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ACS Omega Feb 2024To study transcriptome dynamics without harming cells, it is essential to convert chemical bases. 4-Thiouridine (4sU) is a biocompatible uridine analogue that can be...
To study transcriptome dynamics without harming cells, it is essential to convert chemical bases. 4-Thiouridine (4sU) is a biocompatible uridine analogue that can be converted into a cytidine analogue. Although several reactions can convert 4sU into a cytidine analogue, few studies have compared the features of these reactions. In this study, we performed three reported base conversion reactions, including osmium tetroxide, iodoacetamide, and sodium periodate treatment, as well as a new reaction using 2,4-dinitrofluorobenzene. We compared the reaction time, conversion efficacy, and effects on reverse transcription. These reactions successfully converted 4sU into a cytidine analogue quantitatively using trinucleotides. However, the conversion efficacy and effect on reverse transcription vary depending on the reaction with the RNA transcript. OsO treatment followed by NHCl treatment showed the best base-conversion efficiency. Nevertheless, each reaction has its own advantages and disadvantages as a tool for studying the transcriptome. Therefore, it is crucial to select the appropriate reaction for the target of interest.
PubMed: 38434802
DOI: 10.1021/acsomega.3c08516 -
Carbohydrate Research Dec 2023Bacterial natural products containing heptosides such as septacidin represent interesting scaffolds for the development of drugs to combat antimicrobial resistance....
Bacterial natural products containing heptosides such as septacidin represent interesting scaffolds for the development of drugs to combat antimicrobial resistance. However, very few synthetic strategies have been reported to grant access to these derivatives. Here, we have devised a synthetic pathway to l-glycero-l-glucoheptoside, a key building block en route to septacidin, directly from l-glucose. Importantly, we show that carbon homologation at C6, encompassing oxidation of the C6-OH followed by methylenation, is significantly influenced by the nature of the C4-moiety. In order to observe the effect of various patterns, namely azide (N), p-methoxybenzyloxy (OPMB), and benzyloxy (OBn), a thorough analysis was conducted on the corresponding l-glucosides. The results unveiled a distinct trend where the efficiency of methylenation followed the trend OBn > OPMB > N. Finally, the C6-alkene was dihydroxylated in the presence of osmium tetroxide to yield the expected l/d-glycero-l-glucoheptosides. The lead building block, which features a C-4 azide, was delivered as a phenyl thioglycoside. Added to the suitable masking of the 6,7-diol, this combination enables further functionalization to achieve versatile compounds of biological interest. The study insights into the interplay between substitution at C-4 and carbon homologation at C-6 provide valuable guidance for future endeavors in the synthesis of these carbohydrate molecules.
Topics: Glucose; Azides; Heptoses; Carbon
PubMed: 38016254
DOI: 10.1016/j.carres.2023.108985 -
Journal of Medical Imaging (Bellingham,... Sep 2023Assessing the complex three-dimensional (3D) structure of the cochlea is crucial to understanding the fundamental aspects of signal transduction in the inner ear and is...
PURPOSE
Assessing the complex three-dimensional (3D) structure of the cochlea is crucial to understanding the fundamental aspects of signal transduction in the inner ear and is a prerequisite for the development of novel cochlear implants. X-ray phase-contrast computed tomography offers destruction-free 3D imaging with little sample preparation, thus preserving the delicate structure of the cochlea. The use of heavy metal stains enables higher contrast and resolution and facilitates segmentation of the cochlea.
APPROACH
For μ-CT of small animal and human cochlea, we explore the heavy metal osmium tetroxide (OTO) as a radiocontrast agent and delineate laboratory from synchrotron CT. We investigate how phase retrieval can be used to improve the image quality of the reconstructions, both for stained and unstained specimens.
RESULTS
Image contrast for soft tissue in an aqueous solution is insufficient under the in-house conditions, whereas the OTO stain increases contrast for lipid-rich tissue components, such as the myelin sheaths in nervous tissue, enabling contrast-based rendering of the different components of the auditory nervous system. The overall morphology of the cochlea with the three scalae and membranes is very well represented. Further, the image quality of the reconstructions improves significantly when a phase retrieval scheme is used, which is also suitable for non-ideal laboratory settings. With highly brilliant synchrotron radiation (SR), we achieve high contrast for unstained whole cochleae at the cellular level.
CONCLUSIONS
The OTO stain is suitable for 3D imaging of small animal and human cochlea with laboratory , and relevant pathologies, such as a loss of sensory cells and neurons, can be visualized. With SR and optimized phase retrieval, the cellular level can be reached even for unstained samples in aqueous solution, as demonstrated by the high visibility of single hair cells and spiral ganglion neurons.
PubMed: 37753271
DOI: 10.1117/1.JMI.10.5.053501 -
Ultramicroscopy Nov 2022Muscle samples are commonly chemically fixed or frozen immediately upon collection for biochemical and morphological analysis. Certain fixatives such as glutaraldehyde...
Muscle samples are commonly chemically fixed or frozen immediately upon collection for biochemical and morphological analysis. Certain fixatives such as glutaraldehyde and osmium tetroxide are widely used for transmission electron microscopy (TEM) and lead to adequate preservation of muscle ultrastructure, but do not preserve the molecular features of samples. Methacarn is suggested to be a preferable chemical fixative for light microscopy because it maintains immunohistological features of samples. However, the efficacy of methacarn to preserve ultrastructural features as a primary chemical fixative for TEM is currently unclear. Additionally, cryo-preservation of samples for TEM analysis involves freezing processes such as plunge freezing, slam freezing, or high pressure freezing. High pressure freezing is the considered the gold standard but requires costly equipment and may not be a viable option for many labs collecting tissue samples from remote locations. Dimethyl sulfoxide (DMSO) is a commonly used cryoprotectant that may allow for better structural preservation of samples by impairing ice damage that occurs during plunge/snap freezing. We aimed to assess the effectiveness of methacarn as a primary chemical fixative and determine the effect of pre-coating samples with DMSO before plunge/snap freezing tissues to be prepared for TEM. The micrographs of the methcarn-fixed samples indicate a loss of Z-disk integrity, intermyofibrillar space, mitochondria structure, and lipids. Ultimately, methacarn is not a viable primary fixative for tissue sample preparation for TEM. Similarly, liquid nitrogen freezing of samples wrapped in aluminum foil produced non-uniform Z-disk alignments that appeared smeared with swollen mitochondria. DMSO coating before freezing appears to lessen the alterations to contractile and mitochondrial morphological structures. DMSO appears to be useful for preserving the ultrastructure of sarcomeres if samples are covered before freezing.
Topics: Acetic Acid; Aluminum; Chloroform; Cryopreservation; Dimethyl Sulfoxide; Fixatives; Glutaral; Ice; Methanol; Microscopy, Electron, Transmission; Muscles; Osmium Tetroxide
PubMed: 35988477
DOI: 10.1016/j.ultramic.2022.113600 -
Journal of Neuroscience Methods Jun 2020Dense and unbiased cellular-resolution representations of extended volumetric central nervous system soft-tissue anatomy are difficult to obtain, even in experimental...
BACKGROUND
Dense and unbiased cellular-resolution representations of extended volumetric central nervous system soft-tissue anatomy are difficult to obtain, even in experimental post-mortem settings. Interestingly, X-ray phase-contrast computed tomography (X-PCI-CT), an emerging soft-tissue-sensitive volumetric imaging technique, can provide multiscale organ- to cellular-level morphological visualizations of neuroanatomical structure.
NEW METHOD
Here, we tested different nervous-tissue fixation procedures, conventionally used for transmission electron microscopy, to better establish X-PCI-CT-specific sample-preparation protocols. Extracted rat spinal medullas were alternatively fixed with a standard paraformaldehyde-only aldehyde-based protocol, or in combination with glutaraldehyde. Some specimens were additionally post-fixed with osmium tetroxide. Multiscale X-PCI-CT datasets were collected at several synchrotron radiation facilities, using state-of-the-art setups with effective image voxel sizes of 3.0 to 0.3 μm, and compared to high-field magnetic resonance imaging, histology and vascular fluorescence microscopy data.
RESULTS
Multiscale X-PCI-CT of aldehyde-fixed spinal cord specimens resulted in dense histology-like volumetric representations and quantifications of extended deep spinal micro-vascular networks and of intra-medullary cell populations. Osmium post-fixation increased intra-medullary contrast between white and gray-matter tissues, and enhanced delineation of intra-medullary cellular structure, e.g. axon fibers and motor neuron perikarya.
COMPARISON WITH EXISTING METHODS
Volumetric X-PCI-CT provides complementary contrast and higher spatial resolution compared to 9.4 T MRI. X-PCI-CT's advantage over planar histology is the volumetric nature of the cellular-level data obtained, using samples much larger than those fit for volumetric vascular fluorescence microscopy.
CONCLUSIONS
Deliberately choosing (post-)fixation protocols tailored for optimal nervous-tissue structural preservation is of paramount importance in achieving effective and targeted neuroimaging via the X-PCI-CT technique.
Topics: Aldehydes; Animals; Osmium; Percutaneous Coronary Intervention; Rats; Rodentia; Spinal Cord; X-Ray Microtomography; X-Rays
PubMed: 32353471
DOI: 10.1016/j.jneumeth.2020.108744 -
The Journal of Sexual Medicine Feb 2023It is frequently quoted in mainstream media that the clitoris has "8000 nerve endings." However, no study has yet quantified the number of nerve fibers (axons)...
INTRODUCTION
It is frequently quoted in mainstream media that the clitoris has "8000 nerve endings." However, no study has yet quantified the number of nerve fibers (axons) innervating the human clitoris. The dorsal nerves of the clitoris (DNCs) are the primary source of sensation and somatic clitoral innervation. Therefore, reporting the number of axons in the DNCs is an important step in our understanding of clitoral innervation and sexual response with implications for many fields of medical practice. The purpose of this study is to quantify the mean number of axons in the human DNCs and to report the approximate mean number of nerve fibers that innervate the human glans clitoris.
METHODS
DNC samples were obtained from 7 transmasculine patients undergoing gender-affirming phalloplasty surgery. At the time of nerve coaptation, a small excess of the DNC (5 mm) was collected for analysis at the proximal level of the clitoral body, just distal of the emergence of the DNCs from underneath the pubic symphysis. Samples were placed into 3% glutaraldehyde fixative, postfixed in 1% osmium tetroxide, and serially dehydrated in ethanol and toluene. Samples were then embedded in araldite, sectioned on an ultramicrotome into 1-μm cross sections, and counterstained with 1% toluidine blue. Histomorphometric evaluation was performed at 1000x magnification with a Leitz Laborlux S microscope and image analysis software (Clemex Vision Professional) to obtain an axon counts. Descriptive statistics were performed to yield a mean and standard deviation of the number of axons in the DNCs. Assuming anatomic symmetry between bilateral DNCs, mean total number of somatic nerve fibers innervating the human glans clitoris was obtained by doubling the mean count of the DNCs.
RESULTS
Seven sample DNCs were collected. Of those, 5 were analyzed as 2 did not have sufficient nerve tissue present. The mean number of nerve fibers in the human DNCs was 5140 (SD = 218.4). The mean number of myelinated nerve fibers innervating the human clitoris was 10,281 (SD = 436.8).
CONCLUSION
This study is the first to report the number of axons in the human DNC, at a mean 5140. Given the bilateral nature of clitoral innervation and symmetry of anatomic structures, the approximate mean number of myelinated axons that innervate the human glans clitoris is 10,280. When the uncaptured unmyelinated fibers and contributions from the cavernosal innervation are accounted for, it is clear that far Moree than 8000 axons innervate the human clitoris.
Topics: Female; Humans; Clitoris; Nerve Fibers; Nerve Tissue; Sensation; Sexual Behavior
PubMed: 36763957
DOI: 10.1093/jsxmed/qdac027 -
Journal of Structural Biology Oct 2020Compared with conventional two-dimensional transmission electron microscopy (TEM), focused ion beam scanning electron microscopy (FIB-SEM) can provide more comprehensive...
Compared with conventional two-dimensional transmission electron microscopy (TEM), focused ion beam scanning electron microscopy (FIB-SEM) can provide more comprehensive 3D information on cell substructures at the nanometer scale. Biological samples prepared by cryofixation using high-pressure freezing demonstrate optimal preservation of the morphology of cellular structures, as these are arrested instantly in their near-native states. However, samples from cryofixation often show a weak back-scatter electron signal and bad image contrast in FIB-SEM imaging. In addition, it is impossible to do large amounts of heavy metal staining. This is commonly achieved via established osmium impregnation (OTO) en bloc staining protocols. Here, we compared the FIB-SEM image quality of brain tissues prepared using several common freeze-substitution media, and we developed an approach that overcomes these limitations through a combination of osmium tetroxide, uranyl acetate, tannic acid, and potassium permanganate at proper concentrations, respectively. Using this optimized sample preparation protocol for high-pressure freezing and freeze-substitution, perfect smooth membrane morphology, even of the lipid bilayers of the cell membrane, was readily obtained using FIB-SEM. In addition, our protocol is broadly applicable and we demonstrated successful application to brain tissues, plant tissues, Caenorhabditis elegans, Candida albicans, and chlorella. This approach combines the potential of cryofixation for 3D large volume analysis of subcellular structures with the high-resolution capabilities of FIB-SEM.
Topics: Animals; Cryopreservation; Freeze Substitution; Freezing; Imaging, Three-Dimensional; Metals, Heavy; Mice; Microscopy, Electron, Scanning; Microscopy, Electron, Transmission; Staining and Labeling
PubMed: 32798655
DOI: 10.1016/j.jsb.2020.107600 -
Cancers Jan 2023Hydrodynamic transfection (HT) or hydrodynamic tail vein injection (HTVi) is among the leading technique that is used to deliver plasmid genes mainly into the liver of...
Hydrodynamic transfection (HT) or hydrodynamic tail vein injection (HTVi) is among the leading technique that is used to deliver plasmid genes mainly into the liver of live mice or rats. The DNA constructs are composed of coupled plasmids, while one contains the gene of interest that stably integrate into the hepatocyte genome with help of the other consisting sleeping beauty transposase system. The rapid injection of a large volume of DNA-solution through the tail vein induces an acute cardiac congestion that refluxed into the liver, mainly in acinus zone 3, also found through our EM study. Although, HT mediated hydrodynamic force can permeabilizes the fenestrated sinusoidal endothelium of liver, but the mechanism of plasmid incorporation into the hepatocytes remains unclear. Therefore, in the present study, we have hydrodynamically injected 2 mL volume of empty plasmid (transposon vector) or saline solution (control) into the tail vein of anesthetized C57BL/6J/129Sv mice. Liver tissue was resected at different time points from two animal group conditions, i.e., one time point per animal (1, 5, 10-20, 60 min or 24 and 48 hrs after HT) or multiple time points per animal (0, 1, 2, 5, 10, 20 min) and quickly fixed with buffered 4% osmium tetroxide. The tissues fed with only saline solution was also resected and fixed in the similar way. EM evaluation from the liver ultrathin sections reveals that swiftly after 1 min, the hepatocytes near to the central venule in the acinus zone 3 shows cytoplasmic membrane-bound vesicles. Such vesicles increased in both numbers and size to vacuoles and precisely often found in the proximity to the nucleus. Further, EM affirm these vacuoles are also optically empty and do not contain any electron dense material. Although, some of the other hepatocytes reveals sign of cell damage including swollen mitochondria, dilated endoplasmic reticulum, Golgi apparatus and disrupted plasma membrane, but most of the hepatocytes appeared normal. The ultrastructural findings in the mice injected with empty vector or saline injected control mice were similar. Therefore, we have interpreted the vacuole formation as nonspecific endocytosis without specific interactions at the plasma membrane.
PubMed: 36672277
DOI: 10.3390/cancers15020328 -
International Journal For Parasitology Sep 2021Parasitic infections can be challenging to study because two dimensional light and electron microscopy are often limited in visualising complex and inaccessible...
Parasitic infections can be challenging to study because two dimensional light and electron microscopy are often limited in visualising complex and inaccessible attachment sites. Exemplifying this, Trichuris spp. inhabit a tunnel of epithelial cells within the host caecum and colon. A significant global burden of this infection persists, partly because available anthelminthics lack efficacy, although the mechanisms underlying this remain unknown. Consequently, there is a need to pioneer new approaches to better characterize the parasite niche within the host and investigate how variation in its morphology and integrity may contribute to resistance to therapeutic intervention. To address these aims, we exploited three-dimensional X-ray micro-computed tomography (microCT) to image the mouse whipworm, Trichuris muris, in caeca of wild-type C57BL/6 and SCID mice ex vivo. Using osmium tetroxide staining to effectively enhance the contrast of worms, we found that a subset exhibited preferential positioning towards the bases of the intestinal crypts. Moreover, in one rare event, we demonstrated whipworm traversal of the lamina propria. This morphological variability contradicts widely accepted conclusions from conventional microscopy of the parasite niche, showing Trichuris in close contact with the host proliferative and immune compartments that may facilitate immunomodulation. Furthermore, by using a skeletonization-based approach we demonstrate considerable variation in tunnel length and integrity. The qualitative and quantitative observations provide a new morphological point of reference for future in vitro study of host-Trichuris interactions, and highlight the potential of microCT to characterise enigmatic host-parasite interactions more accurately.
Topics: Animals; Mice; Mice, Inbred C57BL; Mice, SCID; Mucous Membrane; Trichuriasis; Trichuris; X-Ray Microtomography
PubMed: 34216623
DOI: 10.1016/j.ijpara.2021.04.006 -
Methods in Molecular Biology (Clifton,... 2024The study of the localization of secondary metabolites in both plants and the cell cultures on the intravital sections is hampered by the difficulty of obtaining thin,...
The study of the localization of secondary metabolites in both plants and the cell cultures on the intravital sections is hampered by the difficulty of obtaining thin, correctly oriented sections. Techniques for fixing tissues in resins allow these difficulties to be overcome. Properly selected tissue fixation techniques allow using different dyes to identify the compound of interest. In addition, some components of tissue fixation can act as fixatives and as a dye for identifying secondary metabolites. For example, osmium tetroxide, which fixes lipids in tissues, stains phenolic compounds black. This paper describes methods for the detection of phenolic compounds in morphogenic callus culture of buckwheat using osmium tetroxide, Toluidine Blue O dye, and ferric chloride as dyes in epoxy resin-embedded cell culture with double fixation of the material and when material fixed in Karnovsky's fixative.
Topics: Coloring Agents; Osmium Tetroxide; Chlorides; Tolonium Chloride; Fagopyrum; Fixatives; Tissue Fixation; Cell Culture Techniques; Iron; Osmium; Ferric Compounds
PubMed: 38532090
DOI: 10.1007/978-1-0716-3794-4_4