Synthesis of δ-MnO2 via ozonation routine for low temperature formaldehyde removal.

Nowadays, it is still a challenge to prepared high efficiency and low cost formaldehyde (HCHO) removal catalysts in order to tackle the long-living indoor air pollution. Herein, δ-MnO2 is successfully synthesized by a facile ozonation strategy, where Mn2+ is oxidized by ozone (O3) bubble in an alkaline solution. It presents one of the best catalytic properties with a low 100% conversion temperature of 85°C for 50 ppm of HCHO under a GHSV of 48,000 mL/(g·hr). As a comparison, more than 6 times far longer oxidation time is needed if O3 is replaced by O2. Characterizations show that ozonation process generates a different intermediate of tetragonal ß-HMnO2, which would favor the quick transformation into the final product δ-MnO2, as compared with the relatively more thermodynamically stable monoclinic γ-HMnO2 in the O2 process. Finally, HCHO is found to be decomposed into CO2 via formate, dioxymethylene and carbonate species as identified by room temperature in-situ diffuse reflectance infrared fourier transform spectroscopy. All these results show great potency of this facile ozonation routine for the highly active δ-MnO2 synthesis in order to remove the HCHO contamination.

The ATOM-Seq sequence capture panel can accurately predict microsatellite instability status in formalin-fixed tumour samples, alongside routine gene mutation testing.

Microsatellite instability (MSI) occurs across a number of cancers and is associated with different clinical characteristics when compared to microsatellite stable (MSS) cancers. As MSI cancers have different characteristics, routine MSI testing is now recommended for a number of cancer types including colorectal cancer (CRC). Using gene panels for sequencing of known cancer mutations is routinely performed to guide treatment decisions. By adding a number of MSI regions to a small gene panel, the efficacy of simultaneous MSI detection in a series of CRCs was tested. Tumour DNA from formalin-fixed, paraffin-embedded (FFPE) tumours was sequenced using a 23-gene panel kit (ATOM-Seq) provided by GeneFirst. The mismatch repair (MMR) status was obtained for each patient from their routine pathology reports, and compared to MSI predictions from the sequencing data. By testing 29 microsatellite regions in 335 samples the MSI status was correctly classified in 314/319 samples (98.4% concordance), with sixteen failures. By reducing the number of regions in silico, comparable performance could be reached with as few as eight MSI marker positions. This test represents a quick, and accurate means of determining MSI status in FFPE CRC samples, as part of a routine gene mutation assay, and can easily be incorporated into a research or diagnostic setting. This could replace separate mutation and MSI tests with no loss of accuracy, thus improving testing efficiency.

Aqueous extraction of formalin-fixed paraffin-embedded tissue and detection of prion disease using real-time quaking-induced conversion.

OBJECTIVE: The goal of the research presented here is to determine if methods previously developed for the aqueous extraction of PrPSc from formalin-fixed paraffin-embedded tissue (FFPET) are applicable to the detection PrPSc by real-time quaking induced conversion (RT-QuIC). Previous work has utilized aqueous extraction of FFPET for detection of transmissible spongiform encephalopathies (TSEs) utilizing western blot and ELISA. This research extends the range of suitable methods for detection of TSEs in FFPET to RT-QuIC, which is arguably the most sensitive method to detect TSEs. RESULTS: We found complete agreement between the TSE status and the results from RT-QuIC seeded with the aqueous extract of FFPET samples. The method affords the diagnostic assessment TSE status by RT-QuIC of FFPET without the use of organic solvents that would otherwise create a mixed chemical-biological waste for disposal.

Fluorescent probes for formaldehyde based on formaldehyde-promoted C-N cleavage of azanyl carbamates.

Formaldehyde (FA) is an endogenous one-carbon metabolite and an environmental pollutant and carcinogen. Elevated FA levels are associated with many diseases. Methods for the convenient and in situ detection of FA levels are of great significance for understanding FA's biofunctions and signalling pathways. Herein, the NAP-FAP2 series of fluorescent probes for FA detection were developed based on FA-promoted C-N cleavage of 3-nitrophenylazanyl N-arylcarbamate via FA-induced intramolecularity, where the aryl group is the fluorophore 1,8-naphthalimide-4-yl. The 3-nitrophenylazanyl containing reactive group also functions as a fluorescence quenching group via a photo-induced electron transfer mechanism to generate turn-on fluorescence response upon reaction with FA. The probes were applied to explore FA level changes in erastin-induced ferroptosis, and it was found that the FA level increases intracellularly, but not in the endoplasmic reticulum, suggesting that the FA level increases in ferroptosis are not derived from lipid peroxidation.

Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.

Formalin-fixed paraffin-embedded (FFPE) tissue represents a valuable source for translational cancer research. However, the widespread application of various downstream methods remains challenging. Here, we aimed to assess the feasibility of a genomic and gene expression analysis workflow using FFPE breast cancer (BC) tissue. We conducted a systematic literature review for the assessment of concordance between FFPE and fresh-frozen matched tissue samples derived from patients with BC for DNA and RNA downstream applications. The analytical performance of three different nucleic acid extraction kits on FFPE BC clinical samples was compared. We also applied a newly developed targeted DNA Next-Generation Sequencing (NGS) 370-gene panel and the nCounter BC360® platform on simultaneously extracted DNA and RNA, respectively, using FFPE tissue from a phase II clinical trial. Of the 3701 initial search results, 40 articles were included in the systematic review. High degree of concordance was observed in various downstream application platforms. Moreover, the performance of simultaneous DNA/RNA extraction kit was demonstrated with targeted DNA NGS and gene expression profiling. Exclusion of variants below 5% variant allele frequency was essential to overcome FFPE-induced artefacts. Targeted genomic analyses were feasible in simultaneously extracted DNA/RNA from FFPE material, providing insights for their implementation in clinical trials/cohorts.

Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics.

Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences the number, intensity, and reproducibility of identifications. By comparing four deparaffinization and rehydration methods, including heptane, histolene, SubX, and xylene, we found that heptane and methanol produced the lowest coefficients of variation (CVs). Using this, five extraction methods from the literature were modified and evaluated for their performance using kidney, leg muscle, lung, and testicular rat organs. All methods performed well, except for SP3 due to insufficient tissue lysis. Heat n' Beat was the fastest and most reproducible method with the highest digestion efficiency and lowest CVs. S-Trap produced the highest peptide yield, while TFE produced the best phosphopeptide enrichment efficiency. The quantitation of FFPE-derived peptides remains an ongoing challenge with bias in UV and fluorescence assays across methods, most notably in SPEED. Functional enrichment analysis demonstrated that each method favored extracting some gene ontology cellular components over others including chromosome, cytoplasmic, cytoskeleton, endoplasmic reticulum, membrane, mitochondrion, and nucleoplasm protein groups. The outcome is a set of recommendations for choosing the most appropriate method for different settings.

Unraveling the Disulfide-Carbonyl n → π* Interactions in a Gas Phase Molecular Complex and Proteins.

The weak contacts between disulfide linkages and carbonyl groups are anticipated to be important in determining the structure and function of enzymes and proteins. However, the characteristics of the disulfide-carbonyl n → π* (nSS → π* C═O) interactions remain unexplored. Herein, we investigated the nSS → π* C═O interactions in the gas phase and in proteins. Rotational spectroscopic investigation of a model complex of allyl methyl disulfide with formaldehyde identified two structures, both of which are stabilized through a dominant nSS → π* C═O interaction. Surveys of the Protein Data Bank revealed the occurrence of 18 675 nSS → π* C═O interactions associated with 15 320 disulfide bonds in 7105 protein structures. Further theoretical analyses characterize the bonding nature of the nSS → π* C═O interactions. This study provides an in-depth understanding of the stabilizing effect of the nSS → π* C═O interactions in small molecular complexes and biomacromolecules.

Efficient fabrication of cellulose polymer networks via alkaline swelling strategy for wood bonding.

Existing issues with bio-based adhesives, such as complex preparation processes, high energy consumption, and production costs, still need to be addressed. In our study, APTES was grafted onto microcrystalline cellulose (MCC) to generate active aminated cellulose, and then reacted with the epoxide group in glycerol triglycidyl ether (GTE) through a swelling strategy under alkaline solvent, forming a network structure via covalent cross-linking. The adhesive exhibits superior bonding performance and water-resistant property in the bonding strength test of poplar plywood, with a dry shear strength of 2.40 MPa, a wet shear strength of 2.16 MPa after soaking in 63 °C hot water, and a wet shear strength of 1.79 MPa after soaking in boiling water. In terms of cost calculation, the theoretical production cost of AC-GTE adhesive is calculated to be 5303.7 RMB per ton, which is comparable to that of phenol-formaldehyde (PF) resin and other petrochemical-based adhesives, and significantly lower than that of isocyanate-based adhesives. These research results can provide a practical example for producing high-efficiency, aldehyde-free, and low-cost bio-based adhesives.

Synergistically improve the strength and porosity of carbon paper by using a novel phenol formaldehyde resin modified with cellulose nanofiber for proton exchange membrane fuel cells.

To optimize the imbalance between the interfacial bonding and porosity properties of carbon paper (CP) caused by phenol formaldehyde resin (PF) impregnation, and therefore improve the performance of proton exchange membrane fuel cells (PEMFCs), a new approach through cellulose nanofibers grafted with methyl methacrylate (CNFM) as a modified reinforcement and pore-forming agent for PF is investigated. Through suppressing the methylene backbone fracture of CNFM-modified PF during its thermal depolymerization, the interfacial bonding between PF matrix carbon and carbon fibers is enhanced. Compared with unmodified CP, the in-plane resistivity of CNFM-modified CP is reduced by 35.78 %, while the connected porosity increases to 82.26 %, and more homogeneous pore size distribution (PSD) in the range of 20-40 µm is obtained for CNFM-modified CP. Besides, the tensile strength, flexural strength, and air permeability of CNFM-modified CP increase by 72.78 %, 298.4 %, and 103.97 %, respectively. In addition, CNFM-modified CP achieves the peak power density of PEMFCs to 701.81 mW·cm-2, exhibiting 10.98 % improvement compared with commercial CP (632.39 mW·cm-2), evidently achieving an integral promotion of CP and comprehensive performance.

Protocol for high-plex, whole-slide imaging of human formalin-fixed paraffin-embedded tissue using PhenoCycler-Fusion.

Single-cell spatial analysis of proteins is rapidly becoming increasingly important in revealing biological insights. Here, we present a protocol for automated high-plex multi-slide immunofluorescence staining and imaging of human head and neck cancer formalin-fixed paraffin-embedded (FFPE) sections using PhenoCycler-Fusion 2.0 technology. We describe steps for preparing human head and neck cancer FFPE tissues, staining with a panel of immunophenotyping markers, and Flow Cell assembly. We then detail procedures for setting up for a PhenoCycler-Fusion run, post-run Flow Cell removal, and downstream analyses. For complete details on the use and execution of this protocol, please refer to Jhaveri et al.1.

Protocol for assessing GD2 on formalin-fixed paraffin-embedded tissue sections using immunofluorescence staining.

The detection of disialoganglioside GD2 on tumor biopsies, especially in paraffin-embedded tissues, has been challenging due to the glycolipid structure of GD2 and its membrane anchorage. Here, we present an immunofluorescence protocol for the reliable assessment of GD2 on formalin-fixed paraffin-embedded (FFPE) tissues. We describe steps for antigen retrieval with Tris-EDTA buffer and staining with unconjugated anti-GD2 antibody (clone 14.G2a) and horse radish peroxidase (HRP)-conjugated secondary antibody. We then detail procedures for signal amplification using the tyramide signal amplification technique. For complete details on the use and execution of this protocol, please refer to Fischer-Riepe et al.1.

A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues.

Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the cross-linking and pre-analytical variables, these samples have utility for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients' medical histories. Proteomics of formalin-fixed paraffin-embedded (FFPE) tissues also integrates with histological evaluation and molecular pathology strategies, so that additional collection of research biopsies or resected tumor aliquots is not needed. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the protein extraction and proteomics sample preparation from FFPE samples can be onerous, particularly for small (i.e., limited or precious) samples. Therefore, we provide a protocol for a recently introduced kit-based EasyPep method with benchmarking against a modified version of the well-established filter-aided sample preparation strategy using laser-capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables while also supporting the development of methods for spatial proteomics to examine intratumoral heterogeneity. Data are posted in ProteomeXchange (PXD045879).

Enhancing Bioactivity through the Transfer of the 2-(Hydroxymethoxy)Vinyl Moiety: Application in the Modification of Tyrosol and Hinokitiol.

Utilizing Density Functional Theory (DFT) calculations at the B3LYP/QZVP level and incorporating the Conductor-like Polarizable Continuum Model (C-PCM) for solvation, the thermodynamic and chemical activity properties of 21-(hydroxymethoxy)henicosadecaenal, identified in cultured freshwater pearls from the mollusk Hyriopsis cumingii, have been elucidated. The study demonstrates that this compound releases formaldehyde, a potent antimicrobial agent, through dehydrogenation and deprotonation processes in both hydrophilic and lipophilic environments. Moreover, this polyenal exhibits strong anti-reductant properties, effectively scavenging free radicals. These critical properties classify the pearl-derived ingredient as a natural multi-functional compound, serving as a coloring, antiradical, and antimicrobial agent. The 2-(hydroxymethoxy)vinyl (HMV) moiety responsible for the formaldehyde release can be transferred to other compounds, thereby enhancing their biological activity. For instance, tyrosol (4-(2-hydroxyethyl)phenol) can be modified by substituting the less active 2-hydroxyethyl group with the active HMV one, and hinokitiol (4-isopropylotropolone) can be functionalized by attaching this moiety to the tropolone ring. A new type of meso-carrier, structurally modeled on pearls, with active substances loaded both in the layers and the mineral part, has been proposed.

Nanoscale intracellular ultrastructures affected by osmotic pressure using small-angle X-ray scattering.

Although intracellular ultrastructures have typically been studied using microscopic techniques, it is difficult to observe ultrastructures at the submicron scale of living cells due to spatial resolution (fluorescence microscopy) or high vacuum environment (electron microscopy). We investigate the nanometer scale intracellular ultrastructures of living CHO cells in various osmolality using small-angle X-ray scattering (SAXS), and especially the structures of ribosomes, DNA double helix, and plasma membranes in-cell environment are observed. Ribosomes expand and contract in response to osmotic pressure, and the inter-ribosomal correlation occurs under isotonic and hyperosmolality. The DNA double helix is not dependent on the osmotic pressure. Under high osmotic pressure, the plasma membrane folds into form a multilamellar structure with a periodic length of about 6 nm. We also study the ultrastructural changes caused by formaldehyde fixation, freezing and heating.

DropBlot: single-cell western blotting of chemically fixed cancer cells.

Archived patient-derived tissue specimens play a central role in understanding disease and developing therapies. To address specificity and sensitivity shortcomings of existing single-cell resolution proteoform analysis tools, we introduce a hybrid microfluidic platform (DropBlot) designed for proteoform analyses in chemically fixed single cells. DropBlot serially integrates droplet-based encapsulation and lysis of single fixed cells, with on-chip microwell-based antigen retrieval, with single-cell western blotting of target antigens. A water-in-oil droplet formulation withstands the harsh chemical (SDS, 6 M urea) and thermal conditions (98 °C, 1-2 hr) required for effective antigen retrieval, and supports analysis of retrieved protein targets by single-cell electrophoresis. We demonstrate protein-target retrieval from unfixed, paraformaldehyde-fixed (PFA), and methanol-fixed cells. Key protein targets (HER2, GAPDH, EpCAM, Vimentin) retrieved from PFA-fixed cells were resolved and immunoreactive. Relevant to biorepositories, DropBlot profiled targets retrieved from human-derived breast tumor specimens archived for six years, offering a workflow for single-cell protein-biomarker analysis of sparing biospecimens.

Robust Detection of Gene Amplification in Formalin-Fixed Paraffin-Embedded Samples by Fluorescence in situ Hybridization.

Focal gene amplification, such as extrachromosomal DNA (ecDNA), plays an important role in cancer development and therapy resistance. While sequencing-based methodologies enable an unbiased identification of ecDNA, cytogenetic-based techniques, such as fluorescence in situ hybridization (FISH), remain time and cost-effective for identifying ecDNA in clinical specimens. The application of FISH in formalin-fixed paraffin-embedded (FFPE) tissue samples offers a unique avenue for detecting amplified genes, particularly when viable specimens are not available for karyotype examination. However, there is a lack of consensus procedures for this technique. This protocol provides comprehensive, fully optimized, step-by-step instructions for conducting FISH to detect gene amplification, including ecDNA, in FFPE tissue samples which present unique challenges that this protocol aims to overcome and standardize. By following this protocol, researchers can reproducibly acquire high-quality imaging data to assess gene amplification.

A highly sensitive Golgi-targeted fluorescent probe for the simultaneous detection of malondialdehyde and formaldehyde in living systems and foods.

Malondialdehyde (MDA) and formaldehyde (FA) are highly active carbonyl substances widely present in both biological and abiotic systems. The detection of MDA and FA is of great significance for disease diagnosis and food safety monitoring. However, due to the similarity in structural properties between MDA and FA, very few probes for synergistically detecting MDA and FA were reported. In addition, functional abnormalities in the Golgi apparatus are closely related to MDA and FA, but currently there are no fluorescent probes that can detect MDA and FA in the Golgi apparatus. Therefore, we constructed a simple Golgi-targetable fluorescent probe GHA based on hydrazine moiety as the recognition site to produce a pyrazole structure after reaction with MDA and to generate a CN double bond after reaction with FA, allowing MDA and FA to be distinguished due to different emission wavelengths during the recognition process. The probe GHA has good specificity and sensitivity. Under the excitation of 350 nm, the blue fluorescence was significantly enhanced at 424 nm when the probe reacted with MDA, and the detection limit was 71 nM. At the same time, under the same excitation of 350 nm, the reaction with FA showed a significant enhancement of green fluorescence at 520 nm, with a detection limit of 12 nM for FA. And the simultaneous and high-resolution imaging of MDA and FA in the Golgi apparatus of cells was achieved. In addition, the applications of the probe GHA in food demonstrated it can provide a powerful method for food safety monitoring. In summary, this study offers a promising tool for the synergistic identification and determination of MDA and FA in the biosystem and food, facilitating the revelation of their detailed functions in Golgi apparatus and the monitoring of food safety.

A precise microdissection strategy enabled spatial heterogeneity analysis on the targeted region of formalin-fixed paraffin-embedded tissues.

In recent years, the development of spatial transcriptomic technologies has enabled us to gain an in-depth understanding of the spatial heterogeneity of gene expression in biological tissues. However, a simple and efficient tool is required to analyze multiple spatial targets, such as mRNAs, miRNAs, or genetic mutations, at high resolution in formalin-fixed paraffin-embedded (FFPE) tissue sections. In this study, we developed hydrogel pathological sectioning coupled with the previously reported Sampling Junior instrument (HPSJ) to assess the spatial heterogeneity of multiple targets in FFPE sections at a scale of 180 µm. The HPSJ platform was used to demonstrate the spatial heterogeneity of 9 ferroptosis-related genes (TFRC, NCOA4, FTH1, ACSL4, LPCAT3, ALOX12, SLC7A11, GLS2, and GPX4) and 2 miRNAs (miR-185-5p and miR522) in FFPE tissue samples from patients with triple-negative breast cancer (TNBC). The results validated the significant heterogeneity of ferroptosis-related mRNAs and miRNAs. In addition, HPSJ confirmed the spatial heterogeneity of the L858R mutation in 7 operation-sourced and 4 needle-biopsy-sourced FFPE samples from patients with lung adenocarcinoma (LUAD). The successful detection of clinical FFPE samples indicates that HPSJ is a precise, high-throughput, cost-effective, and universal platform for analyzing spatial heterogeneity, which is beneficial for elucidating the mechanisms underlying drug resistance and guiding the prescription of mutant-targeted drugs in patients with tumors.

Pd Nanoclusters-Sensitized MIL-125/TiO2 Nanochannel Arrays for Sensitive and Humidity-Resistant Formaldehyde Detection at Room Temperature.

Among the various hazardous substances, formaldehyde (HCHO), produced worldwide from wood furniture, dyeing auxiliaries, or as a preservative in consumer products, is harmful to human health. In this study, a sensitive room-temperature HCHO sensor, MTiNCs/Pd, has been developed by integrating Pd nanoclusters (PdNCs) into mesoporous MIL-125(Ti)-decorated TiO2 nanochannel arrays (TiNCs). Thanks to the enrichment effect of the mesoporous structure of MIL-125 and the large surface area offered by TiNCs, the resulting gas sensor accesses significantly enhanced HCHO adsorption capacity. The sufficient energetic active defects formed on PdNCs further allow an electron-extracting effect, thus effectively separating the photogenerated electrons and holes at the interface. The resulting HCHO sensor exhibits a short response/recovery time (37 s/12 s) and excellent sensitivity with a low limit of detection (4.51 ppb) under ultraviolet (UV) irradiation. More importantly, the cyclic redox reactions of Pdδ+ in PdNCs facilitated the regeneration of O2-(ads), thus ensuring a stable and excellent gas sensing performance even under a high-humidity environment. As a proof-of-principle of this design, a wearable gas sensing band is developed for the real-time and on-site detection of HCHO in cigarette smoke, with the potential as an independent device for environmental monitoring and other smart sensing systems.

Dynamically crosslinked chiral optics sensing for ultra-sensitive VOCs detection.

Chiroptical sensing with real-time colorimetrical detection has been emerged as quantifiable properties, enantioselective responsiveness, and optical manipulation in environmental monitoring, food safety and other trace identification fields. However, the sensitivity of chiroptical sensing materials remains an immense challenge. Here, we report a dynamically crosslinking strategy to facilitate highly sensitive chiroptical sensing material. Chiral nematic cellulose nanocrystals (CNC) were co-assembled with amino acid by a two-step esterification, of which a precisely tunable helical pitch, a unique spiral conformation with hierarchical and numerous active sites in sensing performance could be trigged by dynamic covalent bond on amines. Such a CNC/amino acid chiral optics features an ultra-trace amount of 0.08 mg/m3 and a high sensitivity of 60 nm/(mg/m3) for formaldehyde gas at a molecule level detection, which is due to the three synergistic adsorption enhancement of dynamic covalent bonded interaction, hydrogen bonded interaction and van der Waals interaction. Meanwhile, an enhancement hierarchical adsorption of CNC/amino acid chiral materials can be readily representative to the precise helical pitch and colorimetrical switch for sensitive visualization reorganization.