses and extracted specific descriptors potentially predicting the progressive outcomes. We identified the activation of ATF4-CHOP axis of the UPR as the key pathway showing the highest correlation with cell death upon DILI compound perturbation. Knocking down main components of the UPR provided partial protection from compound-induced cytotoxicity, indicating a complex interplay among UPR components as well as other stress pathways. Our results suggest that a systematic analysis of the temporal dynamics of ATF4-CHOP axis activation can support the identification of DILI risk for new candidate drugs. published

Nanopore sequencing and phylodynamic modelling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Here, we implement Random Forest models for single nucleotide polymorphism (SNP) polishing to estimate divergence and effective reproduction numbers (Re) of two community-associated, methicillin-resistant Staphylococcus aureus (MRSA) outbreaks in remote Far North Queensland and Papua New Guinea (n = 159). Successive bar-coded panels of S. aureus isolates (2 × 12 per MinION) sequenced at low-coverage (> 5x - 10x) provided sufficient data to accurately infer assembly genotypes with high recall when compared with Illumina references. De novo SNP calling with Clair was followed by SNP polishing using intra- and inter-species models trained on Snippy reference calls. Models achieved sufficient resolution on ST93 outbreak sequence types (> 70 - 90% accuracy and precision) for phylodynamic modelling from lineage-wide hybrid alignments and birth-death skyline models in BEAST2. Our method reproduced phylogenetic topology, geographical source of the outbreaks, and indications of sustained transmission (Re > 1). We provide Nextflow pipelines that implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks using nanopore sequencing.

In a study on the mechanism of stimulated petiole elongation in submerged plants, oxygen concentrations in petioles of the flood-tolerant plant Rumex palustris were measured with micro-electrodes. Short-term submergence lowered petiole partial oxygen pressure to c. 19 kPa whereas prolonged submergence under continuous illumination depressed oxygen levels to c. 8-12 kPa after 24 h. Oxygen levels in petioles depended on the presence of the lamina, even in submerged conditions, and on available light. In darkness, petiole oxygen levels in submerged plants dropped quickly to values as low as 0.5-4 kPa. It is hypothesized that prolonged submergence in the light is accompanied by a decrease in carbon dioxide in the petiole. Submergence-enhanced petiolar elongation rate was compared with emergent plants. Peak daily elongation rates occurred at the end of the dark period in emergent plants, but in the middle of the light period in submerged plants. We suggest that this shift in daily elongation pattern is induced by dependence of growth on photosynthetically derived oxygen in submerged plants. Implications of reduced oxygen for ethylene production are raised. Levels of 1- aminocyclopropane-1-carboxylic acid synthase and 1-aminocyclopropane-1-carboxylic acid oxidase and ethylene sensitivity are cited as potential factors in hypoxia-induced ethylene release.

Prenatal exposure to endocrine disrupting chemicals can interfere with development, and has been associated with social-cognitive functioning and adverse health outcomes later in life. Exposure-associated changes of DNA methylation (DNAm) patterns have been suggested as a possible mediator of this relationship. This study investigated whether prenatal low-dose exposure to polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) is associated with altered DNAm patterns across the genome in a Western urban-industrial population. In 142 mother-infant pairs from the Duisburg Birth Cohort Study, PCBs and PCDD/Fs levels were quantified from maternal blood during late pregnancy and associated with DNAm levels in cord blood using the Illumina EPIC beadchip. The epigenome-wide association studies (EWAS) identified 32 significantly differentially methylated positions (DMPs) and eight differentially methylated regions (DMRs) associated with six congeners of PCB and PCDD in females or males (FDRs < 0.05). DMPs and DMRs mapped to genes involved in neurodevelopment, gene regulation, and immune functioning. Weighted gene correlation network analysis (WGCNA) showed 31 co-methylated modules (FDRs < 0.05) associated with one congener of PCDF levels in females. Results of both analytical strategies indicate that prenatal exposure to PCBs and PCDD/Fs is associated with altered DNAm of genes involved in neurodevelopment, gene expression and immune functioning. DNAm and gene expression levels of several of these genes were previously associated with EDC exposure in rodent models. Follow-up studies will clarify whether these epigenetic changes might contribute to the origin for adverse mental and health outcomes.

Mouse models are frequently used to study chronic liver diseases (CLDs). To assess their translational relevance, we quantified the similarity of commonly used mouse models to human CLDs based on transcriptome data. Gene‐expression data from 372 patients were compared with data from acute and chronic mouse models consisting of 227 mice, and additionally to nine published gene sets of chronic mouse models. Genes consistently altered in humans and mice were mapped to liver cell types based on single‐cell RNA‐sequencing data and validated by immunostaining. Considering the top differentially expressed genes, the similarity between humans and mice varied among the mouse models and depended on the period of damage induction. The highest recall (0.4) and precision (0.33) were observed for the model with 12‐months damage induction by CCl4 and by a Western diet, respectively. Genes consistently up‐regulated between the chronic CCl4 model and human CLDs were enriched in inflammatory and developmental processes, and mostly mapped to cholangiocytes, macrophages, and endothelial and mesenchymal cells. Down‐regulated genes were enriched in metabolic processes and mapped to hepatocytes. Immunostaining confirmed the regulation of selected genes and their cell type specificity. Genes that were up‐regulated in both acute and chronic models showed higher recall and precision with respect to human CLDs than exclusively acute or chronic genes. Conclusion: Similarly regulated genes in human and mouse CLDs were identified. Despite major interspecies differences, mouse models detected 40% of the genes significantly altered in human CLD. The translational relevance of individual genes can be assessed at https://saezlab.shinyapps.io/liverdiseaseatlas/., In the present study, we observed that – although major interspecies differences remain – improved mouse models show up to 40% of the gene expression changes seen in liver tissue of human NAFLD or NASH, which is much higher than previously reported. Moreover, we identified gene sets consistently regulated in human and mouse chronic liver disease. Based on single‐cell RNA‐sequencing data set we mapped liver cell types to those genes and validated them by immunostaining.

The liver plays an important role in xenobiotic metabolism and represents a primary target for toxic substances. Many different in vitro cell models have been developed in the past decades. In this study, we used RNA-sequencing (RNA-Seq) to analyze the following human in vitro liver cell models in comparison to human liver tissue: cancer-derived cell lines (HepG2, HepaRG 3D), induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs), cancerous human liver-derived assays (hPCLiS, human precision cut liver slices), non-cancerous human liver-derived assays (PHH, primary human hepatocytes) and 3D liver microtissues. First, using CellNet, we analyzed whether these liver in vitro cell models were indeed classified as liver, based on their baseline expression profile and gene regulatory networks (GRN). More comprehensive analyses using non-differentially expressed genes (non-DEGs) and differential transcript usage (DTU) were applied to assess the coverage for important liver pathways. Through different analyses, we noticed that 3D liver microtissues exhibited a high similarity with in vivo liver, in terms of CellNet (C/T score: 0.98), non-DEGs (10,363) and pathway coverage (highest for 19 out of 20 liver specific pathways shown) at the beginning of the incubation period (0 h) followed by a decrease during long-term incubation for 168 and 336 h. PHH also showed a high degree of similarity with human liver tissue and allowed stable conditions for a short-term cultivation period of 24 h. Using the same metrics, HepG2 cells illustrated the lowest similarity (C/T: 0.51, non-DEGs: 5623, and pathways coverage: least for 7 out of 20) with human liver tissue. The HepG2 are widely used in hepatotoxicity studies, however, due to their lower similarity, they should be used with caution. HepaRG models, iPSC-HLCs, and hPCLiS ranged clearly behind microtissues and PHH but showed higher similarity to human liver tissue than HepG2 cells. In conclusion, this study offers a resource of RNA-Seq data of several biological replicates of human liver cell models in vitro compared to human liver tissue. Electronic supplementary material The online version of this article (10.1007/s00204-020-02937-6) contains supplementary material, which is available to authorized users.

Background & Aims Oncogenic KrasG12D induces neoplastic transformation of pancreatic acinar cells through acinar-to-ductal metaplasia (ADM), an actin-based morphogenetic process, and drives pancreatic ductal adenocarcinoma (PDAC). mTOR (mechanistic target of rapamycin kinase) complex 1 (mTORC1) and 2 (mTORC2) contain Rptor and Rictor, respectively, and are activated downstream of KrasG12D, thereby contributing to PDAC. Yet, whether and how mTORC1 and mTORC2 impact on ADM and the identity of the actin nucleator(s) mediating such actin rearrangements remain unknown. Methods A mouse model of inflammation-accelerated KrasG12D-driven early pancreatic carcinogenesis was used. Rptor, Rictor, and Arpc4 (actin-related protein 2/3 complex subunit 4) were conditionally ablated in acinar cells to deactivate the function of mTORC1, mTORC2 and the actin-related protein (Arp) 2/3 complex, respectively. Results We found that mTORC1 and mTORC2 are markedly activated in human and mouse ADM lesions, and cooperate to promote KrasG12D-driven ADM in mice and in vitro. They use the Arp2/3 complex as a common downstream effector to induce the remodeling the actin cytoskeleton leading to ADM. In particular, mTORC1 regulates the translation of Rac1 (Rac family small GTPase 1) and the Arp2/3-complex subunit Arp3, whereas mTORC2 activates the Arp2/3 complex by promoting Akt/Rac1 signaling. Consistently, genetic ablation of the Arp2/3 complex prevents KrasG12D-driven ADM in vivo. In acinar cells, the Arp2/3 complex and its actin-nucleation activity mediated the formation of a basolateral actin cortex, which is indispensable for ADM and pre-neoplastic transformation. Conclusions Here, we show that mTORC1 and mTORC2 attain a dual, yet nonredundant regulatory role in ADM and early pancreatic carcinogenesis by promoting Arp2/3 complex function. The role of Arp2/3 complex as a common effector of mTORC1 and mTORC2 fills the gap between oncogenic signals and actin dynamics underlying PDAC initiation.