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• Paper impregnation with 10 % ATP for an effective protection of historical paper against mould development. • 3D surface topography showed no adverse effects of ATP on paper support. • Portable "on the spot" non-invasive FTIR spectroscopy in reflection mode is an effective method for a rapid and highly sensitive detection of mould biofilms. Even though contamination of historical paper by moulds causes aesthetic, physical, and biochemical biodeterioration, dissolving cellulose fibers and inks, the currently applied physical and chemical disinfection methods are either extremely dangerous to human health (ethylene oxide), may harm the underlying support material, or their efficiency is dependent on fungal species, many of which may resist. Therefore, our aim was to test a new paper impregnation agent, aminopropyl-terminated polydimethylsiloxane (ATP), in regards to its biological potency, ease of handling and support material safety. According to the Gelest Inc. (Morrisville, PA 19067) safety data sheet DMS-A31, ATP in solution causes eye irritation, but in dry from is relatively safe. Our biofouling experiments with four cellulase-active fungal strains, originally isolated from historical books, were conducted directly on impregnated and aged paper at verifying concentrations of ATP and at a relative humidity of 95 %. Fungal biofilm development was quantified using micro-invasive fluorescence microscopy and after incubation non-invasive FTIR spectroscopy was also employed. 3D surface topography scan results showed that ATP impregnation at a concentration of 30 % does not harm the visible structural characteristics of the tested paper and no alterations in surface roughness parameters were observed and is therefore safe for the supporting material. At least a 10 % paper impregnation was needed for an effective suppression of fungal biofilm development and tolerance to lower concentrations was species dependent, with Penicillium canescens ZIM-9717 tolerating 1 % of ATP and Aspergillus niger ZIM-9721 tolerating 1 % and 5 % of ATP. Lastly, we have shown that portable "on the spot" non-invasive FTIR spectroscopy in reflection mode can be effectively used for a rapid but highly sensitive detection and monitoring of mould biofilms on paper support materials. This is important, because sampling and fluorescence dye staining in fluorescence microscopy, will harm the integrity of cultural heritage books and documents. Therefore, non-invasive FTIR spectroscopy can provide for an initial overview or insight into the microbiological condition of library and paper materials. [ABSTRACT FROM AUTHOR]

This contribution insight on the cytotoxic and anticancer activities and molecular mechanism of phyto‐reduced silver nanoparticles (AgNPs) in MCF‐7 breast cancer cell lines. A simple, entirely green synthesis process was optimized for the phyto‐reduction of AgNP (~12.7 nm) using aqueous leaf extracts of Indigofera heterantha. The structural and vibrational properties of biosynthesized AgNPs were extensively characterized using UV–Vis spectrophotometer, x‐ray diffraction (XRD), dynamic light scattering (DLS), and Fourier transform Infrared spectroscopy (FTIR), while their shape and morphology was studied through scanning electron microscopy (SEM). The 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) cell viability assay indicates concentration dependent inhibition with IC50, 27.93 ± 2.10 μg/mL against MCF‐7 cells and 294.38 ± 3.87 μg/mL against L929 cells. The manifested anticancer mechanism in MCF‐7 cells was extensively studied using Acridine orange/ethidium bromide (AO/EB), 4′,6‐diamidino‐2‐phenylindole (DAPI) and Annexin‐V/propedium iodide fluorescence microscopic assays. The level of reactive oxygen species (ROS) was measured using DCFH‐DA fluorescent spectroscopy. Overall, the results show that AgNPs exhibit cytotoxic and apoptotic effect on breast cancer MCF‐7 cells by damaging membrane integrity and nuclear fragmentation due to oxidative stress generated by elevated level of ROS. Research Highlights: Biomimetic synthesis of nano dimension size silver nanoparticles (AgNPs).Characterization of AgNPs through UV–Vis, DLS, XRD, FTIR, and SEM.Cytotoxic and anticancer effects of the biosynthesized AgNPs in L929 fibroblast cells and MCF7 breast cancer respectively.Determination of morphological, and nuclear changes triggered by AgNPs in MCF 7 breast cancer cells using fluorescent microscopy and flow cytometry.Apoptosis induction by AgNPs in cancer cells through oxidative stress generated by reactive oxygen species (ROS). [ABSTRACT FROM AUTHOR]

Modulating autophagy and mitophagy, vital cellular quality control systems, offer therapeutic potential for critical illnesses. However, limited drug screening options hinder progress. We present a novel assay using the photoswitchable fluorescent reporter, mito-Kaede, to quantify mitophagy flux. Mito-Kaede's superior UV-induced photoconversion and brightness post-conversion make it ideal for prolonged mitochondrial dynamics tracking. Its specificity in responding to mitophagy, confirmed by parkin-knockout cells, adds value. When coupled with a custom fluid exchange system, enabling efficient medium changes, precise mitophagy observations become feasible. This mitophagy assay, alongside our methodological insights, can decipher mitophagy's role in pathology and supports drug screening efforts.

IntroductionAmong hyperthermophilic organisms, in vivo protein localization is challenging due to the high growth temperatures that can disrupt proper folding and function of mostly mesophilic-derived fluorescent proteins. While protein localization in the thermophilic model archaeon S. acidocaldarius has been achieved using antibodies with fluorescent probes in fixed cells, the use of thermostable fluorescent proteins for live imaging in thermophilic archaea has so far been unsuccessful. Given the significance of live protein localization in the field of archaeal cell biology, we aimed to identify fluorescent proteins for use in S. acidocaldarius.MethodsWe expressed various previously published and optimized thermostable fluorescent proteins along with fusion proteins of interest and analyzed the cells using flow cytometry and (thermo-) fluorescent microscopy.ResultsOf the tested proteins, thermal green protein (TGP) exhibited the brightest fluorescence when expressed in Sulfolobus cells. By optimizing the linker between TGP and a protein of interest, we could additionally successfully fuse proteins with minimal loss of fluorescence. TGP-CdvB and TGP-PCNA1 fusions displayed localization patterns consistent with previous immunolocalization experiments.DiscussionThese initial results in live protein localization in S. acidocaldarius at high temperatures, combined with recent advancements in thermomicroscopy, open new avenues in the field of archaeal cell biology. This progress finally enables localization experiments in thermophilic archaea, which have so far been limited to mesophilic organisms.

DiamondTM Nucleic Acid Dye (DD) has been evaluated for visualizing DNA material on various evidence types, including nuclei in plucked hair roots. While plucked hair roots exhibit a rapid DNA visualization process, shed hairs, even when stained with DD, pose challenges due to the lack of cell nuclei. In the absence of clear cell nuclei, the sole indicator of DNA presence is the fluorescent signal from DD bound to DNA. This study aimed to assess the stability of the fluorescent signal in shed hairs, revealing a rapid decline within 2–3 min post-staining, likely attributed to the cell-free nature of the DNA present on the hair root. Consequently, immediate microscopic visualization and imaging post-staining are crucial during shed hair examination. [ABSTRACT FROM AUTHOR]

Background: Electric eels (Electrophorus sp.) are known for their ability to produce electric organ discharge (EOD) reaching voltages of up to 860 V. Given that gene transfer via intense electrical pulses is a well-established technique in genetic engineering, we hypothesized that electric eels could potentially function as a gene transfer mechanism in their aquatic environment. Methods: To investigate this hypothesis, we immersed zebrafish larvae in water containing DNA encoding the green fluorescent protein (GFP) and exposed them to electric eel's EOD. Results and Discussion: Some embryos exhibited a mosaic expression of green fluorescence, in contrast to the control group without electrical stimulation, which showed little distinct fluorescence. This suggests that electric eel EOD has the potential to function as an electroporator for the transfer of DNA into eukaryotic cells. While electric eel EOD is primarily associated with behaviors related to sensing, predation, and defense, it may incidentally serve as a possible mechanism for gene transfer in natural environment. This investigation represents the initial exploration of the uncharted impact of electric eel EOD, but it does not directly establish its significance within the natural environment. Further research is required to understand the ecological implications of this phenomenon. [ABSTRACT FROM AUTHOR]

The study of arthropod remains from ardiaeological contexts has the potential to reveal. information about the past thot may not necessarily nonbe readily forthcoming from faunal, botanical or artefact miatyses. Yet, iii southern Africa the field of archaeoentomology is practically non-existent. Here, 1 explore the application of excitation (fluorescence) light microscopy to an experimental sample of cruslied arthropod remains of 14 conimon species. It is shown thrit di#crent lighting pathways can reveal -valitable inforination about arthropod sclerites (pieces of their chitinous exoskeleton). and that liltraviolet light iii particular is itseful for distinguishing certain features, some of which appear to be taxon -specific, mid hence helpful for identifying highly fragmented arthropod remains recovered from archaeological settings. Furthermore, excited light can be used effectively to distinguish arthropod reinains from inert sediments and botanical fibres. While a lot of work remains to be dotte, not least of which includes the establishment of a useful arthropod reference collection and the scouring of sedinient samples. Foin excavated sites that have not had the benefit of an archaeoentomological assessment, I hope tliat this paper highlights the potential of excited light microscopy for arthropod identification and will stimulate further research on this topic. [ABSTRACT FROM AUTHOR]

Matrix vesicles are a special class of extracellular vesicles thought to actively contribute to both physiologic and pathologic mineralization. Proteomic studies have shown that matrix vesicles possess high amounts of annexin A5, suggesting that the protein might have multiple roles at the sites of calcification. Currently, Annexin A5 is thought to promote the nucleation of apatitic minerals close to the inner leaflet of the matrix vesicles' membrane enriched in phosphatidylserine and Ca2+. Herein, we aimed at unravelling a possible additional role of annexin A5 by investigating the ability of annexin A5 to adsorb on matrix-vesicle biomimetic liposomes and Langmuir monolayers made of dipalmitoylphosphatidylserine (DPPS) and dipalmitoylphosphatidylcholine (DPPC) in the absence and in the presence of Ca2+. Differential scanning calorimetry and dynamic light scattering measurements showed that Ca2+ at concentrations in the 0.5–2.0 mM range induced the aggregation of liposomes probably due to the formation of DPPS-enriched domains. However, annexin A5 avoided the aggregation of liposomes at Ca2+ concentrations lower than 1.0 mM. Surface pressure versus surface area isotherms showed that the adsorption of annexin A5 on the monolayers made of a mixture of DPPC and DPPS led to a reduction in the area of excess compared to the theoretical values, which confirmed that the protein favored attractive interactions among the membrane lipids. The stabilization of the lipid membranes by annexin A5 was also validated by recording the changes with time of the surface pressure. Finally, fluorescence microscopy images of lipid monolayers revealed the formation of spherical lipid-condensed domains that became unshaped and larger in the presence of annexin A5. Our data support the model that annexin A5 in matrix vesicles is recruited at the membrane sites enriched in phosphatidylserine and Ca2+ not only to contribute to the intraluminal mineral formation but also to stabilize the vesicles' membrane and prevent its premature rupture. [ABSTRACT FROM AUTHOR]

Coordinated cardiomyocyte contraction drives the mammalian heart to beat and circulate blood. No consensus model of cardiomyocyte geometrical arrangement exists, due to the limited spatial resolution of whole heart imaging methods and the piecemeal nature of studies based on histological sections. By combining microscopy and computer vision, we produced the first‐ever three‐dimensional cardiomyocyte orientation reconstruction across mouse ventricular walls at the micrometer scale, representing a gain of three orders of magnitude in spatial resolution. We recovered a cardiomyocyte arrangement aligned to the long‐axis direction of the outer ventricular walls. This cellular network lies in a thin shell and forms a continuum with longitudinally arranged cardiomyocytes in the inner walls, with a complex geometry at the apex. Our reconstruction methods can be applied at fine spatial scales to further understanding of heart wall electrical function and mechanics, and set the stage for the study of micron‐scale fiber remodeling in heart disease. Synopsis: Recovering cardiomyocyte geometry at the cellular scale is of fundamental interest, given the role this organization plays in driving heart wall electrical conduction and mechanics. Confocal microscopy with computer vision methods allow micrometer‐scale reconstruction of cardiomyocyte orientation.Tissue clearing, volumetric imaging using confocal microscopy, and computer vision methods reveal cardiomyocyte orientation in intact sections spanning the entire mouse heart.Direct estimation of cardiomyocyte orientation is obtained at a finer spatial resolution than that resolved by conventional diffusion tensor imaging (DTI).Cellular scale reconstruction reveals a complex geometry of smoothly varying aggregate cardiomyocyte orientations in axial, longitudinal, and apical sections of heart ventricles. [ABSTRACT FROM AUTHOR]

Background: Tuberculosis remains a major public health problem worldwide. Direct Ziehl Nelseen (ZN) is the conventional Laboratory method for diagnosis of TB. However, there are higher chances of missing TB positive cases due to insufficient sensitivity. This would eventually lead to TB transmission and hence mortality. Objective: To determine sensitivity and specificity of ZN diagnostic technique on concentrated and unconcentrated sputum samples as well as to assess how clinical, socio-demographic, and sample variables affect concentrated sputum ZN positivity. Method and Materials: This cross-sectional investigation was carried out in Mulago Hospital, covering adult TB presumptive patients. Sputum samples from 114 patients were collected and processed by both NaOCl concentration and direct ZN diagnostic techniques. Sensitivity and specificity were calculated and tabulated. Prediction of ZN positivity was assessed using Logistic regression analysis. Results: Out of the total 114 samples, 82 (71.9%) were positive by GeneXpert test (the gold standard), whereas by NaOCl concentration method 79 samples (69.3%) were found positive but with direct ZN method 65 samples (57.0%) were found positive, thus an increase of 14 samples (12.3%) in positivity was noted when used NaOCl concentration method which is highly significant with ρ

DNA damage in the brain is influenced by endogenous processes and metabolism along with exogenous exposures. Accumulation of DNA damage in the brain can contribute to various neurological disorders, including neurodegenerative diseases and neuropsychiatric disorders. Traditional methods for assessing DNA damage in the brain, such as immunohistochemistry and mass spectrometry, have provided valuable insights but are limited by their inability to map specific DNA adducts and regional distributions within the brain or genome. Recent advancements in DNA damage detection methods offer new opportunities to address these limitations and further our understanding of DNA damage and repair in the brain. Here, we review emerging techniques offering more precise and sensitive ways to detect and quantify DNA lesions in the brain or neural cells. We highlight the advancements and applications of these techniques and discuss their potential for determining the role of DNA damage in neurological disease.

ABSTRACT In this study, we investigated whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins and virus particles can be detected (i) in post-mortem kidney of fatal coronavirus disease 2019 (COVID-19) patients and (ii) in renal biopsy of patients suffering from kidney failure months after combating a SARS-CoV-2 infection. Using fluorescence microscopy, antibodies against viral proteins [nucleocapsid, membrane (M), non-structural proteins (nsp) 3, 4, and 13] and double-stranded RNA (dsRNA) were validated on SARS-CoV-2-infected Vero cells. dsRNA was detected in lipid-filled electron-lucent (white) compartments in SARS-CoV-2-producing cells. In the kidney of a patient with acute kidney failure, accumulation of SARS-CoV-2 nucleocapsid N protein was detected in tubular epithelium. In contrast, none of the other viral proteins (M, nsp3, 4, 13) nor dsRNA was detected in these regions, suggesting that no viral replication takes place in the kidney of these patients. High-resolution immunoelectron microscopy demonstrated N protein accumulation in Golgi-like structures but absence of intracellular virus particles. The presence of the N protein in Golgi-like structures in kidney of patients suggests that this protein may have an unforeseen role in post-COVID-19 renal complications. IMPORTANCE Even though the coronavirus disease 2019 (COVID-19) pandemic is slowly developing into a conventional infectious disease, the long-term effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infection are still not well understood. One of the problems is that many COVID-19 cases develop acute kidney injuries. Still, it is heavily debated whether SARS-CoV-2 virus enters and actively replicates in kidney tissue and if SARS-CoV-2 virus particles can be detected in kidney during or post-infection. Here, we demonstrated that nucleocapsid N protein was detected in kidney tubular epithelium of patients that already recovered form COVID-19. The presence of the abundantly produced N protein without signs of viral replication could have implications for the recurrence of kidney disease and have a continuing effect on the immune system.

This article presents a modified protocol for embedding and sectioning spheroids and organoids, which are increasingly used in research due to their ability to emulate living tissue. The modifications aim to reduce the distortion and damage of these fragile structures during the embedding and sectioning process. The new method involves using optimized embedding containers, a modified embedding protocol, and optimized temperatures for cryosectioning. A heat-induced antigen retrieval protocol was tested and found to significantly increase immunostaining intensity without compromising spheroid integrity. The combined approach allowed for the creation of thinner cryosections, leading to clearer and more detailed images. The results suggest that the modified protocol could be widely adopted to enhance the imaging of spheroids and organoids. • Paraformaldehyde fixation of spheroids • Antigen retrieval treatment of spheroids • Embedding in freezing medium and cryosectioning

• A simple method for fluorescently labeling yeast histones and how to re-fold them into H2A-H2B dimers and H3/H4 tetramers. • A labeling strategy for histone sub-complexes. • A method for real-time visualization of nucleosomes on dsDNA. Recent advances in single molecule imaging have allowed the evolution of biochemical techniques that directly visualize protein-DNA interactions in real-time. These techniques rely on diffraction limited total internal reflection microscopy (TIRFM), and have significantly improved our understanding of RNA transcription, DNA replication, homologous recombination, and general DNA repair in the context of chromatin. Here we described a general single molecule TIRFM technique called DNA curtains to directly visualize how enzymes function on chromatinized DNA. The goal of this manuscript is to introduce the reader to methods to express and reconstitute nucleosomes on long stretches of DNA, and to directly visualize this process using DNA curtains with TIRFM. [ABSTRACT FROM AUTHOR]

The almond, a commercially important tree nut crop worldwide, is native to the Mediterranean region. Stone fruit trees are affected by at least 14 'Candidatus Phytoplasma' species globally, among which 'Candidatus Phytoplasma asteris' is one of the most widespread phytoplasma infecting Prunus dulcis, causing aster yellows disease. Recently, almond plantations of Nauni region were consistently affected by phytoplasma, as evidenced by visible symptoms, fluorescent microscopic studies and molecular characterization. During several surveys from May to September 2020- 2022, almond aster yellows phytoplasma disease showing symptoms such as chlorosis, inward rolling, reddening, scorching and decline with an incidence as high as 40%. Leaf samples were collected from symptomatic almond trees and the presence of phytoplasma was confirmed through fluorescent microscopic studies by employing DAPI (4, 6-diamino-2-phenylindole) that showed distinctive light blue flourescent phytoplasma bodies in phloem sieve tube elements. The presence of phytoplasma in symptomatic almond trees was further confirmed using nested PCR with specific primer pairs followed by amplification of 16S rDNA and 16S-23S rDNA intergenic spacer (IS) fragments. Sequencing and BLAST analysis of expected amplicon of the 16S rDNA gene confirmed that the almond phytoplasma in Himachal Pradesh was identical to the aster yellows group phytoplasma. Phylogenetic analysis of 16S rDNA almond phytoplasma also grouped 'Prunus dulcis' aster yellows phytoplasma within 16SrI-B subgroup showed 94% nucleotide identity with 'Prunus dulcis' phytoplasma PAEs3 and 'Prunus dulcis' phytoplasma PAE28 from Iran. This research presents the first host report of 'Candidatus Phytoplasma asteris' infecting almonds in India, expanding the knowledge of the diversity and distribution of phytoplasma strains affecting almond trees globally. [ABSTRACT FROM AUTHOR]

Objective: Delayed peripheral nerve repair is complicated by nerve degeneration and atrophy that can prevent identification. We use a murine facial nerve transection model to demonstrate the efficacy of ALM‐488 (bevonescein) in labeling degenerated facial nerves with quantitative image analysis and qualitative survey data. Study Design: Prospective cohort study. Setting: Laboratory. Methods: Ten wild‐type mice underwent transection of the lower facial nerve division with subsequent degeneration. Either 9 (n = 5 mice) or 12 (n = 5 mice) weeks later, mice underwent intravenous infusion of ALM‐488 with in vivo real‐time fluorescence imaging (FL) of the facial nerve. Using ImageJ, the mean gray value of each nerve segment under white light reflectance (WLR) and FL was compared to that of adjacent soft tissue to calculate the signal‐to‐background ratio (SBR). A survey was distributed to evaluate the perceived utility of ALM‐488 in surgeon identification of degenerated nerves. Results: The mean SBR of degenerated nerves was 1.08 (standard deviation [SD]: 0.07) under WLR and 2.11 (SD: 0.31) under FL (p < 0.001). In mice with degenerated nerves, survey participants identified on average 3.01 (SD: 1.84) nerve branches under WLR and 5.73 (SD: 1.88) under FL (p < 0.0001). Under FL, 47 of 48 survey responses correctly identified isolated, degenerated nerves; in contrast, only 12 responses identified degenerated nerves under WLR (p < 0.0001). Conclusion: Preoperative intravenous infusion of ALM‐488 with FL improves the identification of degenerated facial nerves. ALM‐488 also improves surgeon confidence in nerve identification, particularly in degenerated nerve branches that are not visible with WLR. [ABSTRACT FROM AUTHOR]

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with exposure to repetitive head impacts (RHI) and characterized by perivascular accumulations of hyperphosphorylated tau protein (p-tau) at the depths of the cortical sulci. Studies of living athletes exposed to RHI, including concussive and nonconcussive impacts, have shown increased blood–brain barrier permeability, reduced cerebral blood flow, and alterations in vasoreactivity. Blood–brain barrier abnormalities have also been reported in individuals neuropathologically diagnosed with CTE. To further investigate the three-dimensional microvascular changes in individuals diagnosed with CTE and controls, we used SHIELD tissue processing and passive delipidation to optically clear and label blocks of postmortem human dorsolateral frontal cortex. We used fluorescent confocal microscopy to quantitate vascular branch density and fraction volume. We compared the findings in 41 male brain donors, age at death 31–89 years, mean age 64 years, including 12 donors with low CTE (McKee stage I–II), 13 with high CTE (McKee stage III–IV) to 16 age- and sex-matched non-CTE controls (7 with RHI exposure and 9 with no RHI exposure). The density of vessel branches in the gray matter sulcus was significantly greater in CTE cases than in controls. The ratios of sulcus versus gyrus vessel branch density and fraction volume were also greater in CTE than in controls and significantly above one for the CTE group. Hyperphosphorylated tau pathology density correlated with gray matter sulcus fraction volume. These findings point towards increased vascular coverage and branching in the dorsolateral frontal cortex (DLF) sulci in CTE, that correlates with p-tau pathology. [ABSTRACT FROM AUTHOR]

NF-κB signaling has broad effects on cell survival, tissue growth, and proliferation activities. It controls many genes that are involved in inflammation and thus is a key player in many inflammatory diseases. The elevation of NF-κB activators is associated with elevated mortality, especially in cancer and cardiovascular diseases. The zebrafish has emerged as an important model for whole-organism in vivo modeling in translational research. In vertebrates, in-vivo spatial resolution is limited due to normal opacification of skin and subdermal structure. For in vivo imaging, skin transparency by blocking the pigmentation via chemical inhibition is required and the maintenance of this transparency is vital. The Casper(roy−/−, nacre−/−) mutant of zebrafish maintains this transparency throughout its life and serves as an ideal combination of sensitivity and resolution for in vivo stem cell analyses and imaging. We developed an NF-kB:GFP/Casper transparent transgenic zebrafish cellular phenotype to study inflammatory processes in vivo. We outline the experimental setup to generate a transparent transgenic NF-kB/Casper strain of zebrafish through the cross-breeding of Casper and NF-kB transgenic adult fish and have generated F01 in the form of heterozygous progeny. The transgenic F01 progeny was further inbred to generate heterozygous progenies from F1 to F4 generations. Furthermore, it continued to successfully develop the homozygous strain Tg(6xNF-kB:EGFP); Casper(roy−/−, nacre−/−) in the F05 generation. This novel strain of F05 generation showed 100% homozygosity in the transgenic transparent progeny of Tg(6xNF-kB:EGFP); Casper(roy−/−, nacre−/−). The strain has been confirmed by generating the F06 generation of homozygous progeny and again verified and validated for its homogeneity in the F07 generation. The newly developed novel transparent transgenic strain of the NF-kB reporter line has been coined as "Tg(6xNF-kB:EGFP); Casper(roy−/−, nacre−/−)gmc1". We have established a newly generated phenotype of transparent transgenic zebrafish for time-lapse in vivo confocal microscopy to study the cellular phenotype and pathologies at the cellular level over time. This will allow for quantifying the changes in the NF-kB functional activities over time and allow the comparison of control and cardiac-oncology experimental therapeutics. We validated the newly developed Tg(6xNF-kB:EGFP); Casper(roy−/−, nacre−/−)gmc1 homozygous strain of zebrafish by studying the inflammatory response to bacterial lipopolysaccharide (LPS) exposure, tolerance, and the inhibitory role of a potential novel drug candidate against LPS-induced inflammation. The results establish the unique application of newly developed strains by identifying hit and lead drug candidates for experimental therapeutics. [ABSTRACT FROM AUTHOR]

Multiple stains have been historically utilized in electron microscopy to provide proper contrast and superior image quality enabling the discovery of ultrastructures. However, the use of these stains in microbiological viability assessment has been limited. Phosphotungstic acid (PTA) staining is a common negative stain used in scanning electron microscopy (SEM). Here, we investigate the feasibility of a new SEM-PTA assay, aiming to determine both viable and dead microbes. The optimal sample preparation was established by staining bacteria with different PTA concentrations and incubation times. Once the assay conditions were set, we applied the protocol to various samples, evaluating bacterial viability under different conditions, and comparing SEM-PTA results to culture. The five minutes 10% PTA staining exhibited a strong distinction between viable micro-organisms perceived as hypo-dense, and dead micro-organisms displaying intense internal staining which was confirmed by high Tungsten (W) peak on the EDX spectra. SEM-PTA viability count after freezing, freeze-drying, or oxygen exposure, were concordant with culture. To our knowledge, this study is the first contribution towards PTA staining of live and dead bacteria. The SEM-PTA strategy demonstrated the feasibility of a rapid, cost-effective and efficient viability assay, presenting an open-view of the sample, and providing a potentially valuable tool for applications in microbiome investigations and antimicrobial susceptibility testing.

The almond, a commercially important tree nut crop worldwide, is native to the Mediterranean region. Stone fruit trees are affected by at least 14 ‘Candidatus Phytoplasma’ species globally, among which ‘Candidatus Phytoplasma asteris’ is one of the most widespread phytoplasma infecting Prunus dulcis, causing aster yellows disease. Recently, almond plantations of Nauni region were consistently affected by phytoplasma, as evidenced by visible symptoms, fluorescent microscopic studies and molecular characterization. During several surveys from May to September 2020–2022, almond aster yellows phytoplasma disease showing symptoms such as chlorosis, inward rolling, reddening, scorching and decline with an incidence as high as 40%. Leaf samples were collected from symptomatic almond trees and the presence of phytoplasma was confirmed through fluorescent microscopic studies by employing DAPI (4, 6-diamino-2-phenylindole) that showed distinctive light blue flourescent phytoplasma bodies in phloem sieve tube elements. The presence of phytoplasma in symptomatic almond trees was further confirmed using nested PCR with specific primer pairs followed by amplification of 16S rDNA and 16S-23S rDNA intergenic spacer (IS) fragments. Sequencing and BLAST analysis of expected amplicon of the 16S rDNA gene confirmed that the almond phytoplasma in Himachal Pradesh was identical to the aster yellows group phytoplasma. Phylogenetic analysis of 16S rDNA almond phytoplasma also grouped ‘Prunus dulcis’ aster yellows phytoplasma within 16SrI-B subgroup showed 94% nucleotide identity with ‘Prunus dulcis’ phytoplasma PAEs3 and ‘Prunus dulcis’ phytoplasma PAE28 from Iran. This research presents the first host report of ‘Candidatus Phytoplasma asteris’ infecting almonds in India, expanding the knowledge of the diversity and distribution of phytoplasma strains affecting almond trees globally.

Neutrophil extracellular traps (NETs), pathogen-ensnaring structures formed by neutrophils by expelling their DNA into the environment, are believed to play an important role in immunity and autoimmune diseases. In recent years, a growing attention has been put into developing software tools to quantify NETs in fluorescent microscopy images. However, current solutions require large, manually-prepared training data sets, are difficult to use for users without background in computer science, or have limited capabilities. To overcome these problems, we developed Trapalyzer, a computer program for automatic quantification of NETs. Trapalyzer analyzes fluorescent microscopy images of samples double-stained with a cell-permeable and a cell-impermeable dye, such as the popular combination of Hoechst 33342 and SYTOX™Green. The programis designed with emphasis on software ergonomy and accompanied with step-bystep tutorials to make its use easy and intuitive. The installation and configuration of the software takes less than half an hour for an untrained user. In addition to NETs, Trapalyzer detects, classifies and counts neutrophils at different stages of NET formation, allowing for gaining a greater insight into this process. It is the first tool that makes this possible without large training data sets. At the same time, it attains a precision of classification on par with state-of-the-art machine learning algorithms. As an example application, we show how to use Trapalyzer to study NET release in a neutrophil-bacteria co-culture. Here, after configuration, Trapalyzer processed 121 images and detected and classified 16 000 ROIs in approximately three minutes on a personal computer. The software and usage tutorials are available at https://github.com/Czaki/Trapalyzer. [ABSTRACT FROM AUTHOR]

Fluorescently labeled proteins absorb and emit light, appearing as Gaussian spots in fluorescence imaging. When fluorescent tags are added to cytoskeletal polymers such as microtubules, a line of fluorescence and even non-linear structures results. While much progress has been made in techniques for imaging and microscopy, image analysis is less well-developed. Current analysis of fluorescent microtubules uses either manual tools, such as kymographs, or automated software. As a result, our ability to quantify microtubule dynamics and organization from light microscopy remains limited. Despite the development of automated microtubule analysis tools for in vitro studies, analysis of images from cells often depends heavily on manual analysis. One of the main reasons for this disparity is the low signal-to-noise ratio in cells, where background fluorescence is typically higher than in reconstituted systems. Here, we present the Toolkit for Automated Microtubule Tracking (TAMiT), which automatically detects, optimizes, and tracks fluorescent microtubules in living yeast cells with sub-pixel accuracy. Using basic information about microtubule organization, TAMiT detects linear and curved polymers using a geometrical scanning technique. Images are fit via an optimization problem for the microtubule image parameters that are solved using non-linear least squares in Matlab. We benchmark our software using simulated images and show that it reliably detects microtubules, even at low signal-to-noise ratios. Then, we use TAMiT to measure monopolar spindle microtubule bundle number, length, and lifetime in a large dataset that includes several S. pombe mutants that affect microtubule dynamics and bundling. The results from the automated analysis are consistent with previous work and suggest a direct role for CLASP/Cls1 in bundling spindle microtubules. We also illustrate automated tracking of single curved astral microtubules in S. cerevisiae, with measurement of dynamic instability parameters. The results obtained with our fully-automated software are similar to results using hand-tracked measurements. Therefore, TAMiT can facilitate automated analysis of spindle and microtubule dynamics in yeast cells. [ABSTRACT FROM AUTHOR]

We previously developed an incoherent holography technique for use in lattice light sheet (LLS) microscopes that represents a specialized adaptation of light sheet microscopy. Light sheet instruments resolve 3D information by illuminating the sample at 90° to the imaging plane with a sheet of laser light that excites fluorophores in the sample only in a narrow plane. Imaging this plane and then moving it in the imaging z-axis allows construction of the sample volume. Among these types of instruments, LLS microscopy gives higher z-axis resolution and tissue depth penetration. It has a similar working principle to light sheet fluorescence microscopy but uses a lattice configuration of Bessel beams instead of Gaussian beams. Our incoherent light detection technique replaces the glass tube lens of the original LLS with a dual diffractive lens system to retrieve the axial depth of the sample. Here, we show that the system is applicable to all light sheet instruments. To make a direct comparison in the same emission light path, we can imitate the nature of non-Bessel light sheet systems by altering the mask annuli used to create Bessel beams in the LLS system. We change the diffractive mask annuli from a higher NA anulus to a smaller NA anulus. This generates a Gaussian excitation beam similar to conventional light sheet systems. Using this approach, we propose an incoherent light detection system for light sheet 3D imaging by choosing a variable NA and moving only the light sheet while keeping the sample stage and detection microscope objective stationary. [ABSTRACT FROM AUTHOR]

Abstract Background In fluorescence microscopy, co-localization refers to the spatial overlap between different fluorescent labels in cells. The degree of overlap between two or more channels in a microscope may reveal a physical interaction or topological functional interconnection between molecules. Recent advances in the imaging field require the development of specialized computational analysis software for the unbiased assessment of fluorescently labelled microscopy images. Results Here we present SpotitPy, a semi-automated image analysis tool for 2D object-based co-localization. SpotitPy allows the user to select fluorescent labels and perform a semi-automated and robust segmentation of the region of interest in distinct cell types. The workflow integrates advanced pre-processing manipulations for de-noising and in-depth semi-automated quantification of the co-localized fluorescent labels in two different channels. We validated SpotitPy by quantitatively assessing the presence of cytoplasmic ribonucleoprotein granules, e.g. processing (P) bodies, under conditions that challenge mRNA translation, thus highlighting SpotitPy benefits for semi-automatic, accurate analysis of large image datasets in eukaryotic cells. SpotitPy comes in a command line interface or a simple graphical user interphase and can be used as a standalone application. Conclusions Overall, we present a novel and user-friendly tool that performs a semi-automated image analysis for 2D object-based co-localization. SpotitPy can provide reproducible and robust quantifications for large datasets within a limited timeframe. The software is open-source and can be found in the GitHub project repository: ( https://github.com/alexiaales/SpotitPy ).

Abstract Deviation of the H+ concentration from optimum values within the organelles is closely associated with irregular cellular functions that cause the onset of various diseases. Therefore, determining subcellular pH values in live cells and tissues is valuable for diagnostic purposes. In this study, we report a novel ratiometric fluorescence probe 1H-pyrazole-3-carboxylic acid, 4-(benzo[d]thiazol-2-yl)-3-(2,4-dihydroxy-3-methylphenyl)-1H-pyrazole-5-carboxylicacid4-(2-benz othiazolyl)-5-(2,4-dihydroxy-3-methylphenyl), to which we will refer as ThiAKS Green (Thiazole AKyol shifting green), that is pH sensitive. The results presented here show that the probe can penetrate the cell membrane in less than 30 minutes and does not show any detectable toxicity. The measured color shifts up on pH change are linear and most significant around physiological pH (pKa=7.45), thus making this probe suitable for live-cell imaging and intracellular pH measurements. During the long-incubation periods following the application of the probe and the fluorescent microscopy measurements, it shows stable properties and is easy to detect in live cells. In conclusion, the results suggest that ThiAKS Green can be used to obtain precise information on the H+ distribution at various compartments of the live cells.

Deviation of the H+ concentration from optimum values within the organelles is closely associated with irregular cellular functions that cause the onset of various diseases. Therefore, determining subcellular pH values in live cells and tissues is valuable for diagnostic purposes. In this study, we report a novel ratiometric fluorescence probe 1H-pyrazole-3-carboxylic acid, 4-(benzo[d]thiazol-2-yl)-3-(2,4-dihydroxy-3-methylphenyl)-1H-pyrazole-5-carboxylicacid4-(2-benz othiazolyl)-5-(2,4-dihydroxy-3-methylphenyl), to which we will refer as ThiAKS Green (Thiazole AKyol shifting green), that is pH sensitive. The results presented here show that the probe can penetrate the cell membrane in less than 30 minutes and does not show any detectable toxicity. The measured color shifts up on pH change are linear and most significant around physiological pH (pKa=7.45), thus making this probe suitable for live-cell imaging and intracellular pH measurements. During the long-incubation periods following the application of the probe and the fluorescent microscopy measurements, it shows stable properties and is easy to detect in live cells. In conclusion, the results suggest that ThiAKS Green can be used to obtain precise information on the H+ distribution at various compartments of the live cells. [ABSTRACT FROM AUTHOR]

SARS-CoV-2, one of the human RNA viruses, is widely studied around the world. Significant efforts have been made to understand its molecular mechanisms of action and how it interacts with epithelial cells and the human microbiome since it has also been observed in gut microbiome bacteria. Many studies emphasize the importance of surface immunity and also that the mucosal system is critical in the interaction of the pathogen with the cells of the oral, nasal, pharyngeal, and intestinal epithelium. Recent studies have shown how bacteria in the human gut microbiome produce toxins capable of altering the classical mechanisms of interaction of viruses with surface cells. This paper presents a simple approach to highlight the initial behavior of a novel pathogen, SARS-CoV-2, on the human microbiome. The immunofluorescence microscopy technique can be combined with spectral counting performed at mass spectrometry of viral peptides in bacterial cultures, along with identification of the presence of D-amino acids within viral peptides in bacterial cultures and in patients' blood. This approach makes it possible to establish the possible expression or increase of viral RNA viruses in general and SARS-CoV-2, as discussed in this study, and to determine whether or not the microbiome is involved in the pathogenetic mechanisms of the viruses. This novel combined approach can provide information more rapidly, avoiding the biases of virological diagnosis and identifying whether a virus can interact with, bind to, and infect bacteria and epithelial cells. Understanding whether some viruses have bacteriophagic behavior allows vaccine therapies to be focused either toward certain toxins produced by bacteria in the microbiome or toward finding inert or symbiotic viral mutations with the human microbiome. This new knowledge opens a scenario on a possible future vaccine: the probiotics vaccine, engineered with the right resistance to viruses that attach to both the epithelium human surface and gut microbiome bacteria. [ABSTRACT FROM AUTHOR]

The threat of antimicrobial-resistant bacteria is ever increasing and over the past-decades development of novel therapeutic counter measurements have virtually come to a halt. This circumstance calls for interdisciplinary approaches to design, evaluate and validate the mode of action of novel antibacterial compounds. Hereby, carbosilane dendritic systems that exhibit antimicrobial properties have the potential to serve as synthetic and rationally designed molecules for therapeutic use. The bow-tie type topology of BDTL049 was recently investigated against the Gram-positive model organism Bacillus subtilis, revealing strong bactericidal properties. In this study, we follow up on open questions concerning the usability of BDTL049. For this, we synthesized a fluorescent-labeled version of BDTL049 that maintained all antimicrobial features to unravel the interaction of the compound and bacterial membrane. Subsequently, we highlight the bacterial sensitivity against BDTL049 by performing a mutational study of known resistance determinants. Finally, we address the cytotoxicity of the compound in human cells, unexpectedly revealing a high sensitivity of the eukaryotic cells upon BDTL049 exposure. The insights presented here further elaborate on the unique features of BDTL049 as a promising candidate as an antimicrobial agent while not precluding that further rounds of rational designing are needed to decrease cytotoxicity to ultimately pave the way for synthetic antibiotics toward clinical applicability. [ABSTRACT FROM AUTHOR]

Neutrophil extracellular traps (NETs), pathogen-ensnaring structures formed by neutrophils by expelling their DNA into the environment, are believed to play an important role in immunity and autoimmune diseases. In recent years, a growing attention has been put into developing software tools to quantify NETs in fluorescent microscopy images. However, current solutions require large, manually-prepared training data sets, are difficult to use for users without background in computer science, or have limited capabilities. To overcome these problems, we developed Trapalyzer, a computer program for automatic quantification of NETs. Trapalyzer analyzes fluorescent microscopy images of samples double-stained with a cell-permeable and a cell-impermeable dye, such as the popular combination of Hoechst 33342 and SYTOX™ Green. The program is designed with emphasis on software ergonomy and accompanied with step-by-step tutorials to make its use easy and intuitive. The installation and configuration of the software takes less than half an hour for an untrained user. In addition to NETs, Trapalyzer detects, classifies and counts neutrophils at different stages of NET formation, allowing for gaining a greater insight into this process. It is the first tool that makes this possible without large training data sets. At the same time, it attains a precision of classification on par with state-of-the-art machine learning algorithms. As an example application, we show how to use Trapalyzer to study NET release in a neutrophil-bacteria co-culture. Here, after configuration, Trapalyzer processed 121 images and detected and classified 16 000 ROIs in approximately three minutes on a personal computer. The software and usage tutorials are available at https://github.com/Czaki/Trapalyzer.

Dendrites are the primary site of synaptic activity in neurons and changes in synapses are often the first pathological stage in neurodegenerative diseases. Molecular studies of these changes rely on morphological analysis of the imaging of somas and dendritic arbors of cultured or primary neurons. As research on preventing or reversing synaptic degeneration develops, demands increase for user-friendly 2D neurite analyzers without undermining accuracy and reproducibility. The most common method of 2D neurite analysis is manual by using ImageJ. This method relies completely on the user's ability to distinguish the shape and size of dendrites and trace morphology with a series of straight connected lines. Semi-automatic methods have also been developed, such as the NeuronJ plugin for ImageJ. These methods still rely on the user to identify the start and end of the dendrites, but automatically determine the shape, reducing the likelihood of user bias and speeding the process. Some automatic methods have been developed through image processing software, like ImagePro. These programs tend to be expensive, but have been shown to be fast and effective, limiting user interaction. In this study, we compare three methods of neurite analysis-ImageJ, NeuronJ, and ImagePro-in measuring the soma size, number of dendrites, and length of dendrites per cell of embryonic sympathetic rat neurons with BMP-7-induced dendritic growth. Our results indicate that ImageJ and NeuronJ measurements were of similar effectiveness and consistent throughout various images and multiple trials. NeuronJ required less user interaction in measuring the length of dendrites than the manual method and therefore, was faster and less labor intensive. Conversely, ImagePro tended to be inconsistent across images, overestimating both soma size and the number of dendrites per cell while underestimating the length of dendrites. Overall, NeuronJ, in conjunction with ImageJ, is the most reliable and efficient method of 2D neurite analysis tested in the present study.

Medicinal plants are natural resources of diversified therapeutic metabolites. Lavandula stoechas has been used traditionally for the management of different metabolic disorders. However, studies on the anticancer characteristics of certain bioactive compounds present in this plant are very limited. In view of this, the aim of the present study was to isolate oleanolic acid (a triterpenoid) from L. stoechas and assess its anticancer trait against breast carcinoma cells (MCF-7) via induced apoptosis. Initially, oleanolic acid was isolated from the ethyl acetate fraction of L. stoechas using standard extraction protocols. Furthermore, the structure of compound was established using mass spectrometry, FT-IR, 1H NMR, and 2D NMR (HSQC) techniques. In vitro antiproliferative effect of oleanolic acid was assessed against breast carcinoma cells (MCF-7 and MDA-MB-231) and non-cancerous cells (BHK-21) using the MTT assay. Oleanolic acid showed prominent cytotoxicity of 72.44 ± 3.33 and 78.55 ± 2.67 % against MCF-7 and MDA-MB-231 cells with IC50 values of 13.09 and 160.22 µg/mL, respectively. Moreover, the compound showed negligible toxicity against the BHK-21 cell line. Furthermore, the apoptotic features in oleanolic acid-treated MCF-7 cells were determined using fluorescent microscopy, which showed typical nuclear condensation, increased ROS generation, and the loss of outer mitochondrial membrane potentials. The levels of activated caspases in MCF-7 cancer cells were estimated using a fluorescent kit, showing a significant increment in caspase-9 and caspase-7 for oleanolic acid-treated MCF-7 cells. Moreover, oleanolic acid showed down-regulation of the Bcl2 and PDGF genes. Our findings demonstrated the pivotal role of oleanolic acid as pronounced anticancer agent against MCF-7 cell lines by inducing apoptotic mechanism via intrinsic pathway.

Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications. [ABSTRACT FROM AUTHOR]

The possibility of dissemination of bone marrow multipotent stromal cells stained with Vybrant CM-Dil after injection into an intact and resected liver was studied using luminescence microscopy. Labeled cells were found in the kidneys, spleen, lungs, axillary, mesenteric, and inguinal lymph nodes. We observed dissemination of multipotent stromal cells and their detritus throughout the body that occurred only after filtration in the lungs, where most cells underwent destruction. Perivascularly located macrophages in various organs can phagocytize multipotent stromal cells and their detritus from blood vessels. The content of objects labeled with Vybrant CM-Dil in distant organs was significantly lower after multipotent stromal cell injection into the resected liver, which was associated with the deposition of cells in the damaged area of the organ and their partial entry into the abdominal cavity. [ABSTRACT FROM AUTHOR]

Background: In fluorescence microscopy, co-localization refers to the spatial overlap between different fluorescent labels in cells. The degree of overlap between two or more channels in a microscope may reveal a physical interaction or topological functional interconnection between molecules. Recent advances in the imaging field require the development of specialized computational analysis software for the unbiased assessment of fluorescently labelled microscopy images. Results: Here we present SpotitPy, a semi-automated image analysis tool for 2D object-based co-localization. SpotitPy allows the user to select fluorescent labels and perform a semi-automated and robust segmentation of the region of interest in distinct cell types. The workflow integrates advanced pre-processing manipulations for de-noising and in-depth semi-automated quantification of the co-localized fluorescent labels in two different channels. We validated SpotitPy by quantitatively assessing the presence of cytoplasmic ribonucleoprotein granules, e.g. processing (P) bodies, under conditions that challenge mRNA translation, thus highlighting SpotitPy benefits for semi-automatic, accurate analysis of large image datasets in eukaryotic cells. SpotitPy comes in a command line interface or a simple graphical user interphase and can be used as a standalone application. Conclusions: Overall, we present a novel and user-friendly tool that performs a semi-automated image analysis for 2D object-based co-localization. SpotitPy can provide reproducible and robust quantifications for large datasets within a limited timeframe. The software is open-source and can be found in the GitHub project repository: (https://github.com/alexiaales/SpotitPy). [ABSTRACT FROM AUTHOR]

Leukocyte quantification from whole blood can aid in detecting and managing infections, cardiovascular diseases, and immune system responses. In addition to traditional leukocyte quantification devices such as flow cytometers and benchtop fluorescent microscopes, smartphone-based particle quantifiers are becoming popular because they provide results at a fraction of the cost. One major limitation of these smartphone-based devices is their dependence on desktop computers for data processing, which keeps them from reaching their true translation potential as point of care (POC) devices. In this paper, we present a computer vision and machine learning-enabled methodology to count particles imaged from our 3D printed smartphone-coupled fluorescent microscope. Multiple convolution neural networks (CNN) using different filter sizes were implemented and trained with various learning rates (0.001, 0.0001) and batch sizes (8,16,32). The performance of these trained networks was then tested on green fluorescent microparticles and leukocytes and compared against the ground truth obtained using ImageJ. An R2 value of 0.99 was observed. Next, when cross-validation was done to validate the efficacy of the designed CNN architecture, and the predicted results showed a good correlation (R2 = 0.99) when compared against the ground truth. The performance of the trained model was also evaluated on particles conjugated with a different fluorophore and an R2 value of 0.99 was observed, showcasing its efficacy and versatility. This trained model was then integrated into an Application Programming Interface (API) and is available online for the broader community usage.

This work shows the synthesis of four new lanthanide complexes of Gd(III) (1), Eu(III) (2), Dy(III) (3) and Yb(III) (4) ions, using two polydentate ligands F and L in order to evaluate their potential application on the contrast-imaging by fluorescence microscopy (MF), nuclear magnetic resonance (RMI) and as antibacterial agents. We propose a structure where both ligands are bound to the metal centre through -OH, -N- and -COO- groups, exhibiting an apparent coordination number of 7. Moreover, r1 molar relaxivities obtained demonstrates that all the complexes had the capability to accelerate longitudinal relaxation times (T1) of water, with a r1 value of 6.45 mmol-1·L-1·s-1 for compound 1, which was higher than r1 of 2.25 mmol-1·L-1·s-1 corresponding to commercial drug Dotarem® employed for RMI. Furthermore, all quantum yields of fluorescence, in reference to fluorescein, where lower than 1 %, showing a poor performance in emission processes of visible radiation. Stability constants determined as (-log[kap]) were between 21 and 18, being even better than some contrast agents. Compound 2 managed to inhibit the growth of Gram-positive and Gram-negative bacterial strains evaluated with minimum inhibitory concentrations (MICs) of up to 250 mg·L-1, in general the high MICs suggested that the complexes obtained could have a potential application in prokaryotic cell fluorescence contrast. Finally, DNA binding experiments showed that all complexes had the capability to bind DNA strands by a possible intercalation mechanism. [ABSTRACT FROM AUTHOR]

During infection, the giant phiKZ phage forms a specialized structure at the center of the host cell called the phage nucleus. This structure is crucial for safeguarding viral DNA against bacterial nucleases and for segregating the transcriptional activities of late genes. Here, we describe a morphological entity, the early phage infection (EPI) vesicle, which appears to be responsible for earlier gene segregation at the beginning of the infection process. Using cryo-electron microscopy, electron tomography (ET), and fluorescence microscopy with membrane-specific dyes, we demonstrated that the EPI vesicle is enclosed in a lipid bilayer originating, apparently, from the inner membrane of the bacterial cell. Our investigations further disclose that the phiKZ EPI vesicle contains both viral DNA and viral RNA polymerase (vRNAP). We have observed that the EPI vesicle migrates from the cell pole to the center of the bacterial cell together with ChmA, the primary protein of the phage nucleus. The phage DNA is transported into the phage nucleus after phage maturation, but the EPI vesicle remains outside. We hypothesized that the EPI vesicle acts as a membrane transport agent, efficiently delivering phage DNA to the phage nucleus while protecting it from the nucleases of the bacterium., Importance: Our study shed light on the processes of phage phiKZ early infection stage, expanding our understanding of possible strategies for the development of phage infection. We show that phiKZ virion content during injection is packed inside special membrane structures called early phage infection (EPI) membrane vesicles originating from the bacterial inner cell membrane. We demonstrated the EPI vesicle fulfilled the role of the safety transport unit for the phage genome to the phage nucleus, where the phage DNA would be replicated and protected from bacterial immune systems.

Fluorescently labeled proteins absorb and emit light, appearing as Gaussian spots in fluorescence imaging. When fluorescent tags are added to cytoskeletal polymers such as microtubules, a line of fluorescence and even non-linear structures results. While much progress has been made in techniques for imaging and microscopy, image analysis is less well-developed. Current analysis of fluorescent microtubules uses either manual tools, such as kymographs, or automated software. As a result, our ability to quantify microtubule dynamics and organization from light microscopy remains limited. Despite the development of automated microtubule analysis tools for in vitro studies, analysis of images from cells often depends heavily on manual analysis. One of the main reasons for this disparity is the low signal-to-noise ratio in cells, where background fluorescence is typically higher than in reconstituted systems. Here, we present the Toolkit for Automated Microtubule Tracking (TAMiT), which automatically detects, optimizes, and tracks fluorescent microtubules in living yeast cells with sub-pixel accuracy. Using basic information about microtubule organization, TAMiT detects linear and curved polymers using a geometrical scanning technique. Images are fit via an optimization problem for the microtubule image parameters that are solved using non-linear least squares in Matlab. We benchmark our software using simulated images and show that it reliably detects microtubules, even at low signal-to-noise ratios. Then, we use TAMiT to measure monopolar spindle microtubule bundle number, length, and lifetime in a large dataset that includes several S. pombe mutants that affect microtubule dynamics and bundling. The results from the automated analysis are consistent with previous work and suggest a direct role for CLASP/Cls1 in bundling spindle microtubules. We also illustrate automated tracking of single curved astral microtubules in S. cerevisiae, with measurement of dynamic instability parameters. The results obtained with our fully-automated software are similar to results using hand-tracked measurements. Therefore, TAMiT can facilitate automated analysis of spindle and microtubule dynamics in yeast cells.

Bacteria living on the aerial parts of plant come from rhizosphere or/and above ground environment. Leaf associated microbes flourish in harsh conditions, adaptable to other environments, have ability to move across plant and colonize the other parts of plants as well. Imaging of GFP-labelled epiphytic phyllospheric bacteria Pseudomonas sp. MehA-P42 on root, stem and leaves of two sunflower hybrids was done by fluorescence microscopy and CLSM (confocal laser scanning microscope). Phyllo-epiphytic bacteria applied to seeds not even reached and colonized the destined aerial parts but also colonized roots and stem surface of plants. The internal localization (in the inter- and intra-cellular compartments of leaves, stems and roots) of GFP-labeled Pseudomonas sp. MehA-P42 was revealed by CLSM. Phylloepiphytic bacteria isolated from one sunflower variety (Hysun-39) established an association with another variety (Hysun-33) through colonization in and on the root stem and leaves surface. Study indicated the movement of plant associated bacteria along phytosphere as well as the ability of phyllospheric bacterial isolates to adapt the environment and flourish on the plants other than the native. This supports the field application of the phyllospheric bacterial isolates to seeds, roots of plant or in rhizosphere as plant stimulator and biocontrol agent. [ABSTRACT FROM AUTHOR]

Introduction: Multidrug-resistant Mycobacterium tuberculosis (MDR-TB) is one of the leading causes of death in the world. The resource constraints make it difficult to diagnose and monitor the cases of MDR-TB. GeneXpert is a recognized tool used to diagnose the patients of pulmonary tuberculosis in clinical settings across the globe. Methodology: The present one-year cross-sectional study was conducted to estimate the occurrence of MDR-TB in patients with pulmonary TB. A total of 1000 patients suspected of pulmonary tuberculosis were included in this study. A random convenient sampling technique was done to collect the sputum samples (twice) from the patients. Samples were processed for the detection of Mycobacterium tuberculosis using conventional detection methods like the Ziehl Nelson staining method and fluorescent microscopy. Additionally, Cepheid GeneXpert was used for molecular detection of MDR-TB in smear-positive samples of pulmonary tuberculosis by amplifying the rifampicin resistance determining region (RRDR; rpoB gene). All the tests were performed in the biosafety level III lab of District Headquarters Hospital Nankana Sahib. Results: It was observed that 103 (10.3%) individuals were diagnosed as positive for tuberculosis among 1000 patients. Among these 103 TB positive cases, there were 11 (10.7%) patients diagnosed with rifampicin resistance gene (RR-Gene) of Mycobacterium tuberculosis. Conclusions: Overall findings of the study showed that MDR-TB is prevalent in pulmonary TB patients and GeneXpert is the most sensitive technique for early diagnosis of the disease, which may be very helpful in the treatment and control of this public health menace in low and middle-income countries. [ABSTRACT FROM AUTHOR]

In Sohag City, 400 samples were collected from different food markets of different meat products from two companies with high and low prices (e.g., minced meat, kofta sausage, beef burger, and luncheon meat) for determining food fraud. Light, fluorescence, and scanning electron microscopy (SEM) were used to examine the samples. "Special histochemical stains" permit the microscopic examination of different cell types, structures, and/or microorganisms. Histological examination revealed variant tissue types, besides skeletal muscles. Nuchal ligaments, bones, hyaline cartilages, white fibrocartilages, large and medium arteries, cardiac muscles, tendons, and collagenous connective tissues comprised the capsule of a parenchymatous organ. Additionally, a crystal of food additives was recognized using light microscopy and SEM. SEM allows the visualization of bacterial contamination. Using different microscopic anatomy techniques is an efficient methodology for qualitative evaluations of various meat products. No difference in quality was observed between low‐ and high‐priced meat products. [ABSTRACT FROM AUTHOR]