Accessible methods and tools to estimate chemical exposure in humans to support risk assessment: A systematic scoping review.

Exposure assessment is a crucial component of environmental health research, providing essential information on the potential risks associated with various chemicals. A systematic scoping review was conducted to acquire an overview of accessible human exposure assessment methods and computational tools to support and ultimately improve risk assessment. The systematic scoping review was performed in Sysrev, a web platform that introduces machine learning techniques into the review process aiming for increased accuracy and efficiency. Included publications were restricted to a publication date after the year 2000, where exposure methods were properly described. Exposure assessments methods were found to be used for a broad range of environmental chemicals including pesticides, metals, persistent chemicals, volatile organic compounds, and other chemical classes. Our results show that after the year 2000, for all the types of exposure routes, probabilistic analysis, and computational methods to calculate human exposure have increased. Sixty-three mathematical models and toolboxes were identified that have been developed in Europe, North America, and globally. However, only twelve occur frequently and their usefulness were associated with exposure route, chemical classes and input parameters used to estimate exposure. The outcome of the combined associations can function as a basis and/or guide for decision making for the selection of most appropriate method and tool to be used for environmental chemical human exposure assessments in Ontology-driven and artificial intelligence-based repeated dose toxicity testing of chemicals for next generation risk assessment (ONTOX) project and elsewhere. Finally, the choice of input parameters used in each mathematical model and toolbox shown by our analysis can contribute to the harmonization process of the exposure models and tools increasing the prospect for comparison between studies and consistency in the regulatory process in the future.

Transcriptional signals of transformation in human cancer.

BACKGROUND: As normal cells transform into cancers, their cell state changes, which may drive cancer cells into a stem-like or more primordial, foetal, or embryonic cell state. The transcriptomic profile of this final state may encode information about cancer's origin and how cancers relate to their normal cell counterparts. METHODS: Here, we used single-cell atlases to study cancer transformation in transcriptional terms. We utilised bulk transcriptomes across a wide spectrum of adult and childhood cancers, using a previously established method to interrogate their relationship to normal cell states. We extend and validate these findings using single-cell cancer transcriptomes and organ-specific atlases of colorectal and liver cancer. RESULTS: Our bulk transcriptomic data reveals that adult cancers rarely return to an embryonic state, but that a foetal state is a near-universal feature of childhood cancers. This finding was confirmed with single-cell cancer transcriptomes. CONCLUSIONS: Our findings provide a nuanced picture of transformation in human cancer, indicating cancer-specific rather than universal patterns of transformation pervade adult epithelial cancers.

Somatic CNV Detection by Single-Cell Whole-Genome Sequencing in Postmortem Human Brain.

The evidence for a role of somatic mutations, including copy-number variants (CNVs), in neurodegeneration has increased in the last decade. However, the understanding of the types and origins of these mutations, and their exact contributions to disease onset and progression, is still in its infancy. The use of single-cell (or nuclear) whole-genome sequencing (scWGS) has emerged as a powerful tool to answer these questions. In the present chapter, we provide laboratory and bioinformatic protocols used successfully in our lab to detect megabase-scale CNVs in single cells from multiple system atrophy (MSA) human postmortem brains, using immunolabeling prior to selection of nuclei for whole-genome amplification (WGA). We also present an unpublished comparison of scWGS generated from the same control substantia nigra (SN) sample, using the latest versions of popular WGA chemistries, MDA and PicoPLEX. We have used this protocol to focus on brain cell types most relevant to synucleinopathies (dopaminergic [DA] neurons in Parkinson's disease [PD] and oligodendrocytes in MSA), but it can be applied to any tissue and/or cell type with appropriate markers.

Distinct chromosomal "niches" in the genome of Saccharomyces cerevisiae provide the background for genomic innovation and shape the fate of gene duplicates.

Nearly one third of Saccharomyces cerevisiae protein coding sequences correspond to duplicate genes, equally split between small-scale duplicates (SSD) and whole-genome duplicates (WGD). While duplicate genes have distinct properties compared to singletons, to date, there has been no systematic analysis of their positional preferences. In this work, we show that SSD and WGD genes are organized in distinct gene clusters that occupy different genomic regions, with SSD being more peripheral and WGD more centrally positioned close to centromeric chromatin. Duplicate gene clusters differ from the rest of the genome in terms of gene size and spacing, gene expression variability and regulatory complexity, properties that are also shared by singleton genes residing within them. Singletons within duplicate gene clusters have longer promoters, more complex structure and a higher number of protein-protein interactions. Particular chromatin architectures appear to be important for gene evolution, as we find SSD gene-pair co-expression to be strongly associated with the similarity of nucleosome positioning patterns. We propose that specific regions of the yeast genome provide a favourable environment for the generation and maintenance of small-scale gene duplicates, segregating them from WGD-enriched genomic domains. Our findings provide a valuable framework linking genomic innovation with positional genomic preferences.

Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in patients with myeloproliferative neoplasms.

The JAK2-V617F mutation is the most common cause of myeloproliferative neoplasms. Although experiments have revealed that this gain-of-function mutation is associated with myeloid blood cell expansion and increased production of white cells, red cells, and platelets, the transcriptional consequences of the JAK2-V617F mutation in different cellular compartments of the bone marrow have not yet been fully elucidated. To study the direct effects of JAK2-V617F on bone marrow cells in patients with myeloproliferative neoplasms, we performed joint single-cell RNA sequencing and JAK2 genotyping on CD34+-enriched cells from eight patients with newly diagnosed essential thrombocythemia or polycythemia vera. We found that the JAK2-V617F mutation increases the expression of interferon-response genes (e.g., HLAs) and the leptin receptor in hematopoietic progenitor cells. Furthermore, we sequenced a population of CD34- bone marrow monocytes and found that the JAK2 mutation increased expression of intermediate monocyte genes and the fibrocyte-associated surface protein SLAMF7 in these cells.

Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms.

Some cancers originate from a single mutation event in a single cell. Blood cancers known as myeloproliferative neoplasms (MPNs) are thought to originate when a driver mutation is acquired by a hematopoietic stem cell (HSC). However, when the mutation first occurs in individuals and how it affects the behavior of HSCs in their native context is not known. Here we quantified the effect of the JAK2-V617F mutation on the self-renewal and differentiation dynamics of HSCs in treatment-naive individuals with MPNs and reconstructed lineage histories of individual HSCs using somatic mutation patterns. We found that JAK2-V617F mutations occurred in a single HSC several decades before MPN diagnosis-at age 9 ± 2 years in a 34-year-old individual and at age 19 ± 3 years in a 63-year-old individual-and found that mutant HSCs have a selective advantage in both individuals. These results highlight the potential of harnessing somatic mutations to reconstruct cancer lineages.

Complex mosaic structural variations in human fetal brains.

Somatic mosaicism, manifesting as single nucleotide variants (SNVs), mobile element insertions, and structural changes in the DNA, is a common phenomenon in human brain cells, with potential functional consequences. Using a clonal approach, we previously detected 200-400 mosaic SNVs per cell in three human fetal brains (15-21 wk postconception). However, structural variation in the human fetal brain has not yet been investigated. Here, we discover and validate four mosaic structural variants (SVs) in the same brains and resolve their precise breakpoints. The SVs were of kilobase scale and complex, consisting of deletion(s) and rearranged genomic fragments, which sometimes originated from different chromosomes. Sequences at the breakpoints of these rearrangements had microhomologies, suggesting their origin from replication errors. One SV was found in two clones, and we timed its origin to ∼14 wk postconception. No large scale mosaic copy number variants (CNVs) were detectable in normal fetal human brains, suggesting that previously reported megabase-scale CNVs in neurons arise at later stages of development. By reanalysis of public single nuclei data from adult brain neurons, we detected an extrachromosomal circular DNA event. Our study reveals the existence of mosaic SVs in the developing human brain, likely arising from cell proliferation during mid-neurogenesis. Although relatively rare compared to SNVs and present in ∼10% of neurons, SVs in developing human brain affect a comparable number of bases in the genome (∼6200 vs. ∼4000 bp), implying that they may have similar functional consequences.

Influence of Defects and H2O on the Hydrogenation of CO2 to Methanol over Pt Nanoparticles in UiO-67 Metal-Organic Framework.

In catalysts for CO2 hydrogenation, the interface between metal nanoparticles (NPs) and the support material is of high importance for the activity and reaction selectivity. In Pt NP-containing UiO Zr-metal-organic frameworks (MOFs), key intermediates in methanol formation are adsorbed at open Zr-sites at the Pt-MOF interface. In this study, we investigate the dynamic role of the Zr-node and the influence of H2O on the CO2 hydrogenation reaction at 170 °C, through steady state and transient isotope exchange experiments, H2O cofeed measurements, and density functional theory (DFT) calculations. The study revealed that an increased number of Zr-node defects increase the formation rates to both methanol and methane. Transient experiments linked the increase to a higher number of surface intermediates for both products. Experiments involving either dehydrated or prehydrated Zr-nodes showed higher methanol and methane formation rates over the dehydrated Zr-node. Transient experiments suggested that the difference is related to competitive adsorption between methanol and water. DFT calculations and microkinetic modeling support this conclusion and give further insight into the equilibria involved in the competitive adsorption process. The calculations revealed weaker adsorption of methanol in defective or dehydrated nodes, in agreement with the larger gas phase concentration of methanol observed experimentally. The microkinetic model shows that [Zr2(µ-O)2]4+ and [Zr2(µ-OH)(µ-O)(OH)(H2O)]4+ are the main surface species when the concentration of water is lower than the number of defect sites. Lastly, although addition of water was found to promote methanol desorption, water does not change the methanol steady state reaction rate, while it has a substantial inhibiting effect on CH4 formation. These results indicate that water can be used to increase the reaction selectivity to methanol and encourages further detailed investigations of the catalyst system.

One-pot synthesis of cobalt-rhenium nanoparticles taking the unusual ß-Mn type structure.

Using a facile one-pot colloidal method, it is now possible to obtain monodisperse Co1-x Re x nanoparticles (NPs), with excellent control of Re stoichiometry for x < 0.15. Re-incorporation in terms of a solid solution stabilizes the ß-Mn polymorph relative to the hcp/ccp variants of cobalt. The NPs are thermally stable up to 300 °C, which may make them attractive as model catalysts.

Functional Genomics of a Symbiotic Community: Shared Traits in the Olive Fruit Fly Gut Microbiota.

The olive fruit fly Bactrocera oleae is a major pest of olives worldwide and houses a specialized gut microbiota dominated by the obligate symbiont "Candidatus Erwinia dacicola." Candidatus Erwinia dacicola is thought to supplement dietary nitrogen to the host, with only indirect evidence for this hypothesis so far. Here, we sought to investigate the contribution of the symbiosis to insect fitness and explore the ecology of the insect gut. For this purpose, we examined the composition of bacterial communities associated with Cretan olive fruit fly populations, and inspected several genomes and one transcriptome assembly. We identified, and reconstructed the genome of, a novel component of the gut microbiota, Tatumella sp. TA1, which is stably associated with Mediterranean olive fruit fly populations. We also reconstructed a number of pathways related to nitrogen assimilation and interactions with the host. The results show that, despite variation in taxa composition of the gut microbial community, core functions related to the symbiosis are maintained. Functional redundancy between different microbial taxa was observed for genes involved in urea hydrolysis. The latter is encoded in the obligate symbiont genome by a conserved urease operon, likely acquired by horizontal gene transfer, based on phylogenetic evidence. A potential underlying mechanism is the action of mobile elements, especially abundant in the Ca. E. dacicola genome. This finding, along with the identification, in the studied genomes, of extracellular surface structure components that may mediate interactions within the gut community, suggest that ongoing and past genetic exchanges between microbes may have shaped the symbiosis.

Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing.

Synucleinopathies are mostly sporadic neurodegenerative disorders of partly unexplained aetiology, and include Parkinson's disease (PD) and multiple system atrophy (MSA). We have further investigated our recent finding of somatic SNCA (α-synuclein) copy number variants (CNVs, specifically gains) in synucleinopathies, using Fluorescent in-situ Hybridisation for SNCA, and single-cell whole genome sequencing for the first time in a synucleinopathy. In the cingulate cortex, mosaicism levels for SNCA gains were higher in MSA and PD than controls in neurons (> 2% in both diseases), and for MSA also in non-neurons. In MSA substantia nigra (SN), we noted SNCA gains in > 3% of dopaminergic (DA) neurons (identified by neuromelanin) and neuromelanin-negative cells, including olig2-positive oligodendroglia. Cells with CNVs were more likely to have α-synuclein inclusions, in a pattern corresponding to cell categories mostly relevant to the disease: DA neurons in Lewy-body cases, and other cells in the striatonigral degeneration-dominant MSA variant (MSA-SND). Higher mosaicism levels in SN neuromelanin-negative cells may correlate with younger onset in typical MSA-SND, and in cingulate neurons with younger death in PD. Larger sample sizes will, however, be required to confirm these putative findings. We obtained genome-wide somatic CNV profiles from 169 cells from the substantia nigra of two MSA cases, and pons and putamen of one. These showed somatic CNVs in ~ 30% of cells, with clonality and origins in segmental duplications for some. CNVs had distinct profiles based on cell type, with neurons having a mix of gains and losses, and other cells having almost exclusively gains, although control data sets will be required to determine possible disease relevance. We propose that somatic SNCA CNVs may contribute to the aetiology and pathogenesis of synucleinopathies, and that genome-wide somatic CNVs in MSA brain merit further study.

Engineering Functions into Platinum and Platinum-Rhodium Nanoparticles in a One-Step Microwave Irradiation Synthesis.

Platinum (Pt) and platinum-rhodium (PtRh) nanoparticles (NPs) are active catalysts for a range of important industrial reactions, and their response has been shown to be affected by size, morphology, composition, and architectural configuration. We report herein the engineering of these functionalities into NPs by suitably modifying our single-step fabrication process by using microwave irradiation dielectric heating. NPs with different morphologies are acquired by manipulating the reaction kinetics with the concentration of the capping agent while keeping the reaction time constant. Pt@Rh core@shell octopod-cube, Pt-truncated-cube, and cube and small-sphere NPs having "near-monodisperse" distributions and average sizes in the range of 4 to 18 nm are obtained. By increasing the microwave time the composition of Pt@Rh can be tuned, and NPs with a Rh-rich shell and a tunable Pt100-x Rh x (x≤41 at %) core are fabricated. Finally, alloy bimetallic PtRh NPs with controlled composition are designed by simultaneous tuning of the relative molar ratio of the metal precursors and the microwave irradiation time.

Burst nucleation by hot injection for size controlled synthesis of ε-cobalt nanoparticles.

BACKGROUND: Reproducible growth of narrow size distributed ε-Co nanoparticles with a specific size requires full understanding and identification of the role of essential synthesis parameters for the applied synthesis method. For the hot injection methodology, a significant discrepancy with respect to obtained sizes and applied reaction conditions is reported. Currently, a systematic investigation controlling key synthesis parameters as injection-temperature and time, metal to surfactant ratio and reaction holding time in terms of their impact on mean ([Formula: see text]mean) and median ([Formula: see text]median) particle diameter using dichlorobenzene (DCB), Co2(CO)8 and oleic acid (OA) as the reactant matrix is lacking. METHODS: A series of solution-based ε-Co nanoparticles were synthesized using the hot injection method. Suspensions and obtained particles were analyzed by DLS, ICP-OES, (synchrotron)XRD and TEM. Rietveld refinements were used for structural analysis. Mean ([Formula: see text]mean) and median ([Formula: see text]median) particle diameters were calculated with basis in measurements of 250-500 particles for each synthesis. 95 % bias corrected confidence intervals using bootstrapping were calculated for syntheses with three or four replicas. RESULTS: ε-Co NPs in the size range ~4-10 nm with a narrow size distribution are obtained via the hot injection method, using OA as the sole surfactant. Typically the synthesis yield is ~75 %, and the particles form stable colloidal solutions when redispersed in hexane. Reproducibility of the adopted synthesis procedure on replicate syntheses was confirmed. We describe in detail the effects of essential synthesis parameters, such as injection-temperature and time, metal to surfactant ratio and reaction holding time in terms of their impact on mean ([Formula: see text]mean) and median ([Formula: see text]median) particle diameter. CONCLUSIONS: The described synthesis procedure towards ε-Co nanoparticles (NPs) is concluded to be robust when controlling key synthesis parameters, giving targeted particle diameters with a narrow size distribution. We have identified two major synthesis parameters which control particle size, i.e., the metal to surfactant molar ratio and the injection temperature of the hot OA-DCB solution into which the cobalt precursor is injected. By increasing the metal to surfactant molar ratio, the mean particle diameter of the ε-Co NPs has been found to increase. Furthermore, an increase in the injection temperature of the hot OA-DCB solution into which the cobalt precursor is injected, results in a decrease in the mean particle diameter of the ε-Co NPs, when the metal to surfactant molar ratio [Formula: see text] is fixed at ~12.9.

Probing the mechanism of allylic substitution of Morita-Baylis-Hillman acetates (MBHAs) by using the silyl phosphonite paradigm: scope and applications of a versatile transformation.

A P-C bond-forming reaction between silyl phosphonites and Morita-Baylis-Hillman acetates (MBHAs) is explored as a general alternative towards medicinally relevant ß-carboxyphosphinic structural motifs. Conversion rates of diversely substituted MBHAs to phosphinic acids 9 or 14 that were recorded by using (31) P NMR spectroscopy revealed unexpected reactivity differences between ester and nitrile derivatives. These kinetic profiles and DFT calculations support a mechanistic scenario in which observed differences can be explained from the "lateness" of transition states. In addition, we provide experimental evidence suggesting that enolates due to initial P-Michael addition are not formed. Based on the proposed mechanistic scenario in conjunction with DFT calculations, an interpretation of the E/Z stereoselectivity differences between ester and nitriles is proposed. Synthetic opportunities stemming from this transformation are presented, which deal with the preparation of several synthetically capricious phosphinic building blocks, whose access through the classical P-Michael synthetic route is not straightforward.

Electrical response from nanocomposite PDMS-Ag NPs generated by in situ laser ablation in solution.

Laser ablation technique is employed in order to generate polydimethylsiloxane (PDMS)/Ag NPs in situ, starting from a silver target in a solution of PDMS prepolymer and toluene. The produced surfactant-free nanoparticles are characterized by high resolution transmission electron microscopy (HRTEM) and scanning TEM-high angle annular dark field (STEM-HAADF) imaging modes, showing the majority of them to be of the order of 4 nm in diameter with a small percentage of larger Ag-AgCl multidomain NPs, embedded into a PDMS matrix. Low concentrations of carbon onion-like nanoparticles or larger fibers are also formed in the toluene-PDMS prepolymer solution. In accordance with this, UV-vis spectra shows no peak from silver NPs; their small size and their coverage by the PDMS matrix suppresses the signal of surface plasmon absorption. Inductively coupled plasma measurements reveal that the concentration of silver in the polymer is characteristically low, ~0.001% by weight. The electrical properties of the PDMS nanocomposite films are modified, with current versus voltage (I-V) measurements showing a low current of up to a few tenths of a pA at 5 V. The surface resistivity of the films is found to be up to ~10(10) Ω/sq. Under pressure (e.g. stress) applied by a dynamic mechanical analyzer (DMA), the I-V measurements demonstrate the current decreasing during the elastic deformation, and increasing during the plastic deformation.

Water-repellent cellulose fiber networks with multifunctional properties.

We demonstrate a simple but highly efficient technique to introduce multifunctional properties to cellulose fiber networks by wetting them with ethyl-cyanoacrylate monomer solutions containing various suspended organic submicrometer particles or inorganic nanoparticles. Solutions can be applied on cellulosic surfaces by simple solution casting techniques or by dip coating, both being suitable for large area applications. Immediately after solvent evaporation, ethyl-cyanoacrylate starts cross-linking around cellulose fibers under ambient conditions because of naturally occurring surface hydroxyl groups and adsorbed moisture, encapsulating them with a hydrophobic polymer shell. Furthermore, by dispersing various functional particles in the monomer solutions, hydrophobic ethyl-cyanoacrylate nanocomposites with desired functionalities can be formed around the cellulose fibers. To exhibit the versatility of the method, cellulose sheets were functionalized with different ethyl-cyanoacrylate nanocomposite shells comprising submicrometer wax or polytetrafluoroethylene particles for superhydophobicity, MnFe(2)O(4) nanoparticles for magnetic activity, CdSe/ZnS quantum dots for light emission, and silver nanoparticles for antimicrobial activity. Morphological and functional properties of each system have been studied by scanning and transmission electron microscopy, detailed contact angle measurements, light emission spectra and E. coli bacterial growth measurements. A plethora of potential applications can be envisioned for this technique, such as food and industrial packaging, document protection, catalytic cellulosic membranes, textronic (electrofunctional textiles), electromagnetic devices, authentication of valuable documents, and antimicrobial wound healing products to name a few.

Tuning of the characteristics of Au nanoparticles produced by solid target laser ablation into water by changing the irradiation parameters.

We report the production of Au nanoparticles with different average sizes and size distributions, by laser ablation of a solid Au target into pure deionized water. Tuning laser parameters such as pulse duration, energy, and wavelength is possible to tune the size and the size distributions of the produced nanoparticles into the liquid. We demonstrate the possibility of production of highly monodispersed colloidal solutions, in which the average nanoparticle size ranges from 3 to 10 nm, using laser pulses of ns duration. Laser ablation using fs laser pulses can also produce very small nanoparticles, although a small population of bigger nanoparticles is always present. Low and high-resolution transmission electron microscopy (TEM), in combination with UV-Vis spectroscopy have been employed for the characterization of our samples.