Selective visual staining of polyurethane microplastics by novel colorimetric and near-infrared (NIR) fluorescent dye: Application to environmental water and natural soil samples

Microplastics can cause environmental pollution and ecosystem destruction as well as human health problems. Among the types of microplastics, polyurethane (PU) is particularly resistant to heat and difficult to decompose, causing disposal problems, and is evaluated as one of the most hazardous polymers. We present a novel colorimetric and near-infrared (NIR) fluorescence dye, (E)-N-(2-((4-(diphenylamino)benzylidene)amino)phenyl)- 7-nitrobenzo[c][1,2,5]oxadiazol-4-amine (DPNA), designed for selective visual PU microplastic staining. The intramolecular charge transfer (ICT) properties of DPNA are demonstrated through density functional theory (DFT) calculations along with solvatochromic shift. DPNA exhibits red color and red fluorescence emission, showing promising potential as a staining dye. To achieve selective PU microplastic staining, we establish an optimized experimental procedure with the staining dye DPNA by evaluating the staining efficiency under different staining solvent compositions and staining times. DPNA can distinguish PU by both red fluorescence signal and red coloration among different types of microplastics. In addition, DPNA well stain fresh PUs with diverse sizes and at various pH range of 5-9, and the aged PUs can also be dyed as effectively as the fresh PU. Most importantly, DPNA selectively stains PU among 11 types of microplastics and 5 types of natural particles in environmental water and soil with and without any pre-treatments. The adsorption mechanism of DPNA on PU microplastic is demonstrated through field emission scanning electron microscopes (FE-SEM), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), X-ray photoelectron spectroscopy (XPS), and non-covalent interaction (NCI)-reduced density gradient (RDG) analyses, and proposed that intermolecular hydrogen bonding has a significant effect.

Microscopy methods for Clostridioides difficile

Microscopic technologies including light and fluorescent, transmission electron microscopy (TEM), scanning electron microscopy (SEM), and cryo-electron microscopy have been widely utilized to visualize Clostridioides difficile at the molecular, cellular, community, and structural biology level. This comprehensive review summarizes the microscopy tools (fluorescent and reporter system) in their use to study different aspects of C. difficile life cycle and virulence (sporulation, germination) or applications (detection of C. difficile or use of antimicrobials). With these developing techniques, microscopy tools will be able to find broader applications and address more challenging questions to study C. difficile and C. difficile infection.

Interactive effects of cyanobacterial metabolites aeruginosin-98B, anabaenopeptin-B and cylindrospermopsin on physiological parameters and novel in vivo fluorescent indicators in Chironomus aprilinus larvae

We aimed to determine the effects of single cyanobacterial metabolites aeruginosin-B (AER-B), anabaenopeptin-B (ANA-B), cylindrospermopsin (CYL), their binary and ternary mixtures on biomarkers of Chironomus aprilinus larvae: oxygen consumption, fat body structure and two novel fluorescent indicators: imaging of nuclei in cells of body integument, and the catecholamine level. The obtained results showed that oxygen consumption was inhibited by single tested cyanobacterial metabolites except for ANA-B at the lowest concentration (250 μg/L). Although the mixtures of the metabolites inhibited oxygen consumption with antagonistic interactions between the components stimulation was noted in the group exposed to the lowest concentrations of AER-B + CYL (125 μg/L + 125 μg/L, respectively) and the ternary mixture of AER-B + ANA-B + CYL (83.3 μg/L + 83.3 μg/L + 83.3 μg/L, respectively). In vivo fluorescent staining with Hoechst 34580 showed that single AER-B had lower cytotoxic potential on body integument cells than ANA-B and CYL and most binary mixtures except for AER-B + CYL induced synergistic toxicity. Catecholamine level was decreased in animals exposed to single metabolites, their binary and ternary mixtures; however, the interactions between the components in the ternary mixture were antagonistic. Fat body was found to be disrupted in the larvae exposed to single metabolites and their combinations. Antagonistic toxic interactions between the oligopeptide components were found in most binary and the ternary mixtures; however, synergistic effect was noted in the binary mixture of AER-B + CYL. The results suggest that in natural conditions Chironomus larvae and possibly other benthic invertebrates may be affected by cyanobacterial metabolites, however various components and in mixtures and their concentrations may determine varied physiological effects and diverse interactions.

Live Imaging Transverse Sections of Zebrafish Embryo Explants

Vertebrate embryogenesis is a highly dynamic process involving coordinated cell and tissue movements that generate the final embryonic body plan. Many of these movements are difficult to image at high resolution because they occur deep within the embryo along the midline, causing light scattering and requiring longer working distances. Here, we present an explant-based method to image transverse cross sections of living zebrafish embryos. This method allows for the capture of all cell movements at high-resolution throughout the embryonic trunk, including hard-to-image deep tissues. This technique offers an alternative to expensive or computationally difficult microscopy methods. Key features • Generates intact zebrafish explants with minimal tissue disturbance. • Allows for live imaging of deep tissues normally obscured by common confocal microscopy techniques. • Immobilizes tissues for extended periods required for time-lapse imaging. • Utilizes readily available reagents and tools, which can minimize the time and cost of the procedure.

Assembly of phiKZ bacteriophage Inner Body during infection

The giant myovirus phiKZ is characterised by an Inner Body (IB) structure within its capsid, crucial for orderly DNA packaging. The IB is composed of six phiKZ-specific proteins. Notably, four of these IB proteins are co-injected with DNA into the host cell, where they potentially play a role in attacking the bacterial cell. The dynamics of IB assembling within the phiKZ capsid during infection remain poorly understood. In this study, we used fluorescent microscopy to track the localisation of IB proteins fused to fluorescent proteins within the cell throughout the infection process. Our findings reveal that the proteins Gp97 and Gp162 are incorporated into new virion heads during phage head maturation. In contrast, proteins Gp90, Gp93, and Gp95 are likely integrated into the virion shortly before the DNA packaging.

Assessing Phagocytosis of Cryptococcus neoformans Cells in Human Monocytes or the J774 Murine Macrophage Cell Line

Monocyte/macrophage cells play a central role in innate immunity against C. neoformans and C. gattii, species known to cause human disease. Cryptococcus is the only fungal genus known to possess such a large extracellular polysaccharide capsule, which impacts interactions of innate cells with the yeast. This interaction results in different fates, such as phagocytosis and intracellular proliferation and, as the interaction progresses, vomocytosis, cell-to-cell transfer, lysis of macrophages, or yeast killing. Differentiating internalized versus external Cryptococcus cells is thus essential to evaluate monocyte-macrophage phagocytosis. We describe here a protocol that allows quantification of Cryptococcus spp. phagocytosis using quantitative flow cytometry in human monocytes and a murine macrophage cell line (J774).

Electric organ discharge from electric eel facilitates DNA transformation into teleost larvae in laboratory conditions

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.

Advancements in 3D spheroid imaging: Optimised cryosectioning and immunostaining techniques

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.

Annexin A5 stabilizes matrix vesicle-biomimetic lipid membranes: unravelling a new role of annexins in calcification

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.

Calix[4]arene-pyrazole conjugates as potential cancer therapeutics

Tumor selectivity is yet a challenge in chemotherapy-based cancer treatment. A series of calixarenes derivatized at the lower rim with 3-phenyl-1H-pyrazole units with variable upper-rim substituent and conformations of macrocyclic core, alkyl chain length between heterocycle and core, as well as phenolic monomer (5-(4-tert-butylphenyloxy)methoxy-3-phenyl-1H-pyrazole) have been synthesized and characterized in a range of therapeutically relevant cellular models (M-HeLa, MCF7, A-549, PC3, Chang liver, and Wi38) from different target organs/systems. Specific cytotoxicity for M-HeLa cells has been observed in tert-butylcalix[4]arene pyrazoles in 1,3-alternate (compound 7b) and partial cone (compound 7c) conformations with low mutagenicity and haemotoxicity and in vivo toxicity in mice. Compounds 7b,c have induced mitochondrial pathway of apoptosis of M-HeLa cells through caspase-9 activation preceded by the cell cycle arrest at G0/G1 phase. A concomitant overexpression of DNA damage markers in pyrazole-treated M-HeLa cells suggests that calixarene pyrazoles target DNA, which was supported by the presence of interactions between calixarenes and ctDNA at the air-water interface.

DNA curtains to visualize chromatin interactions

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.

First report of 'Candidatus Phytoplasma asteris' associated with yellowing, scorching and decline of almond trees in India

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.

Three dimensional evaluation of cerebrovascular density and branching in chronic traumatic encephalopathy

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.

Rapid microbial viability assay using scanning electron microscopy: a proof-of-concept using Phosphotungstic acid staining

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.

Trophic transfer of microplastics from producer (Lemna minuta) to primary consumer (Cataclysta lemnata) in a freshwater food chain

Contamination by microplastics (0.1 μm-5 mm plastic fragments) is currently one of the major threats to the conservation of aquatic and terrestrial ecosystems worldwide. Growing awareness on this issue has led to an increase in studies on the effects of microplastics on freshwater organisms, although there are still few investigations on possible transfer of this contaminant along water trophic chains from producers to primary consumers. In this study, aquatic herbivorous larvae of the moth Cataclysta lemnata were fed on microplastic-free (control) and contaminated (MPs treatment) Lemna minuta fronds. For the treatments, Lemna plants were grown in mineral water enriched with fluorescent microparticles of poly(styrene-co-methyl methacrylate) (MPs, 100 mg/L) and then fed to the larvae as a food source. Microplastics effects on larvae were tested at 0, 7, 14 and 21 days of exposure, corresponding to sensitive phases of the insect life cycle. Contaminant impact was assessed based on parameters such as viability, body size/weight of the larvae, feeding alterations and regularity of insect life cycle. Using scanning electron and fluorescence microscopy, the presence of microplastics in the larvae was verified. The finding of fluorescent microplastics in both the intestinal lumen and excrement samples showed that larvae ingested contaminated Lemna fronds. In addition, larvae fed contaminated fronds were strongly affected by the presence of microplastic contaminant over time, showing high mortality (90 %) and total inability to complete the life cycle after 21 days by failing to reach the winged adult phase. In control tests, survival rates were higher than in treatments, and 50 % of the larvae managed to pupate and emerge as moths, reaching the adult phase. The results show that there was a trophic transfer of microplastics from producer to primary consumer along a freshwater food chain, generating negative effects on the life cycle of this aquatic herbivore.

Quantitative Image Analysis of Dynamic Cell Behaviors During Border Cell Migration

Drosophila border cells have emerged as a genetically tractable model to investigate dynamic collective cell migration within the context of a developing organ. Studies of live border cell cluster migration have revealed similarities with other migrating collectives, including formation and restriction of cellular protrusions to the front of the cluster, supracellular actomyosin contractility of the entire collective, and intra-collective cell motility. Here, we describe protocols to prepare ex vivo cultures of stage 9 egg chambers followed by live time-lapse imaging of fluorescently labeled border cells to image dynamic cell behaviors. We provide options to perform live imaging using either a widefield epifluorescent microscope or a confocal microscope. We further outline steps to quantify various cellular behaviors and protein dynamics of live migrating border cells using the Fiji image processing package of ImageJ. These methods can be adapted to other migrating cell collectives in cultured tissues and organs.

Quantification of Invadopodia Formation and Matrix Degradation Activity

Cancer cells possess a remarkable capacity to dissociate from a primary tumor, invade the surrounding tissues and vasculature, and eventually form metastases in distant organs. This complex and multistep process remains one of the major causes of mortality in cancer patients worldwide. Multiple studies have highlighted the role of actin-rich structures called invadopodia ("invasive feet"), which adhere to the matrix, contain and secrete matrix-degrading proteinases, and apply protrusive forces generated by the actin cytoskeleton, which drive the invasive process. Here, we describe a fluorescent microscopy-based protocol for imaging and quantifying both invadopodia formation and matrix degradation.

Imaging Chromatin Accessibility by Assay of Transposase-Accessible Chromatin with Visualization

Chromatin accessibility is one of the fundamental structures regulating genome functions including transcription and DNA repair. Recent technological advantages to analyze chromatin accessibility begun to explore the dynamics of local chromatin structures. Here I describe protocols for Assay of Transposase-Accessible Chromatin with Visualization (ATAC-see), which allows us to analyze subnuclear localization of accessible chromatin and quantify accessible chromatin at single-cell level.

SpotitPy: a semi-automated tool for object-based co-localization of fluorescent labels in microscopy images

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 ).

Prevalence, risk factor and diversity of Cryptosporidium in cattle in Latvia

The epidemiology of Cryptosporidium spp. in Latvia was investigated by testing fecal samples from 926 animals aged from one day to 24 years for the presence of Cryptosporidium spp. oocysts. The samples were collected from 87 cattle farms and from four slaughterhouses, and analyzed by conventional and fluorescent microscopy, followed by Cryptosporidium species and C. parvum subtype differentiation. Moreover, using a questionnaire, we surveyed factors that could be relevant as risk factors of Cryptosporidium spp. infection on the farms. Cryptosporidium spp. were shed by 33.8% of the investigated cattle and at least one shedding animal was found on 77.8% of the farms. In the present study, all four Cryptosporidium species reported to commonly infect cattle and two additional Cryptosporidium species (C. scrofarum and C. ubiquitum) were identified. In addition, mix infections of C. parvum/C. bovis, C. bovis/C. ryanae, C. parvum/C. ryanae, C. parvum/C. andersoni and C. bovis/C. andersoni were observed. C. parvum and C. bovis was mostly prevalent in young animals (0-3 months old) and in addition, diarrhea associated with C. parvum infection was observed only in very young animals. Cryptosporidium andersoni and C. ryanae in age group 0-3 months was observed in low prevalence, while a higher proportion of animals with diarrhea associated with C. andersoni infection was observed in very young animals and with C. ryanae in animals age group 4-24 months. Eight previously described C. parvum subtypes were observed. The majority of the subtypes were in the IIa subtype family, while one subtype was identified from the IId subtype family. The most common subtype was IIaA15G2R1, which was found in 34.2% of the C. parvum successfully subtyped samples. The probability of Cryptosporidium spp. associated diarrhea in cattle decreased significantly with the age of the animals and a prolonged period during which calves were fed with milk.

Cell-Free Gene Expression from DNA Brushes

Linear double-stranded DNA polymers coding for synthetic genes immobilized on a surface form a brush as a center for cell-free gene expression, with DNA density 10²-10³ fold higher than in bulk solution reactions. A brush localizes the transcription-translation machinery in cell extracts or in cell-free reconstituted reactions from purified components, creating a concentrated source of RNA and proteins. Newly synthesized molecules can form circuits regulating gene expression in the same brush or adjacent ones. They can also assemble into functional complexes and machines such as ribosomal units, then analyzed by capture on prepatterned antibodies or by cascaded reactions. DNA brushes are arranged as a single center or multiple ones on a glass coverslip, in miniaturized compartments carved in silicon wafers, or in elastomeric microfluidic devices. Brushes create genetically programmable artificial cells with steady-state dynamics of protein synthesis. Here, we provide the basic procedure for surface patterning, DNA immobilization, capture of protein products on antibody traps and fluorescent imaging. The method of DNA brush surface patterning enables simple parallelization of cell-free gene expression reactions for high throughput studies with increased imaging sensitivity.

Spectral Characterization of Purpurin Dye and Its Application in pH Sensing, Cell Imaging and Apoptosis Detection

Purpurin (1,2,4-trihydroxy-9,10-anthraquinone) is a natural red dye obtained from the red madder plant that is widely used in food and dyeing industries. The present study investigated the characteristics of purpurin and its application as a pH-sensitive probe to detect the pH of solutions and intracellular pH of mammalian and bacterial cells. Purpurin exhibited high pH-sensitive behavior, low analytes interference, high stability with pKa of 4.6 and visible colorimetric change. 1H NMR and FTIR studies indicated protonation of phenolic hydroxyl group under acidic condition with hypsochromic shift in the absorption and fluorescence spectra relative to that of basic condition. Cell culture studies using HeLa cells revealed that purpurin is well tolerated by the cells and the fluorescent imaging result indicated excellent cell permeability with possible use of the dye to detect the pH fluctuations in living cells under various physiological conditions such as apoptosis. Microbiological studies indicated that the dye could be used for visualization of bacteria under acidic condition.

Stent-Based Gene Delivery for Coronary Disease

Percutaneous coronary interventions (PCI) are the mainstay for treatment of advanced coronary disease. A majority of PCI involve deployment of a stent in the affected vascular segment. This chapter introduces the concept of using stents as a platform for delivering gene therapies to the vasculature with the overarching aim of mitigating in-stent restenosis (ISR), late stent thrombosis (LST), and neoatherosclerosis (NA), a triad of delayed complications that reduce the overall success rate of PCI. The chapter provides a detailed methodology for coatless reversible attachment of adenoviral (Ad) and adeno-associated viral (AAV) vectors to the metal stent struts along with representative in vitro and in vivo results.

Securinine induces mitotic block in cancer cells by binding to tubulin and inhibiting microtubule assembly: A possible mechanistic basis for its anticancer activity

AIM

Analysis of the anticancer and antimitotic activity of the plant derived alkaloid securinine along with its effect on the organization of cellular microtubules as well as its binding with purified goat brain tubulin in-vitro.

MATERIALS AND METHODS

The cytotoxicity of securinine on different cell lines was conducted using SRB assay. The effect of securinine on the cellular microtubules was analyzed using immunofluorescence microscopy. The binding of securinine on purified goat brain tubulin was evaluated using fluorescent spectroscopy.

KEY FINDINGS

Securinine effectively prevented the proliferation of cervical, breast and lung cancer cells with an IC₅₀ of 6, 10 and 11 μM respectively and induced minimal toxicity in HEK cell line. Securinine at concentrations higher than IC₅₀ induced significant depolymerization in interphase and mitotic microtubules and it suppressed the reassembly of cold depolymerized spindle microtubules in HeLa cells. In the wound healing assay, securinine effectively suppressed the migration of HeLa cells to close the wound. Securinine bound to tubulin with a Kd of 9.7 μM and inhibited the assembly of tubulin into microtubules. The treatment with securinine induced a mitochondrial dependent ROS response in HeLa cells which enhanced the cytotoxic effect of securinine. The result from gene expression studies indicates that securinine induced apoptosis in MCF-7 cells through p53 dependent pathway.

SIGNIFICANCE

Considering the strong anticancer and anti-metastatic property and low toxicity in non-malignant cell lines, we suggest that securinine can be used as a chemotherapeutic drug either alone or in combination with other known anticancer molecules.

ClearSeeAlpha: Advanced Optical Clearing for Whole-Plant Imaging

To understand how the body of plants is made, it is essential to observe the morphology, structure and arrangement of constituent cells. However, the opaque nature of the plant body makes it difficult to observe the internal structures directly under a microscope. To overcome this problem, we developed a reagent, ClearSee, that makes plants transparent, allowing direct observation of the inside of a plant body without inflicting damage on it, e.g. through physical cutting. However, because ClearSee is not effective in making some plant species and tissues transparent, in this study, we further improved its composition to prevent oxidation, and have developed ClearSeeAlpha, which can be applied to a broader range of plant species and tissues. Sodium sulfite, one of the reductants, prevented brown pigmentation due to oxidation during clearing treatment. Using ClearSeeAlpha, we show that it is possible to obtain clear chrysanthemum leaves, tobacco and Torenia pistils and fertilized Arabidopsis thaliana fruits-tissues that have hitherto been challenging to clear. Moreover, we show that the fluorescence intensity of purified fluorescent proteins emitting light of various colors was unaffected in the ClearSeeAlpha solution; only the fluorescence intensity of TagRFP was reduced by about half. ClearSeeAlpha should be useful in the discovery and analysis of biological phenomena occurring deep inside the plant tissues.

Assessment of Cytotoxicity of α-Synuclein in Budding Yeast Using a Spot Growth Assay and Fluorescent Microscopy

The budding yeast Saccharomyces cerevisiae is a model organism amenable both to genetic analysis and cell biology. Due to these advantages, yeast has provided platforms to examine the properties of pathogenic proteins involved in human diseases. The methods used to examine the cytotoxicity and intracellular localization of α-Synuclein, a human neuronal protein implicated in Parkinson's disease, using yeast have been described herein. These methods are readily accessible to researchers or graduate students unfamiliar with experiments using yeast and applicable to larger scale analyses, such as high-throughput genetic and chemical screenings.

Identification of Retinal Ganglion Cells from β-III Stained Fluorescent Microscopic Images

Optic nerve crush in mouse model is widely used for investigating the course following retinal ganglion cell (RGCs) injury. Manual cell counting from β-III tubulin stained microscopic images has been routinely performed to monitor RGCs after an optic nerve crush injury, but is time-consuming and prone to observer variability. This paper describes an automatic technique for RGC identification. We developed and validated (i) a sensitive cell candidate segmentation scheme and (ii) a classifier that removed false positives while retaining true positives. Two major contributions were made in cell candidate segmentation. First, a homomorphic filter was designed to adjust for the inhomogeneous illumination caused by uneven penetration of β-III tubulin antibody. Second, the optimal segmentation parameters for cell detection are highly image-specific. To address this issue, we introduced an offline-online parameter tuning approach. Offline tuning optimized model parameters based on training images and online tuning further optimized the parameters at the testing stage without needing access to the ground truth. In the cell identification stage, 31 geometric, statistical and textural features were extracted from each segmented cell candidate, which was subsequently classified as true or false positives by support vector machine. The homomorphic filter and the online parameter tuning approach together increased cell recall by 28%. The entire pipeline attained a recall, precision and coefficient of determination (r²) of 85.3%, 97.1% and 0.994. The availability of the proposed pipeline will allow efficient, accurate and reproducible RGC quantification required for assessing the death/survival of RGCs in disease models.

Lipophilic Conjugates for Carrier-Free Delivery of RNA Importable into Human Mitochondria

Defects in human mitochondrial genome can cause a wide range of clinical disorders that still do not have efficient therapies. The natural pathway of small noncoding RNA import can be exploited to address therapeutic RNAs into the mitochondria. To create an approach of carrier-free targeting of RNA into living human cells, we designed conjugates containing a cholesterol residue and developed the protocols of chemical synthesis of oligoribonucleotides conjugated with cholesterol residue through cleavable pH-triggered hydrazone bond. The biodegradable conjugates of importable RNA with cholesterol can be internalized by cells in a carrier-free manner; RNA can then be released in the late endosomes due to a change in pH and partially targeted into mitochondria. Here we provide detailed protocols for solid-phase and "in solution" chemical synthesis of oligoribonucleotides conjugated to a cholesterol residue through a hydrazone bond. We describe the optimization of the carrier-free cell transfection with these conjugated RNA molecules and methods for evaluating the cellular and mitochondrial uptake of lipophilic conjugates.

Microscopic evidence for pectin changes in hard-to-cook development of common beans during storage

In this study, pectin changes during Red haricot bean storage under high temperature and high humidity conditions were investigated to understand the hard-to-cook (HTC) development from a microstructural point of view. First, to ensure repeatability of the microscopy results, a classification of the fresh and stored beans (aged at 35 °C and 83% relative humidity) into different hardening levels (the Non-aged, Aged and Very-hard aged sample) was performed based on the texture values of cooked half-cotyledons. Cell wall strength of the cotyledons was evaluated, showing that the aged samples (HTC seeds) exhibit stronger cell walls with more/stronger pectic cross-linkages than the Non-aged sample. After a sequential pectin extraction aiming at removing pectin fractions of different solubility, cell wall autofluorescence and immunolabeling of JIM7, LM9 and 2F4 epitopes in the residual materials were examined. Upon ageing, the samples exhibited an increased Ca²⁺-pectin and ferulic acid-pectin crosslinking, these pectic complexes being accumulated primarily at the intercellular spaces. The results suggest a contribution of both the pectin-cation-phytate hypothesis and the involvement of phenolic-pectin crosslinks in HTC development at the cotyledon during storage of common beans.

Simultaneous express immunoassay of multiple cardiac biomarkers with an automatic platform in human plasma

C-reactive protein, cystatin C, myoglobin, and D-dimer represent the inflammatory or thromboembolic status of the patient and play important roles in early diagnostics of acute myocardial infarction. Each protein can indicate some health problems, but their simultaneous detection can be crucial for differential diagnostics. The express analysis of these proteins in a small drop of plasma was developed using magnetic beads. The suggested method is based on immunomagnetic extraction of the target analyte from plasma samples and its simultaneous labelling by fluorescent dye. Reaction time was optimized for quantification of cardiac biomarkers in the spike solutions and human plasma samples. In this paper, we developed a one-protein detection technique for each cardiac biomarker and united it to a four-protein facility using an automatic platform. The proposed technique requires only 17 μL of the human plasma and takes 14 min for four-protein measuring. The suggested technique covers concentration difference by more than two orders of magnitude and demonstrates analytical applicability by measurements of human plasma samples of 16 volunteers.

Novel use of fluorescent microscopy in determining basement membrane integrity in ambiguous cases

Indistinct basement membrane due to inflammation always poses a problem to the pathologists for commenting on micro-invasive squamous cell carcinoma. In such a situation, even a special stain would not be able to correctly demonstrate the basement membrane, which is necessary for estimating the depth of invasion. In this paper, we have proposed a novel fluorescent microscopy assisted visualization of basement membrane in such difficult situations. To further validate this approach, we then retrospectively investigated twenty such cases under a fluorescent microscope and could able to repeat the same result. As routine hematoxylin and eosin stained sections are required for evaluation, it is technically less demanding and less time-consuming.

CTS tag-based methods for investigating mitochondrial RNA modification factors in Trypanosoma brucei

Unicellular parasite Trypanosoma brucei maintains an elaborate mitochondrial mRNA processing pathway including 3'-5' exonucleolytic trimming of primary precursors, 5' and 3' modifications, and, in most cases, massive U-insertion/deletion editing. Whereas the role of editing in restoring protein coding sequence is apparent, recent developments suggest that terminal modifications are equally critical for generating a stable translationally competent messenger. The enzymatic activities responsible for 5' pyrophosphate hydrolysis, 3' adenylation and uridylation, and 3'-5' decay are positively and negatively regulated by pentatricopeptide repeat-containing (PPR) proteins. These sequence-specific RNA binding factors typically contain arrays of 35-amino acid repeats each of which recognizes a single nucleotide. Here, we introduce a combinatorial CTS affinity tag, which underlies a suite of methods for PPR proteins purification, in vivo RNA binding sites mapping and sub-cellular localization studies. These approaches should be applicable to most trypanosomal RNA binding proteins.

Assays for Autophagy III: Observing Dynamic Protein Trafficking

Macroautophagy, by its very nature, is a protein trafficking process. Cargos are transported and processed. Atg proteins come and go. In this chapter, we present three assays to monitor these dynamic events: a non-radioactive pulse-chase labeling assay to monitor the transport of prApe1 and two fluorescent microscopy-based assays to assess the trafficking of Atg8 and Atg9.

Protocol for Cryopreservation of Endothelial Monolayers

One of the major challenges in the preservation of complex tissues is the cryosensitivity of the endothelium, the single layer of cells lining blood vessels, corneas, and other tissues. The increasing importance of endothelial monolayers in tissue-engineered constructs for transplantation and research warrants the need to develop protocols for the successful cryopreservation of cells in monolayers. In this chapter, we describe a recently published cryopreservation protocol that we developed based on examination of various factors that influence the post-thaw recovery of endothelial monolayers. To efficiently investigate cryopreservation protocol parameters, we employed an interrupted slow-cooling procedure (graded freezing) that allows dissecting loss of cell viability into contributions from slow-cooling injury and rapid-cooling injury. Our optimized protocol involves culturing cells on Rinzl plastic coverslips, using a combination of a penetrating cryoprotectant (5% dimethyl sulfoxide) and a non-penetrating cryoprotectant (6% hydroxyethyl starch), addition of 2% chondroitin sulfate, controlled cooling at 0.2 °C/min or 1 °C/min, and removal of cryoprotectant immediately after thaw. The protocol has been validated for human umbilical vein and porcine corneal endothelial cell monolayers.

Lactoferricin-Derived L5a Cell-Penetrating Peptide for Delivery of DNA into Cells

Cell-penetrating peptides (CPPs) are small peptides which help intracellular delivery of functional macromolecules, including DNAs, RNAs, and proteins, across the cell membrane and into the cytosol, and even into the nucleus in some cases. Delivery of macromolecules can facilitate transfection, aid in gene therapy and transgenesis, and alter gene expression. L5a (RRWQW), originally derived from bovine lactoferricin, is one kind of CPPs which can promote cellular uptake of plasmid DNA and enters cells via direct membrane translocation. The peptide complexes noncovalently with DNA over a short incubation period. DNA plasmid and L5a complex stability is confirmed by a decrease in mobility in a gel retardation assay, and successful transfection is proven by the detection of a reporter gene in cells using fluorescent microscopy. Here, we describe methods to study noncovalent interactions between L5a and plasmid DNA, and the delivery of L5a/DNA complexes into cells. L5a is the one of the smallest CPPs discovered to date, providing a small delivery vehicle for macromolecules in mammalian cells. A small vehicle which can enter the nucleus is ideal for efficient gene uptake, transfer, and therapy. It is simple to complex with DNA plasmids, and its nature allows mammalian cells to be easily transfected.

Rapid identification of a subset of foodborne bacteria in live-cell assays

The detection and identification of microbial pathogens in meat and fresh produce play an essential role in food safety for reducing foodborne illnesses every year. A new approach based on targeting a specific sequence of the 16S rRNA region for each bacterium is proposed and validated. The probe complex consists of a C60, a conjugated RNA detector which targets a specific 16S rRNA sequence, and a complementary fluorescent reporter. The RNA detectors were designed by integrating NIH nucleotide and Vienna RNA Webservice databases, and their specificities were validated by the RDP database. Probe complexes were synthesized for identifying E. coli K12, E. coli O157: H7, S. enterica, Y. enterocolitica, C. perfringens, and L. monocytogenes. First, under controlled conditions of known bacterial mixtures, the efficiency and crosstalk for identifying the foodborne bacteria were quantified to be above 94% and below 5%, respectively. Second, experiments were designed by inoculating meat products by known numbers of bacteria and measuring the limit of detection. In one experiment, 225 g of autoclaved ground chicken was inoculated with 9 E. coli O157:H7, where 6.8 ± 1.2 bacteria with 95% confidence interval were recovered. Third, by positionally printing probe complexes in microwells, specific microorganisms were identified with only one fluorophore. The proposed protocol is a cell-based system, can identify live bacteria in 15 min, requires no amplification, and has the potential to open new surveillance opportunities.Key points• The identification of foodborne bacteria is enabled in live-cell assays.• The limit of detection for 100 g of fresh chicken breast inoculated with 4 bacteria is 2.7 ± 1.4 with 95% confidence interval.• The identification of five bacteria in a coded microwell chip is enabled with only one fluorophore.

The nature and features of organization of reserve polysaccharides in three Pelomyxa species (Archamoebea, Pelobiontida)

The nature and features of organization of reserve polysaccharides in three species of the genus Pelomyxa-P. palustris, P. belevskii, and P. stagnalis-were studied using light and transmission electron microscopy. We applied the periodic acid-Schiff reaction that is a highly selective method for detecting glycogen. The fluorescent dye auramine-SO₂ (Au-SO₂) was used as a Schiff-type reagent. The densely packed aggregates of glycogen that form the morphologically differentiated organelle-like bodies are revealed in the cytoplasm in all studied species. The organization of these bodies is characterized by the species-specific features, while in most cases, their size and number in the cells vary depending on the season of the year. Although in all the cases we studied, these bodies do not have their own boundary membrane, in fact, they are surrounded by membranous structures. These structures differ in a variety of Pelomyxa species. We concluded that there are two groups of species in the genus Pelomyxa. The first one includes organisms containing glycogen structures in the cytoplasm (P. palustris, P. belevskii, P. stagnalis, P. binucleata, P. corona, P. secunda). No inclusions resembling glycogen bodies were found in P. flava, P. paradoxa, P. gruberi, and P. prima that form the second group.

Transient loss of membrane integrity following intracellular ice formation in dimethyl sulfoxide-treated hepatocyte and endothelial cell monolayers

Immediate post-thaw evaluation of membrane integrity has proven to yield overestimates of cell survival under conditions that preclude intracellular ice formation (IIF). However, prominent theories on the mechanisms of intracellular nucleation suggest a damaged membrane can reseal, prompting us to evaluate whether immediate post-thaw assessments of membrane integrity can in fact underestimate cell survival under conditions that promote IIF. HUVEC and HepG2 monolayers were treated with 1.4 M DMSO and frozen to -25 °C under conditions that formed either 0% or 100% IIF. Membrane integrity was evaluated both immediately and 24 h post-thaw, with metabolic activity assessments performed 24 h post-thaw as a secondary measure of survival. Treatment with 1.4 M DMSO and nucleation of 100% IIF resulted in a drastic increase in the relative percent of membrane intact cells following a 24 h culture period (HUVEC: 90.2% ± 0.7%; HepG2: 70.4% ± 4.0%), which correlated with 24 h post-thaw metabolic activity. These differences between the immediate and 24 h post-thaw membrane integrity assessments were significantly more than those seen in the absence of either IIF or DMSO treatment. Therefore, a high incidence of IIF in DMSO-treated monolayers may lead to erroneous underestimates of cell survival when conducting immediate post-thaw assessments of membrane integrity.

Identification of Group A Streptococcus-Containing Autophagosome-Like Vacuoles

Group A Streptococcus (GAS) is one of the major human pathogens that can invade nonphagocytic cells. GAS internalized through endocytosis secretes the pore-forming toxin Streptolysin O (SLO) to escape into the cytoplasm. The cytosolic GAS is selectively captured by autophagic membranes (GAS-containing autophagosome-like vacuoles, GcAVs) and delivered to lysosomes for degradation. Macroautophagy (referred to as autophagy hereafter) is a highly conserved lysosome-mediated catabolic process, which is critical for cellular homeostasis. Autophagy also acts as an intracellular immune system. In this section, we describe how to identify GcAVs in infected cells using fluorescent microscopy.

High-Throughput Calcium Imaging Screen of Toxins' Function in Dissociated Sensory Neurons

Many toxins from a variety of venomous animals and plants have evolved to target neuronal ion channels and receptors. However, a significant obstacle in the study of these toxins is the finding and characterization of their specific molecular target. Here, we describe a method for fast and efficient screening of venom and toxin activity using live-cell calcium imaging. We describe the use of Fura-2, a calcium indictor that changes its fluorescence properties in response to intracellular calcium elevations, to measure the activity of neurons from the dorsal root and trigeminal ganglia. Calcium imaging is an efficient technique for testing many of the venom's components on large numbers of neurons simultaneously. This technique offers a novel tool for low-cost and rapid characterization of functionally active toxins and their target receptors.

Fluorescent analysis of boar sperm capacitation process in vitro

BACKGROUND

Capacitation involves physiological changes that spermatozoa must undergo in the female reproductive tract or in vitro to obtain the ability to bind, penetrate and fertilize the egg. Up to date, several methods have been developed to characterize this complex biological process. The goal of the presented study is to mutually compare several fluorescent techniques, check their ability to detect changes in molecular processes during the capacitation progress and determine their ability to predict the percentage of acrosome reacted (AR) sperm after the exposure to solubilized zona pellucida (ZP). The capacitation process was analyzed using four fluorescent techniques: 1. chlortetracycline (CTC) staining, 2. anti-acrosin antibody (ACR.2) assay, 3. anti-phosphotyrosine (pY) antibody assay, 4. fluorescein isothiocyanate-conjugated phalloidin (FITC-phall) assay. All these methods were tested using fluorescent microscopy and flow cytometry.

RESULTS

All selected methods are capable to detect the capacitation progress of boar sperm in vitro, but there are significant differences in their outcome when using fluorescent microscopy or flow cytometry experimental arrangements and subsequent statistical analysis (KW-ANOVA). Also, the ability to predict the absolute numbers of sperm which will undergo ZP-induced AR differ significantly (CTC and ACR.2 gave the best predictions).

CONCLUSIONS

Our study compared four largely used methods used to characterize capacitation process, highlighted their differences and showed that all are able to detect capacitation progress, CTC and ACR.2 are furthermore able to accurately predict the percentage of AR sperm after ZP-induced AR.

Activation of microglia associated with lentiviral transduction: A semiautomated method of assessment

Lentiviral transduction is a powerful tool and widely used in neuroscience research to manipulate gene expression of cells. However, the injection of lentiviral vectors in the brain is not totally benign, it potentially induces focal neuroinflammation. Upon inflammation, microglial cells get activated and can induce major changes in tissue environment, which may interfere with experimental results. In the current study, two weeks after the injection of control viral construction in the dentate gyrus (DG) of rats, an activation of microglia was detected. To access the activation status, we used a fast and accurate method of phenotype detection - measurement of fractal dimension (FD). Microglial morphology is a key indicator of neuroinflammation, therefore FD of microglial cells may serve as a reliable index of inflammation status in the brain. Here we present a detailed description of image processing procedure of images of individual microglial cells. The method allows to preserve the complex structure of microglial cells and their thin processes on the output image, which is important for accurate FD assessment.

Monitoring stress-induced autophagic engulfment and degradation of the 26S proteasome in mammalian cells

Almost 70 years after the discovery of the lysosome, and about four decades following the unraveling of ubiquitin as a specific "mark of death," the field of protein turnover-the numerous processes it regulates, the pathologies resulting from its dysregulation, and the drugs that have been developed to target them-is still growing exponentially. Accordingly, the need for new technologies and methods is ever growing. One interesting question in the field is the mechanism(s) by which the "predators become prey". We have reported recently that the 26S proteasome, the catalytic arm of the ubiquitin system, is degraded by the autophagy-lysosome machinery, in a process requiring specific ubiquitination of the proteasome, and subsequent recognition by the shuttle protein p62/SQSTM1. Studying the modification(s), recognition sites, engulfment, and breakdown of the 26S proteasome via such "proteaphagy" has required the use of microscopy, subcellular fractionation, 'classical biochemistry', and proteomics. In this chapter, we present the essentials of these protocols, with emphasis on the refinements we have introduced in order for them to better suit the particular study of proteaphagy.

Analysis of Microtubule Dynamics Heterogeneity in Cell Culture

Microtubules (MTs) are dynamic components of the cytoskeleton playing an important role in a large number of cell functions. Individual MTs in living cells undergo stochastic switching between alternate states of growth, shortening and attenuated phase, a phenomenon known as tempered dynamic instability. Dynamic instability of MTs is usually analyzed by labeling MTs with +TIPs, namely, EB proteins. Tracking of +TIP trajectories allows analyzing MT growth in cells with a different density of MTs. Numerous labs now use +TIP to track growing MTs in a variety of cell cultures. However, heterogeneity of MT dynamics is usually underestimated, and rather small sampling for the description of dynamic instability parameters is often used. The strategy described in this chapter is the method for repetitive quantitative analysis of MT growth rate within the same cell that allows minimization of the variation in MT dynamics measurement. We show that variability in MT dynamics within a cell when using repeated measurements is significantly less than between different cells in the same chamber. This approach allows better estimation of the heterogeneity of cells' responses to different treatments. To compare the effects of different MT inhibitors, the protocol using normalized values for MT dynamics and repetitive measurements for each cell is employed. This chapter provides detailed methods for analysis of MT dynamics in tissue cultures. We describe protocols for imaging MT dynamics by fluorescent microscopy, contrast enhancement technique, and MT dynamics analysis using triple color-coded display based on sequential subtraction analysis.

Immunofluorescence staining of live lymph node tissue slices

Explants of lymphoid tissue provide a rare opportunity to assess the organization of the immune system in a living, dynamic environment. Traditionally, ex vivo immunostaining is conducted in fixed tissue sections, while live tissues are analyzed using genetically engineered fluorescent reporters or adoptively transferred, pre-labelled cell populations. Here, we validated a protocol for immunostaining and imaging in live, thick slices of lymph node tissue, thus providing a spatial "map" of the lymph node while maintaining the viability and functionality of the slices. Using anti-B220/CD45R (B cell) as a prototype antibody, the procedure for immunostaining was tested for sufficient signal to noise with respect to staining time, temperature, and wash time, and the specificity was verified in comparison to isotype controls. Immunostaining signal in live tissue slices was detectable to atleast 120 μm deep for both whole antibodies and F(ab')2 fragments using the staining procedure. This procedure revealed the expected changes in B cell organization in lymph nodes from immunized mice. Cell surface staining with most antibodies did not induce cytokine secretion, and cytokine secretion in response to T cell stimulation was unaffected by immunostaining. Staining with known a mitogenic antibody (anti-CD3) simultaneously labelled the cells and activated the tissue, confirming that reagents for live immunostaining must be selected judiciously. As a proof of concept, this method was used to reveal the dynamic distribution of CD69, a T cell activation marker, in lymph node slices before and after ex vivo stimulation.

Mitophagy Dynamics in Caenorhabditis elegans

Mitochondrial selective autophagy (mitophagy) is a critical cellular process for mitochondrial homeostasis and survival both under basal and stress conditions. Distinct cell types display different requirements for mitochondrial turnover depending on their metabolic status, differentiation state, and environmental cues. This points to the necessity of developing novel tools for real-time, tissue-specific assessment of mitophagy. Caenorhabditis elegans is an invaluable model organism for this kind of analysis providing a platform for simultaneous monitoring of mitophagy in vivo in different tissues and cell types, during development, stress conditions, and/or throughout life span. In this chapter we describe three versatile, noninvasive methods, developed for monitoring in vivo early and late mitophagic events in body wall muscles and neuronal cells of C. elegans. These procedures can be readily used and/or provide insights into the generation of novel imaging methods to investigate further the role of mitophagy at the organismal level under normal and pathological conditions.

Determining the Impact of Metabolic Nutrients on Autophagy

Tumorigenesis relies on the ability of cancer cells to obtain necessary nutrients and fulfill increased energy demands associated with rapid proliferation. However, as a result of increased metabolite consumption and poor vascularization, most cancer cells must survive in a nutrient poor and high cellular stress microenvironment. Cancer cells undergo metabolic reprogramming to evade cell death and ensure proliferation; in particular, cancer cells utilize the catabolic process of autophagy. Autophagy creates an intracellular pool of metabolites by sequestering cytosolic macromolecules in double-membrane vesicles targeted for lysosomal degradation. During times of environmental stress and nutrient starvation, autophagy is upregulated through the dynamic interactions between two nutrient sensing proteins, AMP activated protein kinase (AMPK) and mechanistic target of rapamycin (mTOR), in cooperation with Unc-51 like autophagy activating kinase 1 (ULK1). In this way, a lack of metabolic nutrients plays a critical role in inducing autophagy, while the products of autophagy also serve as readily available fuel for the cell. In this chapter, we describe methods to visualize and quantify autophagy using a fluorescent sensor of autophagic membranes. Thus, the impact of specific nutrients on autophagy can be measured using live-cell fluorescent microscopy.

Permeability changes and effect of chemotherapy in brain adjacent to tumor in an experimental model of metastatic brain tumor from breast cancer

Background

Brain tumor vasculature can be significantly compromised and leakier than that of normal brain blood vessels. Little is known if there are vascular permeability alterations in the brain adjacent to tumor (BAT). Changes in BAT permeability may also lead to increased drug permeation in the BAT, which may exert toxicity on cells of the central nervous system. Herein, we studied permeation changes in BAT using quantitative fluorescent microscopy and autoradiography, while the effect of chemotherapy within the BAT region was determined by staining for activated astrocytes.

Methods

Human metastatic breast cancer cells (MDA-MB-231Br) were injected into left ventricle of female NuNu mice. Metastases were allowed to grow for 28 days, after which animals were injected fluorescent tracers Texas Red (625 Da) or Texas Red dextran (3 kDa) or a chemotherapeutic agent ¹⁴C-paclitaxel. The accumulation of tracers and ¹⁴C-paclitaxel in BAT were determined by using quantitative fluorescent microscopy and autoradiography respectively. The effect of chemotherapy in BAT was determined by staining for activated astrocytes.

Results

The mean permeability of texas Red (625 Da) within BAT region increased 1.0 to 2.5-fold when compared to normal brain, whereas, Texas Red dextran (3 kDa) demonstrated mean permeability increase ranging from 1.0 to 1.8-fold compared to normal brain. The K_in values in the BAT for both Texas Red (625 Da) and Texas Red dextran (3 kDa) were found to be 4.32 ± 0.2 × 10⁵ mL/s/g and 1.6 ± 1.4 × 10⁵ mL/s/g respectively and found to be significantly higher than the normal brain. We also found that there is significant increase in accumulation of ¹⁴C-Paclitaxel in BAT compared to the normal brain. We also observed animals treated with chemotherapy (paclitaxel (10 mg/kg), erubilin (1.5 mg/kg) and docetaxel (10 mg/kg)) showed activated astrocytes in BAT.

Conclusions

Our data showed increased permeation of fluorescent tracers and ¹⁴C-paclitaxel in the BAT. This increased permeation lead to elevated levels of activated astrocytes in BAT region in the animals treated with chemotherapy.

Computing neurite outgrowth and arborization in superior cervical ganglion neurons

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.

Cryopreservation of human umbilical vein and porcine corneal endothelial cell monolayers

Cryopreservation of endothelium is one of the major challenges in the cryopreservation of complex tissues. Human umbilical vein endothelial cells (HUVECs) in suspension are available commercially and recently their post-thaw cell membrane integrity was significantly improved by cryopreservation in 5% dimethyl sulfoxide (Me₂SO) and 6% hydroxyethyl starch (HES). However, cryopreservation of cells in monolayers has been elusive. The exact mechanisms of damage during cell monolayer cryopreservation are still under investigation. Here, we show that a combination of different factors contribute to significant progress in cryopreservation of endothelial monolayers. The addition of 2% chondroitin sulfate to 5% Me₂SO and 6% HES and cooling at 0.2 or 1 °C/min led to high membrane integrity (97.3 ± 3.2%) immediately after thaw when HUVECs were cultured on a substrate with a coefficient of thermal expansion similar to that of ice. The optimized cryopreservation protocol was applied to monolayers of primary porcine corneal endothelial cells, and resulted in high post-thaw viability (95.9 ± 3.7% membrane integrity) with metabolic activity 12 h post-thaw comparable to unfrozen control.