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The Application of an Electron Microscope in the Study of Cell Structure

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 3788

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Dr. Ivana Bocina

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Guest Editor

Department of Biology, Faculty of Science, University of Split, 21000 Split, Croatia
Interests: study of tissues and cells, especially renal and intestinal tissues at the level of electron microscopy

Special Issue Information

Dear Colleagues,

In the era of the rapid growth of molecular sciences, immunotherapy, pharmacology and biomedicine in general, it is important to know how different molecular and biochemical mechanisms affect the ultrastructural features of cells and tissues. The electron microscope is an indispensable tool in the study of cell structure, whether we study the basic cell structure or structural changes caused by disease or environmental influence.

This Special Issue focuses on studies that aimed to investigate cell and tissue structure at the level of a transmission (TEM) or scanning (SEM) electron microscope in order to elucidate the pathological changes in cell structure caused by different internal or external factors, and improvements in cell structure caused by various molecular mechanisms or therapeutic treatments. A special focus is given to the immuno-labeling of various proteins expressed in cells exposed to diseases, harmful environmental influences or different treatments. Please note that pure clinical studies are not suitable for the journal but clinical or pure model submission based on biomolecular experiments are very welcome.

Dr. Ivana Bocina
Guest Editor

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Keywords

intracellular structure
organelles
cell surface structure
immuno-labeling

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Published Papers (5 papers)

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23 pages, 13591 KB

Open AccessArticle

Cage-Farming Causes Histopathological Alterations in the Renal Tissues of the Rainbow Trout Oncorhynchus mykiss (Walbaum, 1792)

by Marina Ugrin, María Fernandez Godoy, Ivana Restović, Jerko Hrabar, Nives Kević and Ivana Bočina

Int. J. Mol. Sci. 2025, 26(22), 10876; https://doi.org/10.3390/ijms262210876 - 9 Nov 2025

Viewed by 961

Abstract

Fish are widely recognized as effective bioindicators in ecotoxicological studies due to their repeated exposure to aquatic pollutants that accumulate in metabolically active organs, often leading to histopathological changes. In aquaculture, cage-farmed fish experience continuous environmental and culture-related stress, which can affect renal integrity. The kidney, a central osmoregulatory organ, is particularly sensitive to such conditions. Renal tissues were collected from different growth stages of cage-farmed rainbow trout. Hematoxylin and eosin staining was performed to detect morphological alterations, while transmission electron microscopy was used to assess cellular damage at the ultrastructural level. The expression of fibronectin and caspase-3, markers of extracellular matrix remodeling and apoptosis, respectively, was also evaluated. TEM examination showed pronounced alterations in both the glomeruli and renal tubules, accompanied by increased expression of fibronectin and caspase-3, indicating ongoing tissue remodeling and cellular stress. This study demonstrates that cage-farmed rainbow trout exhibit progressive ultrastructural kidney alterations that appear to be associated with environmental confinement, nutritional practices, and prophylactic treatments. These conditions collectively contribute to renal stress and the onset of nephropathic changes in aquaculture settings. Further research should focus on molecular marker expression to better understand renal adaptation and injury progression under intensive farming conditions. Full article

(This article belongs to the Special Issue The Application of an Electron Microscope in the Study of Cell Structure)

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15 pages, 11561 KB

Open AccessArticle

The Conserved GTPase LepA May Contribute to the Final Proper Stabilization of the 3′ Domain of the 30S Subunit During Ribosome Assembly

by Olesya Kravchenko, Elena Maksimova, Timur Baymukhametov, Irina Eliseeva and Elena Stolboushkina

Int. J. Mol. Sci. 2026, 27(1), 489; https://doi.org/10.3390/ijms27010489 - 3 Jan 2026

Viewed by 719

Abstract

The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal subunit biogenesis. Here, using cryo-electron microscopy, we characterized 30S subunits isolated from an Escherichia coli strain with a deleted lepA gene. The cryo-EM maps for ∆lepA 30S particles were divided into classes corresponding to consecutive assembly intermediates: from particles characterized by unformed helices h44/h45 of the central decoding center (CDR) and highly flexible head, through intermediates with a distorted CDR and a partial stabilization of the head, to near-mature 30S subunits with correctly docked h44 in the CDR, accessible 3′ end of 16S rRNA for translation but significant flexibility in head domain. Cryo-EM analysis of ΔlepA 30S intermediates revealed that they predominantly proceed to nearly mature functional state and exhibit suboptimal flexibility in the head domain. This finding suggests that LepA likely contributes to the final proper stabilization of the 3′ domain of the 30S subunit during ribosome assembly. Full article

(This article belongs to the Special Issue The Application of an Electron Microscope in the Study of Cell Structure)

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29 pages, 14394 KB

Open AccessArticle

Ultrastructural Features, Immune Response, and Junctional Proteins in the Seminiferous Epithelium of SARS-CoV-2-Infected Mice

by Salmo Azambuja de Oliveira, André Acácio Souza da Silva, Barry T. Hinton, Paulo Sérgio Cerri and Estela Sasso-Cerri

Int. J. Mol. Sci. 2026, 27(2), 691; https://doi.org/10.3390/ijms27020691 - 9 Jan 2026

Viewed by 642

Abstract

During the COVID-19 pandemic, the prevalence of death in men was higher than in women. Using transgenic mice expressing the human angiotensin-converting enzyme 2 (hACE2), we demonstrated that SARS-CoV-2 infects Leydig cells and uses its steroidogenic machinery for replication. This study investigates the impact of SARS-CoV-2 in the seminiferous epithelium of K18-hACE2 mice, focusing on the immune response, junctional proteins, and spermatogenesis. The seminiferous tubules (STs) and epithelial (EA) areas were measured. The number of Sertoli cells (SCs), spermatocytes, and damaged ST was quantified. Ultrastructural analysis was performed under transmission electron microscopy. Angiotensin II levels and immunolocalization of hACE2, spike, and nucleocapsid were evaluated. TUNEL and immunoreactions for Ki-67, TNF-α, INF-γ, iNOS, NF-κB, and Conexin-43 were performed and correlated with Jam-α, Stat1, Stat3, and iNOS expressions. hACE2, spike, and nucleocapsid immunolabeling were detected in the epithelium along with high angiotensin II levels in the infected mice. The infection caused a significant reduction in ST, EA, spermatocytes, SCs, Ki-67+ cells, Cx43 immunoexpression, and Jam-a expression. In the epithelium, TNF-α, IFN-γ, iNOS, and nuclear NF-κB immunolabeling increased along with Stat1 upregulation. These findings, combined with the increased epithelial hACE2 and high angiotensin II levels, confirm epithelial responsiveness to the infection and explain the spermatogenic failure and impaired junctional proteins. The presence of viral particles, increased TNF-α immunolabeling, and apoptotic features in Sertoli cells suggests that these sustentacular cells are targets for viral infection in the epithelium, and, due to their extensive projections and ability to phagocytize dying infected germ cells, they may disseminate the viruses throughout the epithelium. Full article

(This article belongs to the Special Issue The Application of an Electron Microscope in the Study of Cell Structure)

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15 pages, 2871 KB

Open AccessArticle

Ultrastructural Study of the Effects of Hybrid Compounds of Natural Monoterpene Carvacrol and Synthetic Cationic Amphiphile DL₄12 on S. aureus and E. faecalis Cells

by Elena S. Ryabova, Alina E. Grigor’eva, Alevtina V. Bardasheva, Anastasiya V. Tupitsyna, Danila A. Zadvornykh, Lyudmila S. Koroleva and Elena I. Ryabchikova

Int. J. Mol. Sci. 2026, 27(5), 2217; https://doi.org/10.3390/ijms27052217 - 26 Feb 2026

Viewed by 370

Abstract

Ultrastructure changes in S. aureus and E. faecalis bacteria incubated with synthetic cationic amphiphile DL₄12 and its hybrids with the natural monoterpene carvacrol were studied. The hybrid compounds DL₄CAR-6, DL₅CAR-6, DLpCAR-6, and DLoCAR-6 contained two carvacrol molecules and differed in central linker structure. The study was conducted on ultrathin sections of bacteria fixed by the Ryter–Kellenberger method and on a Jem 1400 transmission electron microscope (Jeol, Tokyo, Japan). Ultrastructure changes in S. aureus and E. faecalis incubated with compound DL₄12 were species-specific. Destructive changes in S. aureus cells when exposed to DL₄12 compound and all DL₄12-carvacrol hybrids did not differ. DL₄12 and DL₄12-carvacrol hybrids in E. faecalis cells damaged all structures except the cell wall. Compound DL₄12 and its hybrids disrupted the ultrastructure of nucleoid and DNA strands in both bacterial species. Complete disorganization of ribosomes in cells of both bacteria occurred upon incubation with compound DL₄12 and its carvacrol-bearing analog DL₄CAR-6. Inclusions in bacterial cells exposed to all compounds had the same ultrastructure. The study showed that all compounds used possess multitarget properties; the structure of the central linker of hybrid compounds plays a significant role in the nature of their damaging effect on S. aureus and E. faecalis cells. Full article

(This article belongs to the Special Issue The Application of an Electron Microscope in the Study of Cell Structure)

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26 pages, 7070 KB

Open AccessReview

Accomplishments of “Old-Fashioned” Electron Microscopy in the Period of Dominance of Immunofluorescent Methods

by Yury M. Morozov and Pasko Rakic

Int. J. Mol. Sci. 2026, 27(6), 2803; https://doi.org/10.3390/ijms27062803 - 19 Mar 2026

Viewed by 623

Abstract

The goal of this review is to bring to the attention of the scientific community the opportunities of transmission electron microscopy for analyses of biological subjects and resolving complicated cases of data interpretation. Although procedures for electron microscopy are in general more elaborate (particularly for simultaneous immunolabeling of multiple antigens) compared to fluorescent microscopy, they can help view cellular morpho-functional features undetectable using other methods. In this review, we consider several unexpected and serendipitous discoveries made in our laboratory and fulfilled using unique opportunities provided by electron microscopy of ultrathin sections. We are deliberating the following topics: interpretation of unusual results of immunolabeling; a novel method for in situ identification of cells undergoing mitochondrial disorder and necrosis-like death; the sequence of organelles’ reorganization in dying cells; simultaneous rupture of nuclear and plasma membranes in migrating neurons; and the role of cytoskeleton in lateral expansion of the cerebral cortex. Full article

(This article belongs to the Special Issue The Application of an Electron Microscope in the Study of Cell Structure)

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