Methods for Fixing Biofilms of Staphylococcus aureus and Salmonella enterica for Microscopic Examination.

Different methods for fixing biofilms of Staphylococcus aureus and Salmonella enterica for light and electron microscopy were compared. Paraformaldehyde fixation did not preserve biofilm integrity during dehydration; Ito-Karnovsky fixation revealed cell morphology, but did not preserve the matrix. Ruthenium red combined with aldehydes allowed the matrix to be preserved and visualized. An analysis of the ultrastructure of S. aureus and S. enterica cells in biofilms and suspensions at various fixations is presented. The ultrastructure of the biofilm matrix has been described.

A stain with all the fixing's - Enhancement of fingermarks in blood using a combined fixative and aqueous protein stain.

The use of protein stains to enhance fingermark ridge detail in blood is a common technique used by forensic practitioners around the world. Amido Black is one of the most favoured protein stains due to its strong staining ability. The most common formulation of Amido Black is methanol based, with an ability to simultaneously fix and stain the blood impression, however methanol is toxic and can disrupt some surfaces, potentially compromising fingermark detail. If the surface is suspected of being a material that is impacted by methanol, there is an alternative aqueous formulation, which requires a fixative step to set the blood prior to staining so as not to wash away potential ridge detail. The multi-step process of aqueous protein stains is tedious and numerous studies have been conducted to improve the formula to achieve a combined fixing/staining solution that performs like the methanolic reagent. A combined fixative and stain formulation of aqueous based Amido Black was compared to a multi-step formulation with a separate sulfosalicylic acid fixative. Of the 243 split fingermark impressions analysed the majority (63.5 %) showed no preference to either treatment, with a marginally greater proportion of the remaining marks slightly favouring the combined fixative and stain formulation. Given that the new combined formulation performed broadly similarly to the existing multi step formulation, the potential time savings of this simpler approach may be beneficial to implement into operational use.

Assessment of formalin preserved and fresh frozen quadriceps tendon graft-suture constructs for load to failure testing: a biomechanical cadaveric study.

PURPOSE: Fresh-frozen specimen availability and cost may be a barrier for initiation of biomechanical studies where soft tissue is used in a construct with other medical devices. The impact of soft tissue preservation method on the outcomes of biomechanical studies in the specific case of graft-suture constructs is relatively unexplored. This study aimed to observe peak loads and failure modes in biomechanical testing of fresh-frozen (FF) versus formalin embalmed (FE) quadriceps tendon (QT) graft-suture constructs for soft tissue fixation in ACLR and assess suitability of FE QT graft constructs for load-to-fail testing. METHODS: Twenty QT grafts were harvested from human cadaver specimens. Ten grafts came from fresh-frozen donors and 10 from embalmed donors. All grafts were prepared with the modified Prusik knot using a braided composite suture and subjected to tensile loading. Comparisons between the biomechanical properties of the graft-suture constructs were made with unpaired t tests with α = 0.05. RESULTS: FE and FF constructs displayed similar peak loads and failure modes. FF constructs had greater elongation after pre-tensioning than FE (7.3 vs. 5.5 mm, p = 0.02) and greater elongation after cyclic loading than FE constructs (17.5 vs. 10.5 mm, p = 0.01). Hysteresis was greater for FF constructs at the 50th, 100th, 150th, and 200th cycle (p = 0.02, p = 0.07, p < 0.001, p = 0.004, respectively). FE constructs were stiffer than fresh-frozen (103 vs. 84 N/mm, p < 0.001). CONCLUSION: FE constructs were significantly stiffer but displayed similar peak load and failure mode to FF which was reflective of the strength of the suture material. FE grafts can offer an alternative to FF grafts in graft-suture constructs for biomechanical studies where load at failure and knot security and strength is of main interest.

[Recycled formalin: A new environmental mitigation tool in pathology?] / Le formol recyclé : un nouvel outil d'atténuation de l'impact environnemental de l'ACP ?

Formalin is the international gold-standard fixative in pathology laboratories. However it is not the ideal one considering its deleterious effects on individuals and the environment. Complete formalin removal or even substitution does not seem possible in the near future. In this update, we present various tools allowing to integrate the use of formalin into an ecocare approach. Among them, formalin recycling according to the protocol developed by the University Hospital of Bordeaux is simple to implement and delivers rapid and significant results, allowing pathology professionals to meet the sustainable development objectives included in the France 2030 agenda.

An optimized workflow for transcriptomic analysis from archival paraformaldehyde-fixed retinal tissues collected by laser capture microdissection.

RNA sequencing (RNA-seq) coupled with laser capture microdissection (LCM) is a powerful tool for transcriptomic analysis in unfixed fresh-frozen tissues. Fixation of ocular tissues for immunohistochemistry commonly involves the use of paraformaldehyde (PFA) followed by embedding in Optimal Cutting Temperature (OCT) medium for long-term cryopreservation. However, the quality of RNA derived from such archival PFA-fixed/OCT-embedded samples is often compromised, limiting its suitability for transcriptomic studies. In this study, we aimed to develop a methodology to extract high-quality RNA from PFA-fixed canine eyes by utilizing LCM to isolate retinal tissue. We demonstrate the efficacy of an optimized LCM and RNA purification protocol for transcriptomic profiling of PFA-fixed retinal specimens. We compared four pairs of canine retinal tissues, where one eye was subjected to PFA-fixation prior to OCT embedding, while the contralateral eye was embedded fresh frozen (FF) in OCT without fixation. Since the RNA obtained from PFA-fixed retinas were contaminated with genomic DNA, we employed two rounds of DNase I treatment to obtain RNA suitable for RNA-seq. Notably, the quality of sequencing reads and gene sets identified from both PFA-fixed and FF tissues were nearly identical. In summary, our study introduces an optimized workflow for transcriptomic profiling from PFA-fixed archival retina. This refined methodology paves the way for improved transcriptomic analysis of preserved ocular tissue, bridging the gap between optimal sample preservation and high-quality RNA data acquisition.

Century-old chromatin architecture revealed in formalin-fixed vertebrates.

Gene expression is regulated by changes in chromatin architecture intrinsic to cellular differentiation and as an active response to environmental stimuli. Chromatin dynamics are a major driver of phenotypic diversity, regulation of development, and manifestation of disease. Remarkably, we know little about the evolutionary dynamics of chromatin reorganisation through time, data essential to characterise the impact of environmental stress during the ongoing biodiversity extinction crisis (20th-21st century). Linking the disparate fields of chromatin biology and museum science through their common use of the preservative formaldehyde (a constituent of formalin), we have generated historical chromatin profiles in museum specimens up to 117 years old. Historical chromatin profiles are reproducible, tissue-specific, sex-specific, and environmental condition-dependent in vertebrate specimens. Additionally, we show that over-fixation modulates differential chromatin accessibility to enable semi-quantitative estimates of relative gene expression in vertebrates and a yeast model. Our approach transforms formalin-fixed biological collections into an accurate, comprehensive, and global record of environmental impact on gene expression and phenotype.

Glyoxal-methyl-ethylene sulfonic acid fixative enhances the fixation of cytoskeletal structures for Förster resonance energy transfer measurements.

Förster resonance energy transfer (FRET) serves as a tool for measuring protein-protein interactions using various sensor molecules. The tension sensor module relies on FRET technology. In our study, this module was inserted within the actinin molecule to measure the surface tension of the cells. Given that the decay curve of FRET efficiency correlates with surface tension increase, precise and accurate efficiency measurement becomes crucial. Among the methods of FRET measurements, FRET efficiency remains the most accurate if sample fixation is successful. However, when cells were fixed with 4% paraformaldehyde (PFA), the actinin-FRET sensor diffused across the cytoplasm; this prompted us to explore fixation method enhancements. Glyoxal fixative has been reported to improve cytoskeletal morphologies compared to PFA. However, it was not known whether glyoxal fits FRET measurements. Glyoxal necessitates an acetic acid solution for fixation; however, acidic conditions could compromise fluorescence stability. We observed that the pH working range of glyoxal fixative aligns closely with MES (methyl-ethylene sulfonic acid) Good's buffer. Initially, we switched the acidic solution for MES buffer and optimized the fixation procedure for in vitro and in vivo FRET imaging. By comparing FRET measurements on hydrogels with known stiffness to tumor nodules in mouse lung, we estimated in vivo stiffness. The estimated stiffness of cancerous tissue was harder than the reported stiffness of smooth muscle. This discovery shed lights on how cancer cells perceive environmental stiffness during metastasis.

A South African case study on anatomical embalming for human body donation programmes with toxicological considerations.

Body embalming, a practice with deep historical roots across various cultures, forms the backbone of contemporary human body donation educational programmes. In this study, we explored current embalming practices within six South African human anatomical dissection programmes, focusing on the use and volumes of key chemicals-formalin, phenol, and alcohol-and their associated health risks and potential toxicity. We measured and compared aspects of embalming practices such as the duration of body preservation and the annual intake of bodies. Variations in embalming practices and chemical ratios across different South African universities were found. However, the consistent use of formalin, phenol and alcohol were observed across all six programmes. Formaldehyde concentrations used in South African dissection programmes were within the generally acceptable international range. Regarding arterial embalming, South African dissection programmes showed widespread adherence to international embalming practices, with one programme using a substantially lower concentration of formalin. The dual nature of formaldehyde as both an effective preservative and a recognised carcinogen was underscored in relation to human health regarding chemical toxicity. Phenol, like formaldehyde, was consistently used as it is important for the inhibition of bacterial and fungal growth. Alcohol was also consistently used, but there was much greater variation in its volume across South African institutions. Our data showed a slight positive relationship between storage duration and the volumes of formalin and phenol in human embalming fluid. South African regulators enforce stricter exposure limits than those set by the World Health Organisation and various European agencies. While South African institutions operate within internationally acceptable ranges of chemical use that both maximise preservation and minimise toxicity, we acknowledge that these data are preliminary. Further investigation is encouraged to ensure embalming practices effectively protect all those involved and support the educational goals of human anatomical dissection programmes in South Africa.

Feasibility of MALDI-MSI-Based Proteomics Using Bouin-Fixed Pathology Samples: Untapping the Goldmine of Nephropathology Archives.

The application of innovative spatial proteomics techniques, such as those based upon matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) technology, has the potential to impact research in the field of nephropathology. Notwithstanding, the possibility to apply this technology in more routine diagnostic contexts remains limited by the alternative fixatives employed by this ultraspecialized diagnostic field, where most nephropathology laboratories worldwide use bouin-fixed paraffin-embedded (BFPE) samples. Here, the feasibility of performing MALDI-MSI on BFPE renal tissue is explored, evaluating variability within the trypsin-digested proteome as a result of different preanalytical conditions and comparing them with the more standardized formalin-fixed paraffin-embedded (FFPE) counterparts. A large proportion of the features (270, 68.9%) was detected in both BFPE and FFPE renal samples, demonstrating only limited variability in signal intensity (10.22-10.06%). Samples processed with either fixative were able to discriminate the principal parenchyma regions along with diverse renal substructures, such as glomeruli, tubules, and vessels. This was observed when performing an additional "stress test", showing comparable results in both BFPE and FFPE samples when the distribution of several amyloid fingerprint proteins was mapped. These results suggest the utility of BFPE tissue specimens in MSI-based nephropathology research, further widening their application in this field.

Improved Preservation of Mouse Intestinal Tissue Using a Formalin/Acetic Acid Fixative and Quantitative Histological Analysis Using QuPath.

The architecture and morphology of the intestinal tissue from mice or other small animals are difficult to preserve for histological and molecular analysis due to the fragile nature of this tissue. The intestinal mucosa consists of villi and crypts lined with epithelial cells. In between the epithelial folds extends the lamina propria, a loose connective tissue that contains blood and lymph vessels, fibroblasts, and immune cells. Underneath the mucosa are two layers of contractile smooth muscle and nerves. The tissue experiences significant changes during fixation, which can impair the reliability of histologic analysis. Poor-quality histologic sections are not suitable for quantitative image-based tissue analysis. This article offers a new fixative composed of neutral buffered formalin (NBF) and acetic acid, called FA. This fixative significantly improved the histology of mouse intestinal tissue compared to traditional NBF and enabled precise, reproducible histologic molecular analyses using QuPath software. Algorithmic training of QuPath allows for automated segmentation of intestinal compartments, which can be further interrogated for cellular composition and disease-related changes. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Improved preservation of mouse intestinal tissue using a formalin/acetic acid fixative Support Protocol: Quantitative tissue analysis using QuPath.

Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain.

Tissue-clearing and labeling techniques have revolutionized brain-wide imaging and analysis, yet their application to clinical formalin-fixed paraffin-embedded (FFPE) blocks remains challenging. We introduce HIF-Clear, a novel method for efficiently clearing and labeling centimeter-thick FFPE specimens using elevated temperature and concentrated detergents. HIF-Clear with multi-round immunolabeling reveals neuron circuitry regulating multiple neurotransmitter systems in a whole FFPE mouse brain and is able to be used as the evaluation of disease treatment efficiency. HIF-Clear also supports expansion microscopy and can be performed on a non-sectioned 15-year-old FFPE specimen, as well as a 3-month formalin-fixed mouse brain. Thus, HIF-Clear represents a feasible approach for researching archived FFPE specimens for future neuroscientific and 3D neuropathological analyses.

CytoLyt fixation impedes insulinoma-associated protein 1 (INSM1) immunoreactivity compared to formalin fixation.

INTRODUCTION: Insulinoma-associated protein 1 (INSM1) is an immunohistochemical marker commonly used to confirm cytomorphological concordant neuroendocrine tumors/carcinomas (NETs/NECs), demonstrating high utility in small samples. Previous reports have suggested comparable INSM1 staining in CytoLyt-fixed cell blocks and formalin-fixed surgical pathology specimens. This study aimed to assess INSM1 immunoreactivity using both fixation methods and investigate potential factors contributing to its variable expression. MATERIALS AND METHODS: A retrospective query was performed (03/31/21-05/31/22) for NET/NEC cases that had both formalin- and CytoLyt-fixed cell blocks. We collected clinical data and reporting of immunostains for each case. INSM1 staining was evaluated in both fixation methods, and reported as positive, negative, or equivocal. Equivocal INSM1 staining was further scored as a percentage of 1%-100% and intensity of weak (faint staining), moderate (darker staining), and strong (dense staining). RESULTS: Our search identified 20 cases from diverse body sites, including mediastinal lymph nodes (40%), pancreas (35%), lung (20%), and porta hepatis lymph nodes (5%). All cases exhibited a widespread positivity (over 90%) in formalin-fixed cell blocks. In contrast, CytoLyt fixed cells showed a negative stain in 65% of cases and 30% exhibited an equivocal positivity. CONCLUSIONS: While INSM1 is previously reported as a sensitive (75%-100%) and specific (82.7%-100%) marker for NET/NECs, our study found a reduced immunohistochemical staining in CytoLyt-fixed cell blocks. Consequently, false negative INSM1 immunohistochemical results in CytoLyt-fixed cell block material may pose a pitfall in the diagnosis of NET/NEC.

Phenolic Determination in Proembryogenic Cell Complexes of Buckwheat Morphogenic Cell Culture with Osmium Tetroxide, Toluidine Blue O Dye, and Iron Chloride.

The study of the localization of secondary metabolites in both plants and the cell cultures on the intravital sections is hampered by the difficulty of obtaining thin, correctly oriented sections. Techniques for fixing tissues in resins allow these difficulties to be overcome. Properly selected tissue fixation techniques allow using different dyes to identify the compound of interest. In addition, some components of tissue fixation can act as fixatives and as a dye for identifying secondary metabolites. For example, osmium tetroxide, which fixes lipids in tissues, stains phenolic compounds black. This paper describes methods for the detection of phenolic compounds in morphogenic callus culture of buckwheat using osmium tetroxide, Toluidine Blue O dye, and ferric chloride as dyes in epoxy resin-embedded cell culture with double fixation of the material and when material fixed in Karnovsky's fixative.

Cadaver preservative properties of a solution composed of honey, ethyl alcohol, liquid paraffin, distilled water and citric acid: Experiments on rabbit cadavers.

The objective of this study is to assess the efficacy of a solution including honey, ethyl alcohol, liquid paraffin, distilled water and citric acid (HEFS) as a preservative for rabbit cadavers, serving as a potential substitute for formaldehyde. The cadavers underwent preservation using three distinct solutions: 10% formalin, 35% alcohol and HEFS. The cadavers were subjected to a total of four sampling events, occurring at 4-month intervals, in order to collect specimens for microanatomical, histological, microbiological, mycological, colourimetric, texture and odour analysis. In terms of hardness, suitability for dissection and joint mobility metrics, the cadavers fixed with HEFS had superior qualities to those fixed with formalin. The fixation quality of HEFS for histological analyses was deemed acceptable, except kidney and intestinal tissues. In texture analysis, differences only in the elasticity parameter (p < 0.05) in the same sampling period. A total of 10 (13.9) bacteria isolates were identified among which, Metasolibacillus meyeri 3 (30%) was predominantly followed by Staphylococcus aureus 2 (20%), Bacillus siamensis, Bacillus subtilis, Pseudarthrobacter oxydans, Bacillus licheniformis, Bacillus subtilis subsp. subtilis with a proportion of 1 (10%), respectively, by both microbiological and molecular analysis. However, no anaerobic bacteria and fungi were isolated. A considerable percentage of the students had the perception that HEFS was appropriate for utilization in laboratory settings due to its absence of unpleasant odours and detrimental impact on ocular and respiratory functions. In conclusion, we consider that HEFS may serve as a viable substitute for formalin solution in the preservation of rabbit cadavers.

Sirka: An alternative to the formalin fixative.

Formalin fixation is the most essential step of routine histopathology practice. During the last few years, various fixatives have been developed for use in histopathology practice as an alternative to formalin, to overcome its side effects on health. Here we have demonstrated an interesting and novel idea of using sirka or sugar cane vinegar as an alternative to the formalin with the adequate result.

Investigation of the use of gelatine-glycerine and gelatine-polyvinyl alcohol mixtures as tissue consistency preservatives in cadavers fixed with modified SEFS solution.

This study aimed to improve the effectiveness of SEFS, a fixing solution composed of soap and ethanol. This was achieved by modifying the formulation of SEFS. Additionally, this study aimed to preserve the consistency of organs by perfusing cadavers with mixtures of gelatine-glycerin (gelatine-Gls) and gelatine-polyvinyl alcohol (gelatine-PVA) through vascular access. The modified SEFS embalmed cadavers were divided into two groups: Group I was treated with gelatine-glycerin, and Group II was treated with gelatine-polyvinyl alcohol and each group comprised of two goats and three rabbits. Over one year, cadavers were objectively assessed for hardness, colour, and joint range of motion. Additionally, the cadavers were subjectively evaluated after dissection and palpation. For the modified SEFS embalmment haptic and optic examinations of the muscles revealed they maintained a vivid colour tone, closely resembling their natural colour. The thoracic organs displayed natural colour, with the lungs retaining their shape without collapse. Notably, the walls of the atrium and ventricles of the heart remained intact without inward collapse. The use of gelatine-PVA yielded better outcomes than gelatine-Gls in preserving the volumes of both chest and abdominal organs. This was particularly evident in the heart, lungs, liver, spleen, and kidney. Overall, the modified SEFS and gelatin-PVA mixtures were superior in maintaining certain properties better than expected from cadavers.

Modified trichrome stain for faster and improved detection of intestinal protozoan parasites.

Permanent stains such as trichrome have better sensitivity but are time-consuming and the fixative includes toxic mercuric chloride. Thus, a newer modification was tested and found to be a superior, faster and safer staining technique for intestinal parasitic detection. Our study lasted 9 months and a single stool sample was collected from each enrolled patient. We evaluated classical trichrome (T1 - using Schaudinn fixative) with newer modifications, which involved different fixatives with mordant combinations (T2 - acetic acid + hydrated aluminium sulphate, T3 - citric acid + copper sulphate hydrate). Conventional PCR targeting Entamoeba histolytica, Giardia lamblia and Cryptosporidium spp. was taken as the reference. Out of 175 stool samples, 25.1% protozoa were identified by wet mount, 24% by each T1 and T2, 25.7% by T3. Statistically, T3 and T2 had higher sensitivity as compared to T1 and wet mount when PCR was used as reference.

Impact of the quality of resected thyroid cancer tissue sample on next-generation sequencing testing.

Activating rearranged during transfection (RET) proto-oncogene alterations can be identified using next-generation sequencing (NGS) of tumor DNA/RNA. We assessed factors associated with NGS (Oncomine Dx Target Test [ODxTT]) success for resected thyroid cancer (TC) specimens, including sample age, processing conditions, and DNA/RNA quality. TC samples were from three Japanese hospitals, with sample age <1-<10 years, fixative 10%/15% neutralized buffered formalin (NBF), and fixation time ≤48 h/>48 h-≤72 h. NGS success rate was defined as the percentage of samples returning validated NGS results (RET fusion-positive/negative [RNA] or RET mutation-positive/negative [DNA], detected using ODxTT). DNA/RNA quality was assessed with indexes based on electrophoresis (DNA/RNA integrity number, DV200 ) and quantitative polymerase chain reaction (DNA/RNA integrity score [ddCq/ΔCq]). NGS success rate (N = 202) was 90%/93% (DNA/RNA) overall, 98%-100% (DNA and RNA) for samples <3 years old, and 91% (DNA and RNA) for samples ≥3-<5 years old fixed in 10% NBF for ≤48 h. Multivariate logistic regression analysis identified ddCq and ΔCq as significant predictors of DNA and RNA NGS success rates, respectively. Quality assessment of nucleic acid extracted from archival tissue samples is important for achieving high NGS success rates in clinical practice, especially for samples ≥3 years old.

A cost-effective and efficient ex vivo, ex situ human whole brain perfusion protocol for immunohistochemistry.

BACKGROUND: Chemical fixation of the brain can be executed through either the immersion method or the perfusion method. Perfusion fixation allows for better preservation of the brain tissue's ultrastructure, as it provides rapid and uniform delivery of the fixative to the tissue. Still, not all facilities have the expertise to perform perfusion fixation, with initial high cost and complexity of perfusion systems as the main factors limiting its widespread usage. NEW METHOD: Here we present our low-cost approach of whole brain ex situ perfusion fixation to overcome the aforementioned limitations. Our self-made perfusion system, constructed utilising commercially accessible and affordable medical resources alongside laboratory and everyday items, demonstrates the capability to generate superior histological stainings of brain tissue. The perfused tissue can be stored prior to proceeding with IHC for at least one year. RESULTS: Our method yielded high-quality results in histological stainings using both free-floating cryosections and paraffin-embedded tissue sections. The system is fully reusable and complies with the principles of sustainable management. COMPARISON WITH EXISTING METHODS: Our whole brain perfusion system has been assembled from simple components and is able to achieve a linear flow with a pressure of 70 mmHg corresponding to the perfusion pressure of the brain. CONCLUSIONS: Our ex situ method can be especially useful in research settings where expensive perfusion systems are not affordable or in any field with high time pressure, making it suitable for the field of forensic medicine or pathology in general.

Hair fixative traces on footwear - Establishing a link between footwear and the victim's hair after kicks to the head.

Kicking a person laying on the floor in the head is a crime whose forensic investigation could profit from additional microtraces capable of linking a suspected footwear, and by extension its owner, to the victim and their injuries. The transfer of hair fixatives (hair gel, hair wax, hair spray, hair foam, etc.) represents such a trace and was consequently practically evaluated throughout this study. This study consists of two parts: The first part, the differentiation study, encompasses the visual, and instrumental analysis of a variety of different hair fixatives to determine their analysability and differentiation potential. The visual examination was conducted using alternate light sources and filter lenses. Subsequently, the instrumental analysis was carried out, whereby the focus lay on Fourier Transform Infra-red (FT-IR) spectroscopy and Raman spectroscopy. The second part is comprised of different experiments including a test-transfer and pendulum experiments to assess the process and the potential variables of the transfer of hair fixative traces between hair and fabric shoes during a kick. This helped to determine the effect of the kick strength and the behaviour of differing hair products. Retrieval methods to secure hair fixative traces of footwear and from the hair of a victim were developed. These were subsequently tested out on an acute case example..