Fluorescence Microscopy Research Articles

Morphological characteristics of the cerebral cortex of a mini-pig under conditions of gene therapy after experimental stroke

Aim. To study the effectiveness of preventive gene therapy (within 2 days) and gene therapy in the acute phase (after 4 hours) of ischemic stroke in mini-pigs using an autologous leucoconcentrate (AutoLeuc) enriched with recombinant genes of vascular endothelial growth factor (VEGF165), glial cell line-derived neurotrophic factor (GDNF) and neural cell adhesion molecule 1 (NCAM1), as well as the migration of leukocytes transduced with a chimeric adenoviral vector serotype 5 with fiber 35 serotype (Ad5/F35) and the green fluorescent protein (GFP) genome into immune defense organs.Materials and methods. The experiment was conducted on 8-month-old Vietnamese lop-bellied mini-pigs (n=16). An ischemic stroke was created by occlusion of the distal branches of the left middle cerebral artery and the right common carotid artery. Genetically modified AutoLeuc was administered preventively intravenously 2 days before or in the acute phase 4 hours after stroke modelling; the control group was injected with 30 ml of saline solution. The morphology of the cerebral cortex was assessed using histological methods in the areas bordering the infarction and peri-infarction after 21 days. The migration of genetically modified Ad5/F35-GFP leukocytes into the brain, spleen, and submandibular lymph nodes was studied a week after stroke modelling.Results. In the peri-infarction zone, the content of pyknotic neurons in control animals was higher, while the number of capillaries was lower than in the gene therapy groups. In the latter, neurons had a typical morphology with preserved outgrowths; in the control group, the outgrowths were tortuous and fragmented. Fluorescence microscopy after injection of AutoLeuc with Ad5/F35-GFP revealed GFP-positive cells in the spleen and submandibular lymph nodes.Conclusion. 21 days after modeling a stroke in mini-pigs against the background of preventive gene therapy or gene therapy in the acute phase using VEGF165/GDNF/NCAM1 AutoLeuc, greater preservation of neurons and a higher density of capillaries in the peri-infarction zone of ischemic brain damage were established. Leukocytes with Ad5/ F35-GFP were found in the spleen and submandibular lymph nodes.

Biofilm Eradication of Stenotrophomonas maltophilia by Levofloxacin and Trimethoprim-Sulfamethoxazole.

Stenotrophomonas maltophilia is a nonfermenting Gram-negative drug-resistant pathogen that causes healthcare-associated infections. Clinical isolates from Mexico were assessed for biofilm formation using crystal violet staining. Antimicrobial susceptibility was evaluated in planktonic and biofilm cells using the broth microdilution method. The effects of antibiotics on biofilms were visualized using fluorescence microscopy. Fifty isolates were included in this study, of which 14 (28%) were biofilm producers (9 [64%] from blood and 5 [36%] from respiratory samples). In planktonic cells 4/50 (8%) of isolates were resistant to levofloxacin (8.0%) and 22/50 (44%) were resistant to trimethoprim-sulfamethoxazole. All isolates were resistant to levofloxacin and trimethoprim-sulfamethoxazole in biofilm cells. Bacterial biofilms treated with different concentrations of both antibiotics were completely disrupted. In conclusion, S. maltophilia isolated from blood had higher biofilm production than those isolated from respiratory samples. Biofilm production was associated with increased antibiotic resistance. Antibiotic monotherapy might not be the best course of action for the treatment of S. maltophilia infections in Mexico, because it might cause biofilm production and antimicrobial resistance.

Utilizing quantitative phase microscopy to localize fluorescence in three dimensions via the transport of intensity equation.

We demonstrate the use of a novel, to the best of our knowledge, localization algorithm for digitally refocusing fluorescence images from a three-dimensional cell culture. Simultaneous phase and fluorescence intensity images are collected through a multimodal system that combines digital holography via quantitative phase microscopy (QPM) and fluorescence microscopy. Defocused fluorescence images are localized to a specific z-plane within the three-dimensional (3D) matrix using the transport of intensity equation (TIE) and depth-resolved information derived from the QPM measurements. This technique is applied to cells stained with different fluorescent tags suspended in 3D collagen hydrogel cultures. Experimental findings demonstrate the localization of defocused images, facilitating the analysis and comparison of cells within the hydrogel matrix. This method holds promise for comprehensive cellular imaging of fluorescence labeling in three-dimensional environments, enabling detailed investigations into cellular behavior and interactions.

Muga (Antheraea assamensis) silk electrospun scaffold for biomedical applications

Abstract Wild silk varieties are less explored in the field of biomaterials than cultivated mulberry silk (Bombyx Mori). In the present work, an electrospun scaffold was produced from wild silk, muga (Antheraea assamensis), and it was assessed for the properties required for biomaterials. Scanning electron microscopy images showed that the electrospun fibers were formed without beads, and the majority of the fibers had diameters in the range of 500–900 nm. The scaffold started to decompose at 210 °C, which is higher than the temperature used for sterilization of the scaffold. The PBS uptake percentage was found to be 400 %, which is sufficient for the absorption of the medium used during cell culture. The scaffold had a hemolysis value of less than 5 %, which indicates that the scaffold exhibits good blood compatibility. The MTT assay showed cell viability of more than 80 % after 24 h and 48 h, and fluorescence microscopy showed that cells adhered and spread on the surface of the scaffold. The results show that muga silk electrospun mat can be used as an ideal biomaterial.

Synthesis of novel hydrophilic celastrol nanoformulation by entrapment within calcium phosphate nanoparticle and study of its antioxidant activity against neurotoxin-induced damage in human neuroblastoma cells

Celastrol, a pentacyclic triterpenoid found in Chinese herb Tripterygium wilfordii, is considered as one of the top-five natural medicinal compounds with high antioxidant property. However, celastrol has poor aqueous solubility and thereby low bioavailability, restricting its clinical application as drug. To overcome this problem, we nanonized celastrol by entrapping it within hydrophilic nanocarrier – calcium phosphate nanoparticle. The synthesized calcium phosphate celastrol nanoparticle (CPCN) had average size of 35 nm, spherical shape, significant stability with (−) 37 mV zeta potential, celastrol entrapment efficiency around 75 % and low celastrol release kinetics spanning over 7 days, as measured by different techniques like FESEM, AFM, DLS, and spectrophotometry. Studies on the antioxidant potency of CPCN by flow cytometry and fluorescence microscopy depicted that the toxicity developed in human neuroblastoma cells SH-SY5Y by treatment with the selective neurotoxin MPP+ iodide (N-Methyl-4-phenylpyridinium iodide) got reduced by pretreatment of the cells with CPCN. Determination of cellular ROS content, depolarization level of mitochondrial membrane potential, cell cycle analysis and nuclear damage in MPP+-exposed cells demonstrated that CPCN had about 65 % more antioxidant efficacy over that of bulk celastrol. Thus, the nanonization process transformed hydrophobic celastrol into hydrophilic CPCN, having high potentiality to be developed as an effective antioxidant drug.

A Fluorogenic Pseudoinfection Assay to Probe Transfer and Distribution of Influenza Viral Contents to Target Vesicles.

Fusion of enveloped viruses with endosomal membranes and subsequent release of the viral genome into the cytoplasm are crucial to the viral infection cycle. It is often modeled by performing fusion between virus particles and target lipid vesicles. We utilized fluorescence microscopy to characterize the kinetic aspects of the transfer of influenza viral ribonucleoprotein (vRNP) complexes to target vesicles and their spatial distribution within the fused volumes to gain deeper insight into the mechanistic aspects of endosomal escape. The fluorogenic RNA-binding dye QuantiFluor (Promega) was found to be well-suited for direct and sensitive microscopic observation of vRNPs which facilitated background-free detection and kinetic analysis of fusion events on a single particle level. To determine the extent to which the viral contents are transferred to the target vesicles through the fusion pore, we carried out virus-vesicle fusion in a side-by-side fashion. Measurement of the Euclidean distances between the centroids of superlocalized membrane and content dye signals within the fused volumes allowed determination of any symmetry (or the lack thereof) between them as expected in the event of transfer (or the lack thereof) of vRNPs, respectively. We found that, in the case of fusion between viruses and 100 nm target vesicles, ∼39% of the events led to transfer of viral contents to the target vesicles. This methodology provides a rapid, generic, and cell-free way to assess the inhibitory effects of antiviral drugs and therapeutics on the endosomal escape behavior of enveloped viruses.

Macro-Calcium Carbonate-Hydrogel Hybrid Spheroids: Design and Biomedical Applications.

In advancing tissue engineering, we introduce a particle system combining the strength of calcium carbonate with the flexibility of hydrogels enhanced with alkaline phosphatase (ALP) for improved bone regeneration. Our innovation lies in creating large hybrid macrospheroids by bonding mineral nanostructured microparticles loaded with ALP through hydrogel polymerization. These composite macrospheroids address critical challenges in cell seeding, growth, and handling within three-dimensional (3D) environments. We conducted extensive characterization of these particles using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), mechanical property assessment, and fluorescence microscopy. The results demonstrate that the hybrid macrospheroids significantly enhance cell manipulation and growth in three-dimensional structures. Specifically, ALP-loaded macrospheroids showed a marked improvement in osteogenic activity, promoting effective bone tissue regeneration. This study not only showcases a unique approach to overcoming the limitations of traditional hydrogels in tissue engineering but also opens pathways for bone tissue regeneration. Our findings offer a promising tool for cell seeding and growth in 3D structures, potentially revolutionizing practices in tissue engineering and regenerative medicine.

Glioma-associated oncogene (GLI)-specific decoy oligodeoxynucleotide induces apoptosis and attenuates proliferation, colony formation, and migration in liver cancer cells

Aim: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-associated death. The Sonic Hedgehog (SHH) signaling pathway participates in the initiation, progression, migration, and recurrence of HCC cancer stem cells. Furthermore, SHH regulates various cellular behaviors such as proliferation, differentiation, survival, self-renewal, epithelial-mesenchymal transition (EMT), and SHH autoregulation. Glioma-associated oncogene (GLI) family zinc finger are key transcription factors in the development of many organs and are deregulated in cancer. In this study, Huh-7 cells were treated with GLI-specific decoy oligodeoxynucleotide (ODN) to evaluate its anticancer impact. Methods: The transfection efficiency of GLI-specific decoy ODN was measured using fluorescent microscopy. Then, the effects of GLI-specific decoy ODN on apoptosis, viability, proliferation rate, colony formation, and migration capacities of Huh-7 cells were assessed. Furthermore, the expression of genes associated with the alteration of SHH was assessed. Results: Treatment of Huh-7 cells with GLI-specific decoy ODN decreased cell viability (56.36% ± 3%). Expression of certain genes such as c-MYC , SNAI2 , ZEB1 , and PROM1 decreased dramatically, while the expression of CDH1 increased significantly. Furthermore, the treated cells’ proliferation, colony formation, and migration capacity decreased considerably. This treatment induced apoptosis in the Huh-7 cells. Conclusion: Inhibition of the SHH signaling pathway using GLI-specific decoy ODN led to a decline in the growth rate of HCC cells, decreased migration, and attenuated EMT progression.

Induction of Apoptosis and ROS Production in Liver Cancer Cells by Saponin Fraction from Alcea rosea L. Seeds

Background: Natural compounds are essential targets in anticancer research due to the toxic effects of current chemotherapy and drug resistance. Methods: Saponin extraction from Alcea rosea L. was carried out using 20% methanol and liquid-liquid extraction coupled with the Solid phase extraction (SPE) approach. The saponin fraction was explored for its cytotoxic activity against Huh-7 and MDA-MB-231 cancer cell lines and a non–cancer cell line (HUVEC). The cytotoxic activity and oxidative stress were assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and 2,7 dichlorofluorescein diacetate dyes respectively. The apoptotic potential was investigated using DAPI and acridine orange-ethidium bromide dual staining. Result: The saponin fraction exhibited cytotoxic potential against the cell lines investigated. The IC50 values of the saponin fraction were 49.02, 300 and 325 µg\mL against Huh-7, MDA-MB-231 and HUVEC cell lines, respectively. The cytotoxicity for the extract was dose-dependent. The saponin fraction calculated selectivity index (SI) value indicated high selectivity towards Huh-7 cells (SI = 6.62) compared with normal HUVEC cells. Huh-7 cells treated with saponin fraction showed cellular and nuclear morphological changes, such as apoptotic body formation and chromatin condensation, as observed using light and fluorescent microscopy. However, further investigation is required to assess the the saponin fraction as a potential therapeutic agent.

Novel silica coated trimetallic ferrite functionalized with amino acid-based protic ionic liquid (Mn0.5Fe0.25Ca0.25Fe2O4-SiO2@[L-Tyr][HSO4]): A versatile bio-nanostructure to catalyze green synthesis of poly-substituted hydroquinolines and pyrido[2,3-d]pyrimidine-triones

In this research a magnetized inorganic-bioorganic nanocomposite prepared through coating the Mn0.5Fe0.25Ca0.25Fe2O4 core by silica layer, and consequent functionalization by the L-tyrosinium hydrogen sulfate ionic liquid. The structure of the hybrid nanocomposite (Mn0.5Fe0.25Ca0.25Fe2O4-SiO2@[L-Tyr][HSO4]) studied by density functional theory (DFT) calculations which contains L-Tyr protonation step and the chemisorption of L-Tyr cation on silica layer. The novel synthesized bio-nanocomposite (Mn0.5Fe0.25Ca0.25Fe2O4-SiO2@[L-Tyr][HSO4]) characterized by Fourier-transform infrared spectroscopy (FT-IR), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDAX), vibrating-sample magnetometery (VSM), thermogravimetric (TGA/DSC), X-ray powder diffractometery (XRD), X-ray fluorescence (XRF), and transmission electron microscopy (TEM) analysis. The hybrid bio-nanocomposite applied for solvent-free diastereoselective synthesis of dispiro[tetrahydroquinoline-bis(2,2-dimethyl[1,3]dioxane-4,6-dione)] derivatives via one-pot pseudo eight-component reaction of meldrum’s acid, aromatic aldehydes, and arylamines at 50 °C. Also, the bio-nanocatalyst utilized for the aqua-mediated green synthesis of 5-aryl-5,6-dihydropyrido[2,3-d]pyrimidine-2,4,7(1H,3H,8H)-triones at 70 °C through the reaction of meldrum’s acid, aryl aldehydes, and 6-aminouracil. The recovery and reusability of the bio-nanohybrid also examined within 2 runs successfully.

Single-walled Carbon Nanotubes Wrapped with Charged Polysaccharides Enhance Extracellular Electron Transfer.

Microbial electrochemical systems (MESs) rely on the microbes' ability to transfer charges from their anaerobic respiratory processes to electrodes through extracellular electron transfer (EET). To increase the generally low output signal in devices, advanced bioelectrical interfaces tend to augment this problem by attaching conducting nanoparticles, such as positively charged multiwalled carbon nanotubes (CNTs), to the base carbon electrode to electrostatically attract the negatively charged bacterial cell membrane. On the other hand, some reports point to the importance of the magnitude of the surface charge of functionalized single-walled CNTs (SWCNTs) as well as the size of functional groups for interaction with the cell membrane, rather than their polarity. To shed light on these phenomena, in this study, we prepared and characterized well-solubilized aqueous dispersions of SWCNTs functionalized by either positively or negatively charged cellulose-derivative polymers, as well as with positively charged or neutral small molecular surfactants, and tested the electrochemical performance of Shewanella oneidensis MR-1 in MESs in the presence of these functionalized SWCNTs. By simple injection into the MESs, the positively charged polymeric SWCNTs attached to the base carbon felt (CF) electrode, and as fluorescence microscopy revealed, allowed bacteria to attach to these structures. As a result, EET currents continuously increased over several days of monitoring, without bacterial growth in the electrolyte. Negatively charged polymeric SWCNTs also resulted in continuously increasing EET currents and a large number of bacteria on CF, although SWCNTs did not attach to CF. In contrast, SWCNTs functionalized by small-sized surfactants led to a decrease in both currents and the amount of bacteria in the solution, presumably due to the detachment of surfactants from SWCNTs and their detrimental interaction with cells. We expect our results will help researchers in designing materials for smart bioelectrical interfaces for low-scale microbial energy harvesting, sensing, and energy conversion applications.

Surface-Functionalized Halo-Tag Gold Nanoprobes for Live-Cell Long-Term Super-Resolution Imaging of Endoplasmic Reticulum Dynamics.

Super-resolution fluorescence microscopy has emerged as a powerful tool for studying endoplasmic reticulum (ER) dynamics in living cells. However, the lack of high-brightness, high-photostability, and stable labeling probes makes long-term super-resolution imaging of the ER still challenging. Herein, we reported a surface-functionalized Halo-tag gold nanofluorescent probe (GNP-Atto565-fR8-CA) that exhibits excellent brightness, photostability, and biocompatibility. GNP-Atto565-fR8-CA can simultaneously load multiple Atto565 dye molecules, significantly improving its brightness. Modifying the cell-penetrating peptide fR8 enables GNP-Atto565-fR8-CA to be efficiently delivered into the cytoplasm, overcoming the challenge of their easy entrapment in vesicles. Fluorescent labeling of ER proteins via Halo tags enables high specificity and stable labeling of GNP-Atto565-fR8-CA to the ER. The SIM super-resolution imaging results showed that GNP-Atto565-fR8-CA can track and observe the long-term dynamic process of the ER, and can also be used for long-term super-resolution imaging of the dynamic interactions between the ER and other organelles. This work offers a practical tool to study live-cell ER ultrastructure and dynamics.

3D Culture Analysis of Cancer Cell Adherence to Ex Vivo Lung Microexplants.

Ex vivo 3D culture of human tissue explants addresses many limitations of traditional monolayer cell culture techniques, namely the lack of cellular heterogeneity and absence of 3D intercellular spatial relationships, but presents challenges with regard to repeatability due to the difficulty of acquiring multiple tissue samples from the same donor. In this study, we used a cryopreserved bank of human lung microexplants , ~1 mm3 fragments of peripheral lung from donors undergoing lung resection surgery, and a liquid-like-solid (LLS) 3D culture matrix to describe a method for the analysis of non-small cell lung cancer (NSCLC) adhesion to human lung tissue. H226 (squamous cell carcinoma), H441 (lung adenocarcinoma), and H460 (large cell carcinoma) cell lines were co-cultured with lung microexplants. Confocal fluorescence microscopy was used to visualize the adherence of each cell line to lung microexplants. Adherent cancer cells were quantified following filtration of non-adherent cells, digestion of cultured microexplants, and flow cytometry. This method was used to evaluate the role of integrins in cancer cell adherence. A statistically significant decrease in the adherence of H460 cells to lung microexplants was observed when anti-integrins were administered to H460 cells prior to co-culture with lung microexplants.

HaloTag as a substrate-based macroautophagy reporter

Macroautophagy is a conserved cellular degradation pathway that, upon upregulation, confers resilience toward various stress conditions, including protection against proteotoxicity associated with neurodegenerative diseases, leading to cell survival. Monitoring autophagy regulation in living cells is important to understand its role in physiology and pathology, which remains challenging. Here, we report that when HaloTag is expressed within a cell of interest and reacts with tetramethylrhodamine (TMR; its ligand attached to a fluorophore), the rate of fluorescent TMR-HaloTag conjugate accumulation in autophagosomes and lysosomes, observed by fluorescence microscopy, reflects the rate of autophagy. Notably, we found that TMR-HaloTag conjugates were mainly degraded by the proteasome (~95%) under basal conditions, while lysosomal degradation (~10% upon pharmacological autophagy activation) was slow and incomplete, forming a degraded product that remained fluorescent within a SDS-PAGE gel, in agreement with previous reports that HaloTag is resistant to lysosomal degradation when fused to proteins of interest. Autophagy activation is distinguished from autophagy inhibition by the increased production of the degraded TMR-HaloTag band relative to the full-length TMR-HaloTag band as assessed by SDS-PAGE and by a faster rate of TMR-HaloTag conjugate lysosomal puncta accumulation as observed by fluorescence microscopy. Pharmacological proteasome inhibition leads to accumulation of TMR-HaloTag in lysosomes, indicating possible cross talk between autophagy and proteasomal degradation.

Peptide lipidation and shortening optimises antibacterial, antibiofilm and membranolytic actions of an amphiphilic polylysine-polyphenyalanine octapeptide

The demand for broad-spectrum antibacterial agents continues with increasing rates of resistance of microbial pathogens to traditional antibiotics. Peptides and lipopeptides are gaining traction as promising novel, class-reference antibiotics for tackling difficult-to-treat infections caused by multi-drug resistant bacteria. To identify novel candidates and expand treatment options in clinical settings, we explored the in vitro antibacterial potential and mode of action of a short octapeptide combining a cationic block of four lysines and a highly hydrophobic segment of four phenylalanines (K4F4), and two K4F4-inspired lipopeptides (Palmitoyl-K4F4 and K4-NH-Palmitoyl). Preliminary AI-based screening had revealed the antimicrobial potential of the K4F4 peptide coupled with limited haemolytic activity. Broth dilution and haemolytic assays have confirmed these in silico predictions. Overall, our lipidated peptides were more active at lower MIC values compared to non-lipidated species, indicating the beneficial impact of tailing lipidation on design of peptide-based antimicrobials. An integrated view of the membrane-active mechanism of these novel therapeutic templates was obtained using a combination of flow cytometry, fluorescence microscopy and dye-based permeabilization assays. K4F4 and its lipidated derivatives act via a fast-disrupting mechanism without inducing bacterial resistance mechanisms in a long-term exposure assay. A K4F4-inspired lipopeptide together with its shorter version (K4-NH-Palmitoyl), were more stable in environments closer emulating physiological conditions, showing a higher antibacterial response in physiological salts and serum than their parent peptide. Our findings reveal the antibacterial and antibiofilm potential of a novel polylysine-polyphenyalanine peptide and highlight the significant contribution of lipidation and shortening as molecular engineering strategies to improve and guide the future design of next-generation membrane-targeting antibiotics.

Calcite recrystallization and its impact on speleothem geochemistry

Speleothems are among the most important archives for past climatic and environmental change. Calcite recrystallization can modify the authigenic structure and geochemical composition of the speleothems and affect the reliability of calcite stalagmites as repositories of authigenic geochemical proxies of past climates and environments. The criteria for distinguishing primary from secondary speleothem calcite, and the conditions (open or semi-closed) of speleothem calcite recrystallization remain poorly understood. Thus, in this study, we investigated the fabric, geochemical composition, and recrystallization dynamics of a partially recrystallized calcite stalagmite (DDH-Z-2) from Didonghe Cave in Shaanxi Province, China, through petrographic observations, fluorescence microscopy, and geochemical analyses (stable isotopes, trace elements, UTh isotopes). We found that: (1) in the DDH-Z-2 stalagmite, open elongated columnar calcite recrystallized into compact elongated columnar calcite. Particulate organic matter and fulvic and humic acids were removed during recrystallization, while aromatic compounds were preserved and became incorporated into the secondary calcite; (2) calcite recrystallization was affected by multiple factors, including external fluid chemistry, primary calcite microstructure, and organic matter; (3) calcite recrystallization occurred under open, fluid-buffered conditions for alteration of the stable isotopes (δ18O and δ13C) and trace elements (Mg, Sr, U). The effect of external fluid composition on trace element (Mg, Sr) composition of secondary calcite varied across the stages of calcite recrystallization. Caution should, therefore, be exercised when using geochemical proxies in stalagmites composed of inclusion-free elongated columnar calcite: such calcite is likely to be recrystallized, and thus record the composition of reactive fluids at the time of recrystallization. Regarding the geochemical system of speleothem diagenesis, the contribution of the parent material and the sources of reactive fluids are key factors to consider.

Establishment of a 3D organoid culture model for the investigation of adult slow-cycling putative intestinal stem cells.

The study of intestinal stem cells is a prerequisite for the development of therapies aimed at regenerating the gut. To enable investigation of adult slow-cycling H2B-GFP-retaining putative small intestinal (SI) stem cells in vitro, we have developed a three-dimensional (3D) SI organoid culture model based on the Tet-Op histone 2 B (H2B)-green fluorescent protein (GFP) fusion protein (Tet-Op-H2B-GFP) transgenic mouse. SI crypts were isolated from 6- to 12-week-old Tet-Op-H2B-GFP transgenic mice and cultured with appropriate growth factors and an animal-derived matrix (Matrigel). For in vitro transgene expression, doxycycline was added to the culture medium for 24h. By pulse-chase experiments, H2B-GFP expression and retention were assessed through direct GFP fluorescence observations, both by confocal and fluorescence microscopy and by immunohistochemistry. The percentages of H2B-GFP-retaining putative SI stem cells and H2B-GFP-retaining Paneth cells persisting in organoids were determined by scoring relevant GFP-positive cells. Our results indicate that 24 h exposure to doxycycline (pulse) induced ubiquitous expression of H2B-GFP in the SI organoids. During subsequent culture, in the absence of doxycycline (chase), there was a gradual loss (due to cell division) of H2B-GFP. At 6-day chase, slow-cycling H2B-GFP-retaining putative SI stem cells and H2B-GFP-retaining Paneth cells were detected in the SI organoids. The developed culture model allows detection of slow-cycling H2B-GFP-retaining putative SI stem cells and will enable the study of self-renewal and regeneration for further characterization of these cells.

Ionic liquid-assisted sample preparation mediates sensitive proteomic analysis of Bacillus subtilis spores

Endospore-forming bacteria are ubiquitous. Bacterial endospores are multilayered proteinaceous structures that protects the bacterial genome during stress conditions. They are also responsible for a wide range of critical clinical infections in humans. Precise analysis of spore-forming pathogens remains a major challenge in the field of proteomics because spore structures are highly resistant to conventional solubilizers and denaturing agents, such as sodium dodecyl sulfate and urea. We present an ionic liquid-assisted (i-soln) technique of sample preparation, called pTRUST, which enables shotgun analysis of Bacillus subtilis spores even when the starting materials are in the sub-microgram range. In proteomic analysis, this technique shows 50–2000-fold higher sensitivity than other conventional gel-based or gel-free methods (including one-pot sample processing). Using this technique, we identified 445 proteins with high confidence from trace amounts of highly pure spore preparations, including 52 of the 79 proteins (approximately 70%) previously demonstrated to be localized in spores in the SubtiWiki database and detected through direct protein analysis. Consequently, 393 additional proteins were identified as candidates for spore constitutive proteins. Twenty of these newly identified candidates were produced as green fluorescent protein fusion proteins, and each was evaluated for authenticity as a spore constituent using fluorescence microscopy analysis. The pTRUST method's sensitivity and reliability using the i-soln system, together with hitherto unreported proteins in spores, will enable an array of spore research for biological and clinical applications.

An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single cells

High-throughput volumetric fluorescent microscopy pipelines can spatially integrate whole-brain structure and function at the foundational level of single cells. However, conventional fluorescent protein (FP) modifications used to discriminate single cells possess limited efficacy or are detrimental to cellular health. Here, we introduce a synthetic and nondeleterious nuclear localization signal (NLS) tag strategy, called "Arginine-rich NLS" (ArgiNLS), that optimizes genetic labeling and downstream image segmentation of single cells by restricting FP localization near-exclusively in the nucleus through a poly-arginine mechanism. A single N-terminal ArgiNLS tag provides modular nuclear restriction consistently across spectrally separate FP variants. ArgiNLS performance in vivo displays functional conservation across major cortical cell classes and in response to both local and systemic brain-wide AAV administration. Crucially, the high signal-to-noise ratio afforded by ArgiNLS enhances machine learning-automated segmentation of single cells due to rapid classifier training and enrichment of labeled cell detection within 2D brain sections or 3D volumetric whole-brain image datasets, derived from both staining-amplified and native signal. This genetic strategy provides a simple and flexible basis for precise image segmentation of genetically labeled single cells at scale and paired with behavioral procedures.

Neutrophil extracellular traps as markers of infectious and aseptic inflammation

One of the important problems of medicine is the search for new reliable markers of inflammation that would allow us to determine the type of inflammatory process. The aim of the study was to identify specific markers of infectious and aseptic inflammation based on the analysis of morphological variants of neutrophil extracellular traps (NETs). The study included 26 patients with various nosological forms of inflammation in the abdominal cavity (12 with acute appendicitis, 8 with acute cholecystitis, 6 with a diagnosis of pancreatitis/ pancreonecrosis) after surgery. The study also included 20 patients with post-COVID and a group of 10 volunteers no clinical manifestations of the disease, but at the same time had contacts with flu patients. Neutrophils were isolated using gradient centrifugation. Fluorescence microscopies with the dye SYBR Green (JSC “Evrogen”, Russia) were used for NET visualization and counting. NETs in the morphological form of neutrophils web structure were found in the blood of surgical patients with acute appendicitis who had a favorable course of the postoperative period. In a group of volunteers who were exposed to influenza but did not have symptoms of an infectious disease, we also found neutrophils web structure. In all patients with abdominal inflammation complicated by abdominal abscess, in addition to neutrophil web structure, abnormal forms of NETs were recorded, in particular, NETs in the form of single filaments. In the post-COVID patients an absolute absence of neutrophilis web structure was revealed. In all post-COVID patients, NETs are found only in the form of single filaments. The results of subsequent experiments showed that collagen peptides are inducers of the formation of NETs in the form of single filaments. The detection of neutrophils web structure is a sign of an infectious inflammatory process. NETs in the morphological form of single filaments are markers of aseptic inflammation, as well as a sign of endothelial damage.