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Formalin, an aqueous solution of formaldehyde, has been the gold standard for fixation of histological samples for over a century. Despite its considerable advantages, growing evidence points to objective toxicity, particularly highlighting its carcinogenicity and mutagenic effects. In 2016, the European Union proposed a ban, but a temporary permission was granted in consideration of its fundamental role in the medical-diagnostic field. In the present study, we tested an innovative fixative, glyoxal acid-free (GAF) (a glyoxal solution deprived of acids), which allows optimal tissue fixation at structural and molecular level combined with the absence of toxicity and carcinogenic activity. An open-label, non-inferiority, multicentric trial was performed comparing fixation of histological specimens with GAF fixative vs standard phosphate-buffered formalin (PBF), evaluating the morphological preservation and the diagnostic value with four binary score questions answered by both the central pathology reviewer and local center reviewers. The mean of total score in the GAF vs PBF fixative groups was 3.7 ± 0.5 vs 3.9 ± 0.3 for the central reviewer and 3.8 ± 0.5 vs 4.0 ± 0.1 for the local pathologist reviewers, respectively. In terms of median value, similar results were observed between the two fixative groups, with a median value of 4.0. Data collected indicate the non-inferiority of GAF as compared to PBF for all organs tested. The present clinical performance study, performed following the international standard for performance evaluation of in vitro diagnostic medical devices, highlights the capability of GAF to ensure both structural preservation and diagnostic value of the preparations.

Plywood is widely used in construction, such as for flooring and interior walls, as well as in the manufacture of household items such as furniture and cabinets. Such items are made of wood veneers that are bonded together with adhesives such as urea–formaldehyde and phenol–formaldehyde resins 1 , 2 . Researchers in academia and industry have long aimed to synthesize lignin–phenol–formaldehyde resin adhesives using biomass-derived lignin, a phenolic polymer that can be used to substitute the petroleum-derived phenol 3 , 4 , 5 – 6 . However, lignin–phenol–formaldehyde resin adhesives are less attractive to plywood manufacturers than urea–formaldehyde and phenol–formaldehyde resins owing to their appearance and cost. Here we report a simple and practical strategy for preparing lignin-based wood adhesives from lignocellulosic biomass. Our strategy involves separation of uncondensed or slightly condensed lignins from biomass followed by direct application of a suspension of the lignin and water as an adhesive on wood veneers. Plywood products with superior performances could be prepared with such lignin adhesives at a wide range of hot-pressing temperatures, enabling the use of these adhesives as promising alternatives to traditional wood adhesives in different market segments. Mechanistic studies indicate that the adhesion mechanism of such lignin adhesives may involve softening of lignin by water, filling of vessels with softened lignin and crosslinking of lignins in adhesives with those in the cell wall. A straightforward strategy for preparing lignin-based wood adhesives from lignocellulosic biomass is described, with the resulting adhesives demonstrating performance attractive for plywood manufacture.

Practical, high-yield lignin depolymerization methods could greatly increase biorefinery productivity and profitability. However, development of these methods is limited by the presence of interunit carbon-carbon bonds within native lignin, and further by formation of such linkages during lignin extraction. We report that adding formaldehyde during biomass pretreatment produces a soluble lignin fraction that can be converted to guaiacyl and syringyl monomers at near theoretical yields during subsequent hydrogenolysis (47 mole % of Klason lignin for beech and 78 mole % for a high-syringyl transgenic poplar). These yields were three to seven times those obtained without formaldehyde, which prevented lignin condensation by forming 1,3-dioxane structures with lignin side-chain hydroxyl groups. By depolymerizing cellulose, hemicelluloses, and lignin separately, monomer yields were between 76 and 90 mole % for these three major biomass fractions.

Cancer pharmacogenetic studies use archival tumor samples as a DNA source when germline DNA is unavailable. Genotyping DNA from formalin-fixed paraffin embedded tumors (FFPE-T) may be inaccurate due to FFPE storage, genetic aberrations, and/or insufficient DNA extraction. Our objective was to assess the extent and source of genotyping inaccuracy from FFPE-T DNA and demonstrate analytical validity of FFPE-T genotyping of candidate single nucleotide polymorphisms (SNPs) for pharmacogenetic analyses. Cancer pharmacogenetics SNPs were genotyped by Sequenom MassARRAYs in DNA harvested from matched FFPE-T, FFPE lymph node (FFPE-LN), and whole blood leukocyte samples obtained from breast cancer patients. No- and discordant-call rates were calculated for each tissue type and SNP. Analytical validity was defined as any SNP with <5% discordance between FFPE-T and blood and <10% discordance plus no-calls. Matched samples from 114 patients were genotyped for 247 SNPs. No-call rate in FFPE-T was greater than FFPE-LN and blood (4.3% vs. 3.0% vs. 0.5%, p < 0.001). Discordant-call rate between FFPE-T and blood was very low, but greater than that between FFPE-LN and blood (1.1% vs. 0.3%, p < 0.001). Samples with heterozygous genotypes were more likely to be no- or discordantly-called in either tissue (p < 0.001). Analytical validity of FFPE-T genotyping was demonstrated for 218 (88%) SNPs. No- and discordant-call rates were below concerning thresholds, confirming that most SNPs can be accurately genotyped from FFPE-T on our Sequenom platform. FFPE-T is a viable DNA source for prospective–retrospective pharmacogenetic analyses of clinical trial cohorts. •Genotyping DNA from FFPE-T specimens is highly concordant (≈99%) with genotyping germline DNA.•The small loss of genotyping performance is attributable to inadequate DNA yield, not genetic rearrangement.•Analytic validity of genotyping from FFPE-T on our Sequenom array was documented for 218 cancer pharmacogenetics SNPs.•FFPE-T DNA is a viable alternative for prospective–retrospective pharmacogenetic analyses of clinical trials.

The folate-driven one-carbon (1C) cycle is a fundamental metabolic hub in cells that enables the synthesis of nucleotides and amino acids and epigenetic modifications. This cycle might also release formaldehyde, a potent protein and DNA crosslinking agent that organisms produce in substantial quantities. Here we show that supplementation with tetrahydrofolate, the essential cofactor of this cycle, and other oxidation-prone folate derivatives kills human, mouse and chicken cells that cannot detoxify formaldehyde or that lack DNA crosslink repair. Notably, formaldehyde is generated from oxidative decomposition of the folate backbone. Furthermore, we find that formaldehyde detoxification in human cells generates formate, and thereby promotes nucleotide synthesis. This supply of 1C units is sufficient to sustain the growth of cells that are unable to use serine, which is the predominant source of 1C units. These findings identify an unexpected source of formaldehyde and, more generally, indicate that the detoxification of this ubiquitous endogenous genotoxin creates a benign 1C unit that can sustain essential metabolism. The mechanism by which formaldehyde, a potent DNA and protein crosslinking agent, is generated from folate is described, with implications for the treatment of certain cancers. Formaldehyde detoxification fuels one-carbon metabolism Folate is an essential cofactor in one-carbon (1C) metabolism, a group of biochemical cycles involved in nucleotide and amino acid synthesis. Ketan Patel and co-workers elucidate the route by which folate derivatives produce intracellular formaldehyde in vivo . Formaldehyde causes DNA and protein crosslinking and is toxic to cells lacking protection against this compound. Endogenous formaldehyde detoxification by the alcohol dehydrogenase ADH5 generates formate, a benign 1C unit, driving nucleotide synthesis. By this route, formaldehyde provides a source of 1C units that can sustain essential metabolism and cell growth in the absence of the amino acid serine. This work shows how formaldehyde fits into key metabolic pathways and provides clues as to how some features of these cycles could be used to target certain cancer cells.

Isoprene is the dominant non-methane organic compound emitted to the atmosphere 1 – 3 . It drives ozone and aerosol production, modulates atmospheric oxidation and interacts with the global nitrogen cycle 4 – 8 . Isoprene emissions are highly uncertain 1 , 9 , as is the nonlinear chemistry coupling isoprene and the hydroxyl radical, OH—its primary sink 10 – 13 . Here we present global isoprene measurements taken from space using the Cross-track Infrared Sounder. Together with observations of formaldehyde, an isoprene oxidation product, these measurements provide constraints on isoprene emissions and atmospheric oxidation. We find that the isoprene–formaldehyde relationships measured from space are broadly consistent with the current understanding of isoprene–OH chemistry, with no indication of missing OH recycling at low nitrogen oxide concentrations. We analyse these datasets over four global isoprene hotspots in relation to model predictions, and present a quantification of isoprene emissions based directly on satellite measurements of isoprene itself. A major discrepancy emerges over Amazonia, where current underestimates of natural nitrogen oxide emissions bias modelled OH and hence isoprene. Over southern Africa, we find that a prominent isoprene hotspot is missing from bottom-up predictions. A multi-year analysis sheds light on interannual isoprene variability, and suggests the influence of the El Niño/Southern Oscillation. Direct satellite measurements of atmospheric isoprene are compared with model predictions, showing broad agreement but highlighting spatial and temporal biases in modelled isoprene and nitrogen oxide emissions.

Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein–protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful. Here we report mass spectrometry data that reveal formaldehyde cross-links to be the dimerization product of two formaldehyde-induced amino acid modifications. By integrating the revised mechanism into a customized search algorithm, we identify hundreds of cross-links from in situ formaldehyde fixation of human cells. Interestingly, many of the cross-links could not be mapped onto known atomic structures, and thus provide new structural insights. These findings enhance the use of formaldehyde cross-linking and mass spectrometry for structural studies. Formaldehyde (FA) is a popular cross-linking reagent, but applying it for cross-linking mass spectrometry (XLMS) has been largely unsuccessful. Here, the authors show that cross-links in structured proteins are the product of two FA molecules and identify hundreds of FA cross-links by XLMS in vitro and in situ.

Noncoding RNA sequences, including long noncoding RNAs, small nucleolar RNAs, and untranslated mRNA regions, accomplish many of their diverse functions through direct interactions with RNA-binding proteins (RBPs). Recent efforts have identified hundreds of new RBPs that lack known RNA-binding domains, thus underscoring the complexity and diversity of RNA–protein complexes. Recent progress has expanded the number of methods for studying RNA–protein interactions in two general categories: approaches that characterize proteins bound to an RNA of interest (RNA-centric), and those that examine RNAs bound to a protein of interest (protein-centric). Each method has unique strengths and limitations, which makes it important to select optimal approaches for the biological question being addressed. Here we review methods for the study of RNA–protein interactions, with a focus on their suitability for specific applications.This Review discusses the strengths and limitations of methods to probe RNA–protein interactions.

We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more efficiently and with less backward flux than any naturally occurring one-carbon assimilation pathway. When supplemented with enzymes carrying out the other steps in the pathway, FLS converts formate into dihydroxyacetone phosphate and other central metabolites in vitro. These results demonstrate how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway. Significance This paper describes the development of a computationally designed enzyme that is the cornerstone of a novel metabolic pathway. This enzyme, formolase, performs a carboligation reaction, directly fixing one-carbon units into three-carbon units that feed into central metabolism. By combining formolase with several naturally occurring enzymes, we created a new carbon fixation pathway, the formolase pathway, which assimilates one-carbon units via formate. Unlike native carbon fixation pathways, this pathway is linear, not oxygen sensitive, and consists of a small number of thermodynamically favorable steps. We demonstrate in vitro pathway function as a proof of principle of how protein design in a pathway context can lead to new efficient metabolic pathways.

Electronic (e-)cigarettes have emerged in recent years as putative alternative to conventional tobacco cigarettes. These products do not contain typical carcinogens that are present in tobacco smoke, due to the lack of combustion. However, besides nicotine, hazards can also arise from other constituents of liquids, such as solvents, flavors, additives and contaminants. In this study, we have analyzed 28 liquids of seven manufacturers purchased in Germany. We confirm the presence of a wide range of flavors to enhance palatability. Although glycerol and propylene glycol were detected in all samples, these solvents had been replaced by ethylene glycol as dominant compound in five products. Ethylene glycol is associated with markedly enhanced toxicological hazards when compared to conventionally used glycerol and propylene glycol. Additional additives, such as coumarin and acetamide, that raise concerns for human health were detected in certain samples. Ten out of 28 products had been declared “free-of-nicotine” by the manufacturer. Among these ten, seven liquids were identified containing nicotine in the range of 0.1–15 µg/ml. This suggests that “carry over” of ingredients may occur during the production of cartridges. We have further analyzed the formation of carbonylic compounds in one widely distributed nicotine-free brand. Significant amounts of formaldehyde, acetaldehyde and propionaldehyde were only found at 150 °C by headspace GC–MS analysis. In addition, an enhanced formation of aldehydes was found in defined puff fractions, using an adopted machine smoking protocol. However, this effect was delayed and only observed during the last third of the smoking procedure. In the emissions of these fractions, which represent up to 40 % of total vapor volume, similar levels of formaldehyde were detected when compared to conventional tobacco cigarettes. By contrast, carbonylic compounds were hardly detectable in earlier collected fractions. Our data demonstrate the necessity of standardized machine smoking protocols to reliably address putative risks of e-cigarettes for consumers.