A Hitchhiker's guide to high-dimensional tissue imaging with multiplexed ion beam imaging.

Advancements in multiplexed tissue imaging technologies are vital in shaping our understanding of tissue microenvironmental influences in disease contexts. These technologies now allow us to relate the phenotype of individual cells to their higher-order roles in tissue organization and function. Multiplexed Ion Beam Imaging (MIBI) is one of such technologies, which uses metal isotope-labeled antibodies and secondary ion mass spectrometry (SIMS) to image more than 40 protein markers simultaneously within a single tissue section. Here, we describe an optimized MIBI workflow for high-plex analysis of Formalin-Fixed Paraffin-Embedded (FFPE) tissues following antigen retrieval, metal isotope-conjugated antibody staining, imaging using the MIBI instrument, and subsequent data processing and analysis. While this workflow is focused on imaging human FFPE samples using the MIBI, this workflow can be easily extended to model systems, biological questions, and multiplexed imaging modalities.

Evaluation of DNAmAge in paired fresh, frozen, and formalin-fixed paraffin-embedded heart tissues.

The continued development in methylome analysis has enabled a more precise assessment of DNA methylation, but treatment of target tissue prior to analysis may affect DNA analysis. Prediction of age based on methylation levels in the genome (DNAmAge) has gained much interest in disease predisposition (biological age estimation), but also in chronological donor age estimation in crime case samples. Various epigenetic clocks were designed to predict the age. However, it remains unknown how the storage of the tissues affects the DNAmAge estimation. In this study, we investigated the storage method impact of DNAmAge by the comparing the DNAmAge of the two commonly used storage methods, freezing and formalin-fixation and paraffin-embedding (FFPE) to DNAmAge of fresh tissue. This was carried out by comparing paired heart tissue samples of fresh tissue, samples stored by freezing and FFPE to chronological age and whole blood samples from the same individuals. Illumina EPIC beadchip array was used for methylation analysis and the DNAmAge was evaluated with the following epigenetic clocks: Horvath, Hannum, Levine, Horvath skin+blood clock (Horvath2), PedBE, Wu, BLUP, EN, and TL. We observed differences in DNAmAge among the storage conditions. FFPE samples showed a lower DNAmAge compared to that of frozen and fresh samples. Additionally, the DNAmAge of the heart tissue was lower than that of the whole blood and the chronological age. This highlights caution when evaluating DNAmAge for FFPE samples as the results were underestimated compared with fresh and frozen tissue samples. Furthermore, the study also emphasizes the need for a DNAmAge model based on heart tissue samples for an accurate age estimation.

Machine-Learning-Assisted Descriptors Identification for Indoor Formaldehyde Oxidation Catalysts.

The development of highly efficient catalysts for formaldehyde (HCHO) oxidation is of significant interest for the improvement of indoor air quality. Up to 400 works relating to the catalytic oxidation of HCHO have been published to date; however, their analysis for collective inference through conventional literature search is still a challenging task. A machine learning (ML) framework was presented to predict catalyst performance from experimental descriptors based on an HCHO oxidation catalysts database. MnOx, CeO2, Co3O4, TiO2, FeOx, ZrO2, Al2O3, SiO2, and carbon-based catalysts with different promoters were compiled from the literature. Notably, 20 descriptors including reaction catalyst composition, reaction conditions, and catalyst physical properties were collected for data mining (2263 data points). Furthermore, the eXtreme Gradient Boosting algorithm was employed, which successfully predicted the conversion efficiency of HCHO with an R-square value of 0.81. Shapley additive analysis suggested Pt/MnO2 and Ag/Ce-Co3O4 exhibited excellent catalytic performance of HCHO oxidation based on the analysis of the entire database. Validated by experimental tests and theoretical simulations, the key descriptor identified by ML, i.e., the first promoter, was further described as metal-support interactions. This study highlights ML as a useful tool for database establishment and the catalyst rational design strategy based on the importance of analysis between experimental descriptors and the performance of complex catalytic systems.

Solution and gaseous phase sensing of formaldehyde with economical triphenylmethane based sensors: a tool to estimate formaldehyde content in stored fish samples.

The use of formalin to preserve raw food items such as fish, meat, vegetables etc. is very commonly practiced in the present day. Also, formaldehyde (FA), which is the main constituent of formalin solution, is known to cause serious health issues on exposure. Considering the ill effects of formaldehyde, herein we report synthesis of highly sensitive triphenylmethane based formaldehyde (FA) sensors from a single step reaction of inexpensive reagents namely 4-hydroxy benzaldehyde and 2,6-dimethyl phenol. The synthetic method also provides highly pure product in bulk quantity. The analytical activity of the triphenylmethane sensor 1 with a limit of detection (LOD) value of 2.31 × 10-6 M for FA was significantly enhanced through induced deprotonation and thereafter a LOD value of 1.82 × 10-8 M could be achieved. To the best of our knowledge, the LOD value of the deprotonated form (sensor 2) for FA was superior to those of all the FA optical sensors reported so far. The mechanism of sensing was demonstrated by 1H-NMR titration and recording mass spectra before and after addition of FA to a solution of sensor 2. Both sensor 1 and sensor 2 exhibit quenching in emission upon addition of FA. A fluorescence study also demonstrates enhancement in analytical activity of the sensor upon induced deprotonation. Then the sensor was effectively immobilized into a hydrophilic and biocompatible starch-PVA polymer matrix which enabled detection of FA in a 100% aqueous system reversibly. Again, quick and effective sensing of FA in real food samples (stored fish) with the help of a computational application was demonstrated. The sensors have significant practical applicability as they effectively detect FA in real food samples qualitatively and quantitatively.

A facile cellulose finishing strategy through in-situ growth of sliver-doped manganese dioxide assisted by amine-quinone for improving indoor living quality.

Nowadays, various harmful indoor pollutants especially including bacteria and residual formaldehyde (HCHO) seriously threaten human health and reduce the quality of public life. Herein, a universal substrate-independence finishing approach for efficiently solving these hybrid indoor threats is demonstrated, in which amine-quinone network (AQN) was employed as reduction agent to guide in-situ growth of Ag@MnO2 particles, and also acted as an adhesion interlayer to firmly anchor nanoparticles onto diverse textiles, especially for cotton fabrics. In contrast with traditional hydrothermal or calcine methods, the highly reactive AQN ensures the efficient generation of functional nanoparticles under mild conditions without any additional catalysts. During the AQN-guided reduction, the doping of Ag atoms onto cellulose fiber surface optimized the crystallinity and oxygen vacancy of MnO2, providing cotton efficient antibacterial efficiency over 90 % after 30 min of contact, companying with encouraging UV-shielding and indoor HCHO purification properties. Besides, even after 30 cycles of standard washing, the Ag@MnO2-decorated textiles can effectively degrade HCHO while well-maintaining their inherent properties. In summary, the presented AQN-mediated strategy of efficiently guiding the deposition of functional particles on fibers has broad application prospects in the green and sustainable functionalization of textiles.

Cu-doped Fe3O4 nanoparticles for efficient detoxification of epsilon toxin: Toward substituting magnetically recyclable detoxifying agent for formaldehyde.

This research presents the synthesis and characterization of Cu-doped Fe3O4 (Cu-Fe3O4) nanoparticles as a magnetically recoverable and reusable detoxifying agent for the efficient and long-lasting neutralization of bacterial toxins. The nanoparticles were synthesized using the combustion synthesis method and characterized through SEM, XRD, BET, TGA, and VSM techniques. The detoxification potential of Cu-Fe3O4 was compared with traditional formaldehyde (FA) in detoxifying epsilon toxin (ETx) from Clostridium perfringens Type D, the causative agent of enterotoxemia in ruminants. In vivo residual toxicity tests revealed that Cu-Fe3O4 could detoxify ETx at a concentration of 2.0 mg mL-1 within 4 days at room temperature (RT) and 2 days at 37 °C, outperforming FA (12 and 6 days at RT and 37 °C, respectively). Characterization studies using dynamic light scattering (DLS) and circular dichroism (CD) highlighted lower conformational changes in Cu-Fe3O4-detoxified ETx compared to FA-detoxified ETx. Moreover, Cu-Fe3O4-detoxified ETx exhibited exceptional storage stability at 4 °C and RT for 6 months, maintaining an irreversible structure with no residual toxicity. The particles demonstrated remarkable reusability, with the ability to undergo five continuous detoxification batches. This study provides valuable insights into the development of an efficient and safe detoxifying agent, enabling the production of toxoids with a native-like structure. The magnetically recoverable and reusable nature of Cu-Fe3O4 nanoparticles offers practical advantages for easy recovery and reuse in detoxification reactions.

Density functional theory-based screening of Ti4C3O2-loaded single atoms for efficient selective catalytic oxidation of formaldehyde.

Indoor formaldehyde (HCHO) pollution poses a major risk to human health. Low-temperature catalytic oxidation is an effective method for HCHO removal. The high activity and selectivity of single atomic catalysts provide a possibility for the development of efficient non-precious metal catalysts. In this study, the most stable single-atom catalyst Ti-Ti4C3O2 was screened by density functional theory among many single atomic catalysts with two-dimensional (2D) monolayer Ti4C3O2 as the support. The computational results show that Ti-Ti4C3O2 is highly selective to HCHO and O2 in complex environments. The HCHO oxidation reaction pathways are proposed based on the Eley-Rideal (E-R) and Langmuir-Hinshelwood (L-H) mechanisms. According to the reaction energy and energy span models, the E-R mechanism has a lower maximum energy barrier and higher catalytic efficiency than the L-H mechanism. In addition, the stability of the Ti-Ti4C3O2 structure and active center was verified by diffusion energy barrier and ab initio molecular dynamics simulations. The above results indicate that Ti-Ti4C3O2 is a promising non-precious metal catalyst. The present study provides detailed theoretical insights into the catalytic oxidation of HCHO by Ti-Ti4C3O2, as well as an idea for the development of efficient non-precious metal catalysts based on 2D materials.

Photocatalytic oxidation of formaldehyde under visible light using BiVO4-TiO2 synthesized via ultrasonic blending.

Formaldehyde (HCHO) is one of the primary indoor air pollutants, and efficiently eliminating it, especially at low concentrations, remains challenging. In this study, BiVO4-TiO2 catalyst was developed using ultrasonic blending technology for the photocatalytic oxidation of low-level indoor HCHO. The crystal structure, surface morphology, element distribution, and active oxidation species of the catalyst were examined using XRD, SEM, TEM, UV-Vis, EDS, and ESR techniques. Our results demonstrated that the BiVO4-TiO2 catalyst, prepared by ultrasonic blending, exhibited good oxidation performance and stability. The HCHO concentration reduced from 1.050 to 0.030 mg/m3 within 48 h, achieving a removal rate of 97.1%. The synergy between BiVO4 and TiO2 enhanced the efficiency of separating photogenerated carriers and minimized the likelihood of recombination between photogenerated electrons and holes. Additionally, this synergy significantly enhanced the presence of hydroxyl radicals (·OH) on the catalyst, resulting in an oxidation performance superior to that of either BiVO4 or TiO2. Our research offers valuable insights for the development of new photocatalysts to address HCHO pollution.

Theoretical investigation of the carbonyl-ene reaction between encapsulated formaldehyde and propylene over M-Cu-BTC paddlewheels (M= Be, Mg, and Ca): A DFT study.

Formaldehyde is a VOC gas that plays a key role in air pollution. To limit emissions into the environment, the utilization of this waste as a raw material is a promising way. In this work, the M06-L functional calculation was used to investigate the structure, electronic properties, and catalytic activity of group IIA metals (Be, Mg, and Ca) partial substitution on Cu-BTC paddlewheels for formaldehyde encapsulation and carbonyl-ene reaction with propylene. Formaldehyde is absorbed by the metal center of the paddlewheel via its oxygen atom. The adsorption of formaldehyde on the substituted metal sites increased as compared to the parent Cu-BTC which can facilitate formaldehyde to react with propylene. The adsorption free energies are predicted to be -15.1 (Be-Cu-BTC), -14.7 (Mg-Cu-BTC), and -14.5 (Ca-Cu-BTC) kcal mol-1, respectively. The substituted metal has a slight effect on the Lewis acidity of the Cu ion in the paddlewheel. The adsorption free energy of formaldehyde, similar to that found in the pristine Cu-BTC, is observed. For the carbonyl-ene reaction, the reaction is proposed via a single step involving the C-C bond formation between two reactants and one hydrogen of propylene methyl group moves to formaldehyde oxygen, simultaneously. It was found that the substituted metals do not affect the catalytic performance of the Cu center for this reaction. The activation energies for the reaction at the Cu center are in the range of 22.0-23.4 kcal mol-1, which are slightly different from Cu-BTC (21.5 kcal mol-1). Interestingly, the catalytic activity of this reaction on the substituted metal is greater than that on the Cu center. The catalytic activities are in the order Be-Cu-BTC (13.3 kcal mol-1) > Mg-Cu-BTC (15.9 kcal mol-1) > Ca-Cu-BTC (17.8 kcal mol-1). Among them, the Be site of the bimetallic Be-Cu-BTC paddlewheel is predicted as a promising candidate catalyst.

Heat 'n Beat: A Universal High-Throughput End-to-End Proteomics Sample Processing Platform in under an Hour.

Proteomic analysis by mass spectrometry of small (≤2 mg) solid tissue samples from diverse formats requires high throughput and comprehensive proteome coverage. We developed a nearly universal, rapid, and robust protocol for sample preparation, suitable for high-throughput projects that encompass most cell or tissue types. This end-to-end workflow extends from original sample to loading the mass spectrometer and is centered on a one-tube homogenization and digestion method called Heat 'n Beat (HnB). It is applicable to most tissues, regardless of how they were fixed or embedded. Sample preparation was divided into separate challenges. The initial sample washing and final peptide cleanup steps were adapted to three tissue sources: fresh frozen (FF), optimal cutting temperature (OCT) compound embedded (FF-OCT), and formalin-fixed paraffin embedded (FFPE). Third, for core processing, tissue disruption and lysis were decreased to a 7 min heat and homogenization treatment, and reduction, alkylation, and proteolysis were optimized into a single step. The refinements produced near doubled peptide yield when compared to our earlier method ABLE delivered a consistently high digestion efficiency of 85-90%, reported by ProteinPilot, and required only 38 min for core processing in a single tube, with the total processing time being 53-63 min. The robustness of HnB was demonstrated on six organ types, a cell line, and a cancer biopsy. Its suitability for high-throughput applications was demonstrated on a set of 1171 FF-OCT human cancer biopsies, which were processed for end-to-end completion in 92 h, producing highly consistent peptide yield and quality for over 3513 MS runs.

Co-adsorption enhancement of formaldehyde/carbon dioxide over modified hexagonal boron nitride for whole-surface capture purification.

Simultaneous capture of formaldehyde (HCHO) and carbon dioxide (CO2) in indoor air is promising of achieving indoor-air purification. Of all potential adsorbents, hexagonal boron nitride (h-BN) is one of the most suitable species owing to facile formation of attraction points. Therefore, in this study, performances of HCHO and CO2 being adsorbed over pure/modified h-BN are systematically investigated via density functional theory (DFT) calculations. Minutely speaking, direct interaction between HCHO and CO2, single-point adsorption enhancement of HCHO over modified h-BN, co-adsorption reinforcement of HCHO/CO2 as well as relevant thermodynamic characteristics are major research contents. According to calculation results, there is relatively strong attraction between HCHO and CO2 owing to hydrogen bonds, which is in favor of co-adsorption of HCHO/CO2. As to single-adsorption of HCHO, C-doped h-BN shows better adsorption features than P-doped h-BN and C/P-doped h-BN is slightly weakened in adsorption ability due to surficial deformation caused by P atoms. For co-adsorption of HCHO/CO2, CO2 is the protagonist via formation of quasi-carbonate with the help of delocalized π-orbital electrons. Regarding effects of temperatures on adsorption strengths, they depend on interelectronic interactions among dopant atoms and finally derives from dispersion of π bonds across adsorbents. Overall, this study provides detailed mechanisms for co-capture of HCHO/CO2 to accomplish indoor-air purification.

Synthesis and characterization of a bio-aldehyde-based lignin adhesive with desirable water resistance.

Wood-based panels find widespread application in the furniture and construction industries. However, over 90 % of adhesives used are synthesized with formaldehyde, leading to formaldehyde emission and associated health risks. In this study, an entirely bio-based adhesive (OSL) was innovatively proposed through the condensation of multi-aldehyde derived from the oxidization of sucrose (OS) with sodium lignosulfonate (L). This approach positioned oxidized sucrose (OS) as a viable substitute for formaldehyde, ensuring safety, simplicity, and enhance water resistance upon reaction with L. The optimization of the OSL adhesive preparation process involved determining the oxidant level for high sucrose conversion to aldehyde (13 % based on sucrose), the mass ratio of OS to L (0.8), and hot-pressing temperature (200 °C). Notably, the shear strength of 3-plywood bonded with the developed adhesive (1.04 MPa) increased to 1.42 MPa after being immersed in hot water at 63 ±â€¯3 °C for 3 h. Additionally, the plywood specimens exhibited excellent performance after soaking in boiling water for 3 h, resulting in a shear strength of 1.03 MPa. Chemical analysis using Fourier-transform infrared spectroscopy (FTIR), 1H nuclear magnetic resonance (NMR), and X-ray photoelectron spectroscopy (XPS) confirmed an addition reaction between L and OS, forming a dense network structure, effectively enhanceing the water resistance of OSL adhesives. Furthermore, compared with lignin-formaldehyde resin adhesive (LF), the OSL adhesive exhibited superior wet shear strength. This study offered an innovative approach for developing lignin-based adhesives utilizing a biomass aldehyde (OS), as a promising substitute for formaldehyde in the wood industry. The findings indicated that this approach may advance lignin-based adhesives, ensuring resistance to strength deterioration under highly humid environmental conditions.

Effect of Lignin Structure Characteristics on the Performance of Lignin Based Phenol Formaldehyde Adhesives.

As the second most abundant biopolymer, lignin remains underutilized in various industrial applications. Various forms of lignin generated from different methods affect its physical and chemical properties to a certain extent. To promote the broader commercial utilization of currently available industrial lignins, lignin sulfonate (SL), kraft lignin (KL), and organosolv lignin (OL) are utilized to partially replace phenol in the synthesis of phenol formaldehyde (PF) adhesives. The impact of lignin production process on the effectiveness of lignin-based phenolic (LPF) adhesives is examined based on the structural analysis of the selected industrial lignin. The results show that OL has more phenolic hydroxyl groups, lower molecular weight, and greater number of reactive sites than the other two types of lignins. The maximum replacement rate of phenol by OL reaches 70% w/w, resulting in organosolv lignin phenolic (OLPF) adhesives with a viscosity of 960 mPa·s, a minimal free formaldehyde content of 0.157%, and a shear strength of 1.84 MPa. It exhibits better performance compared with the other two types of lignin-based adhesives and meets the requirements of national standards.

Bonding performance and surface characterization of cold-bonded acetylated beech (Fagus sylvatica L.) laminated veneer lumber.

Acetylation of wood with acetic anhydride reduces the wood-moisture interaction, improves the dimensional stability and resistance against biodegradation. However, the adhesive bonding is affected by the modification, which is crucial to manufacture engineered wood products, such as laminated veneer lumber (LVL). In this study we report the bonding of 8-layered acetylated beech (Fagus sylvatica L.) LVL boards to 2-layered LVL beams. The beams were glued together at room temperature adding three common load-bearing construction adhesives: melamine-urea-formaldehyde (MUF), phenol-resorcinol-formaldehyde (PRF), and one-component polyurethane (PUR). The bonding performance was tested by assessing its dry and wet tensile shear strength (TSS) and wood failure percentage (WF). Also evaluated were the material's density and moisture content (MC). The surface was characterized prior to bonding by its pH, roughness, and contact angle (CA). The adhesive penetration was observed by fluorescence microscopy. Aside from MUF, applying PRF and PUR adhesives achieved good bonding performance on acetylated LVL and references. Acetylated LVL displayed a more hydrophobic behaviour, a higher pH, a somewhat smoother surface, and an increased density.

Synthesis and characterization of microencapsulated paraffin with melamine-urea-formaldehyde shell modified with lignin.

The study aims to fabricate MUF/paraffin microcapsules with lignin nanoparticles (LNPs)/ melamine-urea-formaldehyde (MUF) resin as hybrid shell material with different LNPs addition were synthesized in oil-in-water emulsion stabilized synergistically by styrene/maleic anhydride (SMA) and LNPs. The morphological characterization of LNPs was observed by transmission electron microscopy (TEM). The particle size of LNPs, the mean particle size and ξ potentials of SMA/LNPs mixture at pH =4.5 were investigated by zeta potential measurement. Field emission scanning electron microscopy (FE-SEM), Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), thermogravimetric analyzer (TGA), and differential scanning calorimetry (DSC) were characterized the morphologies, crystallography, chemical component, thermal stability and phase change properties of MUF/paraffin microcapsules with different LNPs addition. The results showed that MUF/paraffin microcapsules were spherical. The LNPs did not influence the chemical structure or crystal type of MUF/paraffin microcapsules. When the LNPs addition was 0.15 g, the melting enthalpy and crystallization enthalpy is respectively 130.03 and 121.92 J/g and the encapsulation efficiency of MicroC-15 is 61.04 %.

Surficial engineering of active hydroxyls for ambient formaldehyde oxidation via enhanced Lewis acidity over Zr-doped cryptomelane materials.

Lewis acids of solid catalysts have been featured for a pivotal role in promoting various reactions. Regarding the oxidation protocol to remove formaldehyde, the inherent drawback of the best-studied MnO2 materials in acidic sites has eventually caused deficiency of active hydroxyls to sustain low-temperature activity. Herein, the cryptomelane-type MnO2 was targeted and it was tuned via incorporation of Zr metal, exhibiting great advances in not only the complete HCHO-to-CO2 degradation but also cycling performance. Zr species were existent in doping state in the MnO2 lattice, rendering lower crystallinity and breaking the regular growth of MnO2 crystallites, which thereby tripled surface area and created larger volume of smaller mesopores. Meantime, the local electronic properties of Mn atoms were also changed by Zr doping, i.e., more low-valence Mn species were formed due to the electron transfer from Zr to Mn. The results of infrared studies demonstrate the higher possession of Lewis acid sites on ZrMn, and this high degree of electrophilic agents favored the production of hydroxyl species. Furthermore, the reactivity of surface hydroxyls, as investigated by CO temperature programmed reduction and temperature programmed desorption of adsorbed O2, was obviously improved as well after Zr modification. It is speculated jointly with the characterizations of the post-reaction catalysts that the accelerated production of active hydroxyls helped rapidly convert formaldehyde into key intermediate-formate, which was then degraded into CO2, avoiding the side reaction path with undesired intermediate-hydrocarbonate-over the pristine MnO2, where active sites were blocked and formaldehyde oxidation was inhibited. Additionally, Zr decoration could stabilize Lewis acidity to be more resistant to heat degeneration, and this merit brought about advantageous thermal recyclability for cycled application.

Histochemical and morphological evaluation of a glyoxal acid-free fixative.

The application of most chemical fixatives, such as formalin, in the anatomic pathology laboratory requires safety training and hazardous chemical monitoring due to the toxicity and health risks associated with their use. Consequently, the use of formalin has been banned in most applications in Europe; the primary exception is its use in the histology laboratory in lieu of a suitable and safer alternative. Glyoxal based solutions, several of which are available commercially, are the most promising alternative fixatives, because they are based on a mechanism of fixation similar to that of formalin. Unlike formalin, however, glyoxal based solutions do not dissociate from water and therefore do not require ventilation measures such as a fume hood. A primary barrier to the adoption of commercially available glyoxal based solutions is their low pH, which can produce undesirable morphological and antigenic tissue alterations; however, a recently available neutral pH glyoxal product (glyoxal acid free) (GAF) has been developed to mitigate the challenges of low pH. We compared the morphology and histochemistry among tissues fixed in 10% neutral buffered formalin, a commercially available acidic glyoxal product (Prefer), and GAF. Tissues fixed in formalin and Prefer exhibited similar morphology and staining properties; tissues fixed with 2% GAF exhibited deleterious effects.

Hot alkaline lysis gDNA extraction from formalin-fixed archival tissues.

Formalin fixation of natural history specimens and histopathological material has historically been viewed as an impediment to successful genomic analysis. However, the development of extraction methods specifically tailored to contend with heavily crosslinked archival tissues, re-contextualises millions of previously overlooked specimens as viable molecular assets. Here, we present an easy-to-follow protocol for screening archival wet specimens for molecular viability and subsequent genomic DNA extraction suitable for sequencing. The protocol begins with non-destructive assessment of specimen degradation and preservation media conditions to allow both museum curators and researchers to select specimens most likely to yield an acceptable proportion (20-60%) of mappable endogenous DNA during short-read DNA sequencing. The extraction protocol uses hot alkaline lysis in buffer (0.1M NaOH, 1% SDS, pH 13) to simultaneously lyse and de-crosslink the tissue. To maximise DNA recovery, phenol:chloroform extraction is coupled with a small-fragment optimised SPRI bead clean up. Applied to well-preserved archival tissues, the protocol can yield 1-2 µg DNA per 50 mg of tissue with mean fragment sizes typically ranging from 50-150 bp, which is suitable to recover genomic DNA sufficient to reconstruct complete mitochondrial genomes and achieve up to 25X nuclear genome coverage. We provide guidance for read mapping to a reference genome and discuss the limitations of relying on small fragments for SNP genotyping and de novo genome assembly. This protocol opens the door to broader-scale genetic and phylogenetic analysis of historical specimens, contributing to a deeper understanding of evolutionary trends and adaptation in response to changing environments.

Morphological changes in striated muscle fibres caused by components of the Thiel embalming method.

BACKGROUND: Thiel-fixed body donors are highly valued for surgical training courses. The pronounced flexibility of Thiel-fixed tissue has been postulated to be caused by histologically visible fragmentation of striated muscle. The aim of this study was to analyse whether a specific ingredient, pH, decay, or autolysis could cause this fragmentation in order to modulate the Thiel solution to adapt specimen flexibility specifically to the needs of different courses. MATERIALS AND METHODS: Striated muscle of the mouse was fixed for different time periods in formalin, Thiel solution, and its individual ingredients, and analysed by light microscopy. Further, pH-values of Thiel solution and its ingredients were measured. In addition, unfixed muscle tissue was histologically analysed including Gram staining to investigate a relationship between autolysis, decomposition, and fragmentation. RESULTS: Muscle fixed with Thiel solution for 3 months was slightly more fragmentated than muscle fixed for 1 day. Fragmentation was more pronounced after 1 year of immersion. Three individual salt ingredients showed slight fragmentation. Decay and autolysis had no effect on fragmentation, which occurred regardless of the pH of all solutions. CONCLUSIONS: Fragmentation of Thiel-fixed muscle is dependent on fixation time and most likely occurs due to salts present in the Thiel solution. Adjustment of the salt composition in the Thiel solution with verification of the influence on the fixation effect, fragmentation and flexibility of the cadavers could be performed in further studies.