Microscopic and spectroscopic analysis of atmospheric iron-containing single particles in Lhasa, Tibet

The Tibetan Plateau, known as the "Third Pole", is currently in a state of perturbation caused by intensified human activity. In this study, 56 samples were obtained at the five sampling sites in typical area of Lhasa city and their physical and chemical properties were investigated by TEM/EDS, STXM, and NEXAFS spectroscopy. After careful examination of 3387 single particles, the results showed that Fe should be one of the most frequent metal elements. The Fe-containing single particles in irregular shape and micrometer size was about 7.8% and might be mainly from local sources. Meanwhile, the Fe was located on the subsurface of single particles and might be existed in the form of iron oxide. Interestingly, the core-shell structure of iron-containing particles were about 38.8% and might be present as single-, dual- or triple-core shell structure and multi-core shell structure with the Fe/Si ratios of 17.5, 10.5, 2.9 and 1.2, respectively. Meanwhile, iron and manganese were found to coexist with identical distributions in the single particles, which might induce a synergistic effect between iron and manganese in catalytic oxidation. Finally, the solid spherical structure of Fe-containing particles without an external layer were about 53.4%. The elements of Fe and Mn were co-existed, and might be presented as iron oxide-manganese oxide-silica composite. Moreover, the ferrous and ferric forms of iron might be co-existed. Such information can be valuable in expanding our understanding of Fe-containing particles in the Tibetan Plateau atmosphere.

Evaluating the biological (antidiabetic) potential of TEM, FTIR, XRD, and UV-spectra observed berberis lyceum conjugated silver nanoparticles

Diabetes is a life-threatening disease that affects different parts of the body including the liver, kidney, and pancreas. The core root of diabetes is mainly linked to oxidative stress produced by reactive oxygen species (ROS). Berberis lyceum Royle (BLR) is the source of natural products. It comprises numerous bioactive compounds having antioxidant activities. In the current investigation, silver nanoparticles from BLR root extract were synthesized, characterized, and assessed for antidiabetic potential. UV spectrophotometry, Transmission electron microscopy (TEM), Fourier transform infra-red spectroscopy (FTIR), and x-ray diffraction (XRD) were applied for the characterization of NPs. It was evident from the morphological studies that the synthesized NPs were spherical and the average size was 11.02 nm. Results revealed that BLR-AgNPs showed higher radical scavenging activity as compared to BLR extract. Moreover, BLR-AgNPs displayed superior in vivo and in vitro antidiabetic activity in comparison to BLR extract. Glucose level (116.5 ± 5.1 mg/dL), liver function test (ALAT: 54.038 ± 6.2 IU/L; ASAT: 104.42 ± 13.9 IU/L; ALP: 192.6 ± 2.4 IU/L; bilirubin: 1.434 ± 0.14 mg/dL; total protein: 5.14 ± 0.24 mg/dL), renal function test (urea: 39.6 ± 0.63 mg/dL; uric acid: 21.4 ± 0.94 mg/dL; creatinine: 0.798 ± 0.03 mg/dL; albumin: 4.14 ± 0.2 mg/dL), lipid profile level (cholesterol: 101.62 ± 3 mg/dL; triglyceride: 110.42 ± 7 mg/dL; HDL-C: 29.7 ± 3 mg/dL; LDL-C: 47.056 ± 1 mg/dL; VLDL-C: 22.0 ± 1.3 mg/dL) and hematology (WBCs: 3.82 ± 0.24 103 /μL; RBCs: 4.78 ± 0.42 106 /μL; Hb: 12.6 ± 1.0 g/dL; Hematocrit: 39.4 ± 3.7%; MCV: 65.8 ± 3 fL; platelets: 312 ± 22.4; neutrophils: 34.8 ± 1.87; eosinophils: 3.08 ± 0.43; monocytes: 3.08 ± 0.28; lymphocytes: 75.6 ± 3.77) confirmed the significant antidiabetic potential of BLR-AgNPs. Histopathological examination authenticated that BLR-AgNPs caused a significant revival in the morphology of the liver, kidney, and pancreas. Hence, findings of the study suggested the BLR-AgNPs as a potent antidiabetic agent and could be an appropriate nanomedicine to prevent diabetes in future. RESEARCH HIGHLIGHTS: Berberis lyceum extract as a reducing, capping, and stabilization agent for the BLR-AgNPs synthesis Evaluation of α-amylase inhibition, antioxidant, and α-glucosidase inhibition potential Thorough characterization using Fourier transform infrared spectroscopy, Transmission electron microscopy, x-ray diffraction, and UV-VIS spectrophotometer, which is 1st of its kind In-vivo antidiabetic activity evaluation through multiple biomarkers.

A systematic study of the effect of lipid architecture on cytotoxicity and cellular uptake of cationic cubosomes

HYPOTHESIS

Lipid nanoparticles containing a cationic lipid are increasingly used in drug and gene delivery as they can display improved cellular uptake, enhanced loading for anionic cargo such as siRNA and mRNA or exhibit additional functionality such as cytotoxicity against cancer cells. This research study tests the hypothesis that the molecular structure of the cationic lipid influences the structure of the lipid nanoparticle, the cellular uptake, and the resultant cytotoxicity.

EXPERIMENTS

Three potentially cytotoxic cationic lipids, with systematic variations to the hydrophobic moiety, were designed and synthesised. All the three cationic lipids synthesised contain pharmacophores such as the bicyclic coumarin group (CCA12), the tricyclic etodolac moiety (ETD12), or the large pentacyclic triterpenoid "ursolic" group (U12) conjugated to a quaternary ammonium cationic lipid containing twin C12 chains. The cationic lipids were doped into monoolein cubosomes at a range of concentrations from 0.1 mol% to 5 mol% and the effect of the lipid molecular architecture on the cubosome phase behaviour was assessed using a combination of Small Angle X-Ray Scattering (SAXS), Dynamic Light Scattering (DLS), zeta-potential and cryo-Transmission Electron Microscopy (Cryo-TEM). The resulting cytotoxicity of these particles against a range of cancerous and non-cancerous cell-lines was assessed, along with their cellular uptake.

FINDINGS

The molecular architecture of the cationic lipid was linked to the internal nanostructure of the resulting cationic cubosomes with a transition to more curved cubic and hexagonal phases generally observed. Cubosomes formed from the cationic lipid CCA12 were found to have improved cellular uptake and significantly higher cytotoxicity than the cationic lipids ETD12 and U12 against the gastric cancer cell-line (AGS) at lipid concentrations ≥ 75 µg/mL. CCA12 cationic cubosomes also displayed reasonable cytotoxicity against the prostate cancer PC-3 cell-line at lipid concentrations ≥ 100 µg/mL. In contrast, 2.5 mol% ETD12 and 2.5 mol% U12 cubosomes were generally non-toxic against both cancerous and non-cancerous cell lines over the entire concentration range tested. The molecular architecture of the cationic lipid was found to influence the cubosome phase behaviour, the cellular uptake and the toxicity although further studies are necessary to determine the exact relationship between structure and cellular uptake across a range of cell lines.

Malformation of the endoplasmic reticulum system evolving into giant inclusions and Auer bodies in acute promyelocytic leukemia: an ultrastructural study of 6 cases

The endoplasmic reticulum（ER）is the largest membranous network serving as a region for protein, lipid and steroid synthesis, transport and storage. Detailed information about ER-cisternae, ER-tubules and rough endoplasmic reticulum (rER) is scarce in human blood cells. This study describes a series of giant inclusions and Auer bodies in promyeloblasts in six patients with acute promyelocytic leukemia (APL), by light microscopy, transmission electron microscopy (TEM) and cytochemical stains. TEM revealed that giant inclusions and pro-Auer bodies were associated with rER and surrounded by tubular structures composed of degenerated or redundant membrane in promyeloblasts, which corresponded with elements of the ER system. This paper reveals that in the promyeloblasts of APL, ER is the source of and transforms progressively into giant inclusions and Auer bodies.

Heterogeneity of mesenchymal cells in human amniotic membrane at term

There is increasing interest in understanding the tissue biology of human amniotic membrane (hAM) given its applications in medicine. One cellular component is mesenchymal cells, which can be extracted, cultured and differentiated "in vitro" into various cell types. These studies show that there is heterogeneity among mesenchymal cells. The aim of this work is to study the membrane in situ to determine whether this cellular heterogeneity exists. The hAMs were obtained from caesarean deliveries at term and analyzed by histological techniques. Types I-III mesenchymal cells and Hofbauer were distinguished by light microscopy. Histochemically, mesenchymal cell types showed successively increasing positivity to: PAS, vimentin, fibronectin, and Concanavalin-A; VGEF, TGF-β2, PDGF-C, FGF-2. By the semiquantitative point of view, the percentage of Type II cells was 60%, significantly higher than the other types. With transmission electron microscopy, an intermediate cell type between II-III was observed. Strong vesiculation of the rough endoplasmic reticulum (RER) with exocytosis was observed. In addition, an accumulation of a similar material to the extracellular matrix in the RER caused its dilation especially in type IIITEM cells. Some of this material acquired a globular structure. These structures were also found free in the extracellular matrix. In conclusion, the mesenchymal cells of the fibroblastic layer of the hAMs studied are heterogeneous, with some undifferentiated and others with a probably senescent fibroblastic phenotype with accumulation in their RER of fibronectin. These results may be of interest to extract mesenchymal cells from hAMs for use in regenerative medicine and to better understand the mechanisms of fetal membrane rupture.

Ultrastructural characterization and quantification of hemocytes in engorged female Amblyomma sculptum ticks

Amblyomma sculptum (formerly Amblyomma cajennense) ticks have been implicated in the transmission of pathogens that cause diseases in animals and humans. Their wide geographic distribution and high impact on animal health and zoonotic disease transmission highlight the importance of studying and implementing effective control measures to mitigate the risks associated with this tick species. The aim of this study was to quantify and characterize the morphology and the ultrastructure of different types of hemocytes in the hemolymph in engorged A. sculptum females fed on rabbits. The hemolymph samples were collected by perforation of the cuticle in the dorsal region. Hemocyte types, sizes, and differential counts were determined using light microscopy, while ultrastructural analysis of hemocytes was performed using transmission electron microscopy. The average number of total hemocytes in the hemolymph was 1024 ± 597.6 cells µL-1. Five morphologically distinct cell types were identified in A. sculptum females: prohemocytes (6 % ± 8.8), plasmatocytes (10 % ± 7.7), granulocytes (78 % ± 12.2), spherulocytes (5 % ± 4.48), and oenocytoids (1 % ± 1.6). In general, prohemocytes were the smallest hemocytes. The ultrastructural morphology of A. sculptum hemocytes described in the present study agrees with the findings for other hard ticks. This is the first study to investigate ultrastructural characteristics of hemocytes of female A. sculptum ticks.

Ultrastructural diversity in the shell of Artemia resting eggs

The shell of Artemia resting egg, which is a delicate multilayered envelope surrounding the inside diapause embryo, plays an important role in the survival strategy of Artemia. To date, the ultrastructure of resting eggshell has been studied for only handful populations, and knowledge about the diversity of shell structure is still limited. In this paper, resting eggs from 13 Artemia populations were studied by transmission electron microscopy. Results show that the basic configuration of resting eggshell is quite conservative, but variations are not uncommon in the fine ultrastructure of each main layer of the shell (e.g., the shape and distribution of the radially oriented pores in the cortical layer; the size, number and arrangement of chambers in the alveolar layer; and the development state of outer cuticular membrane [OCM]). The ultrastructural variation of eggshell seems not to be linked with species and reproductive mode of Artemia. Resting eggs from very high habitats (4300+ m above sea level [a.s.l.]) on Qinghai-Tibet Plateau and certain tropical salterns have a hypoplastic OCM, which may be related to the adaptation to habitat conditions such as low oxygen concentration. RESEARCH HIGHLIGHTS: Comparative study on resting eggs from 13 Artemia populations reveals high diversity in the fine structure of eggshell. Resting eggs from very high (4300+ m a.s.l.) habitats commonly have a hypoplastic OCM.

Exploring the antibiofilm and toxicity of tin oxide nanoparticles: Insights from in vitro and in vivo investigations

BACKGROUND INFORMATION

The advancement of biological-mediated nanoscience towards higher levels and novel benchmarks is readily apparent, owing to the use of non-toxic synthesis processes and the incorporation of various additional benefits. This study aimed to synthesize stable tin oxide nanoparticles (SnO2-NPs) using S. rhizophila as a mediator.

METHODS

The nanoparticles that were created by biosynthesis was examined using several analytical techniques, including Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM), X-ray diffraction (XRD), UV-visible (UV-vis) spectroscopy, and energy dispersive X-ray spectroscopy (EDS).

RESULTS

The results obtained from the characterization techniques suggest that S. rhizophila effectively catalyzed the reduction of SnCl2 to SnO2-NPs duration of 90 min at ambient temperature with the ƛmax of 328 nm. The size of the nano crystallite formations was measured to be 23 nm. The present study investigates nanoscale applications' antibacterial efficacy against four bacterial strains, including Klebsiella Sp, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. The observed zone of inhibition for the nanoparticles (NPs) varied from 10 to 25 mm. The research findings demonstrate that the nanoparticles (NPs) are effective as antibacterial, phytotoxic, and cytotoxic agents.

Oligomerization states of the Mycobacterium tuberculosis RNA polymerase core and holoenzymes

During the past few decades, a wealth of knowledge has been made available for the transcription machinery in bacteria from the structural, functional and mechanistic point of view. However, comparatively little is known about the homooligomerization of the multisubunit M. tuberculosis RNA polymerase (RNAP) enzyme and its functional relevance. While E. coli RNAP has been extensively studied, many aspects of RNAP of the deadly pathogenic M. tuberculosis are still unclear. We used biophysical and biochemical methods to study the oligomerization states of the core and holoenzymes of M. tuberculosis RNAP. By size exclusion chromatography and negative staining Transmission Electron Microscopy (TEM) studies and quantitative analysis of the TEM images, we demonstrate that the in vivo reconstituted RNAP core enzyme (α2ββ'ω) can also exist as dimers in vitro. Using similar methods, we also show that the holoenzyme (core + σA) does not dimerize in vitro and exist mostly as monomers. It is tempting to suggest that the oligomeric changes that we see in presence of σA factor might have functional relevance in the cellular process. Although reported previously in E. coli, to our knowledge we report here for the first time the study of oligomeric nature of M. tuberculosis RNAP in presence and absence of σA factor.

Amperometry and Electron Microscopy show Stress Granules Induce Homotypic Fusion of Catecholamine Vesicles

An overreactive stress granule (SG) pathway and long-lived, stable SGs formation are thought to participate in the progress of neurodegenerative diseases (NDs). To understand if and how SGs contribute to disorders of neurotransmitter release in NDs, we examined the interaction between extracellular isolated SGs and vesicles. Amperometry shows that the vesicular content increases and dynamics of vesicle opening slow down after vesicles are treated with SGs, suggesting larger vesicles are formed. Data from transmission electron microscopy (TEM) clearly shows that a portion of large dense-core vesicles (LDCVs) with double/multiple cores appear, thus confirming that SGs induce homotypic fusion between LDCVs. This might be a protective step to help cells to survive following high oxidative stress. A hypothetical mechanism is proposed whereby enriched mRNA or protein in the shell of SGs is likely to bind intrinsically disordered protein (IDP) regions of vesicle associated membrane protein (VAMP) driving a disrupted membrane between two closely buddled vesicles to fuse with each other to form double-core vesicles. Our results show that SGs induce homotypic fusion of LDCVs, providing better understanding of how SGs intervene in pathological processes and opening a new direction to investigations of SGs involved neurodegenerative disease.

The synergistic effect of multiple organic macromolecules on the formation of calcium oxalate raphides of Musa spp

Needle-like calcium oxalate crystals called raphides are unique structures in the plant kingdom. Multiple biomacromolecules work together in the regulatory and transportation pathways to form raphides; however, the mechanism by which this occurs remains unknown. Using banana (Musa spp.), this study combined in vivo methods including confocal microscopy, transmission electron microscopy, and Q Exactive mass spectrometry to identify the main biomolecules, such as vesicles, together with the compositions of lipids and proteins in the crystal chamber, which is the membrane compartment that surrounds each raphide during its formation. Simulations of the vesicle transportation process and the synthesis of elongated calcium oxalate crystals in vitro were then conducted, and the results suggested that the vesicles carrying amorphous calcium oxalate and proteins embedded in raphides are transported along actin filaments. These vesicles subsequently fuse with the crystal chamber, utilizing the proteins embedded in the raphides as a template for the final formation of the structure. Our findings contribute to the fundamental understanding of the regulation of the diverse biomacromolecules that are crucial for raphide formation. Moreover, the implications of these findings extend to other fields such as materials science, and particularly the synthesis of functionalized materials.

Unveiling Cryptosporidium parvum sporozoite-derived extracellular vesicles: profiling, origin, and protein composition

Cryptosporidium parvum is a common cause of a zoonotic disease and a main cause of diarrhea in newborns. Effective drugs or vaccines are still lacking. Oocyst is the infective form of the parasite; after its ingestion, the oocyst excysts and releases four sporozoites into the host intestine that rapidly attack the enterocytes. The membrane protein CpRom1 is a large rhomboid protease that is expressed by sporozoites and recognized as antigen by the host immune system. In this study, we observed the release of CpRom1 with extracellular vesicles (EVs) that was not previously described. To investigate this phenomenon, we isolated and resolved EVs from the excystation medium by differential ultracentrifugation. Fluorescence flow cytometry and transmission electron microscopy (TEM) experiments identified two types of sporozoite-derived vesicles: large extracellular vesicles (LEVs) and small extracellular vesicles (SEVs). Nanoparticle tracking analysis (NTA) revealed mode diameter of 181 nm for LEVs and 105 nm for SEVs, respectively. Immunodetection experiments proved the presence of CpRom1 and the Golgi protein CpGRASP in LEVs, while immune-electron microscopy trials demonstrated the localization of CpRom1 on the LEVs surface. TEM and scanning electron microscopy (SEM) showed that LEVs were generated by means of the budding of the outer membrane of sporozoites; conversely, the origin of SEVs remained uncertain. Distinct protein compositions were observed between LEVs and SEVs as evidenced by their corresponding electrophoretic profiles. Indeed, a dedicated proteomic analysis identified 5 and 16 proteins unique for LEVs and SEVs, respectively. Overall, 60 proteins were identified in the proteome of both types of vesicles and most of these proteins (48 in number) were already identified in the molecular cargo of extracellular vesicles from other organisms. Noteworthy, we identified 12 proteins unique to Cryptosporidium spp. and this last group included the immunodominant parasite antigen glycoprotein GP60, which is one of the most abundant proteins in both LEVs and SEVs.

Enhanced extracellular vesicles mediated uttroside B (Utt-B) delivery to Hepatocellular carcinoma cell: Pharmacokinetics based on PBPK modelling

Our prior investigation has confirmed that the anti-hepatocellular carcinoma activity of the plant saponin, specifically Uttroside B (Utt-B), derived from the leaves of Solanum nigrum Linn. This study concentrated on formulating a novel biocompatible nanocarrier utilizing Extracellular vesicles (EVs) to enhance the delivery of plant saponin into cells. The physicochemical attributes of Extracellular Vesicles/UttrosideB (EVs/Utt-B) were comprehensively characterized through techniques such as Transmission Electron Microscopy (TEM) and Fourier-transform infrared spectroscopy (FTIR). Despite the promising therapeutic potential of this uttroside B, mechanistic know-how about its entry into cells is still in its infancy. Our research sheds light on the extracellular vesicle-mediated mechanism facilitating the entry of the saponin into cells, a phenomenon confirmed through the use of by confocal microscopy. We further analysed drug-releasing kinetics and simulated the Pharmacokinetics by PBPK modelling. The simulated pharmacokinetics revealed the bioavailability of Uttroside-B in oral administration against intravenous administration.

Genetically Fused Resilin-like Polypeptide-Coiled Coil Bundlemer Conjugates Exhibit Tunable Multistimuli-Responsiveness and Undergo Nanofibrillar Assembly

Peptide-based materials are diverse candidates for self-assembly into modularly designed and stimuli-responsive nanostructures with precisely tunable compositions. Here, we genetically fused computationally designed coiled coil-forming peptides to the N- and C-termini of compositionally distinct multistimuli-responsive resilin-like polypeptides (RLPs) of various lengths. The successful expression of these hybrid polypeptides in bacterial hosts was confirmed through techniques such as gel electrophoresis, mass spectrometry, and amino acid analysis. Circular dichroism spectroscopy and ultraviolet-visible turbidimetry demonstrated that despite the fusion of disparate structural and responsive units, the coiled coils remained stable in the hybrid polypeptides, and the sequence-encoded differences in thermoresponsive phase separation of the RLPs were preserved. Cryogenic transmission electron microscopy and coarse-grained modeling showed that after thermal annealing in solution, the hybrid polypeptides adopted a closed loop conformation and assembled into nanofibrils capable of further hierarchically organizing into cluster structures and ribbon-like structures mediated by the self-association tendency of the RLPs.

Localization and quantitative distribution of a chromatin structural protein Topoisomerase II on plant chromosome using HVTEM and UHVTEM

Topoisomerase II (TopoII) is an essential structural protein of the metaphase chromosome. It maintains the axial compaction of chromosomes during metaphase. It is localized at the axial region of chromosomes and accumulates at the centromeric region in metaphase chromosomes. However, little is known about TopoII localization and distribution in plant chromosomes, except for several publications. We used high voltage transmission electron microscopy (HVTEM) and ultra-high voltage transmission electron microscopy (UHVTEM) in conjunction with immunogold labeling and visualization techniques to detect TopoII and investigate its localization, alignment, and density on the barley chromosome at 1.4 nm scale. We found that HVTEM and UHVTEM combined with immunogold labeling is suitable for the detection of structural proteins, including a single molecule of TopoII. This is because the average size of the gold particles for TopoII visualization after silver enhancement is 8.9 ± 3.9 nm, which is well detected. We found that 31,005 TopoII molecules are distributed along the barley chromosomes in an unspecific pattern at the chromosome arms and accumulate specifically at the nucleolus organizer regions (NORs) and centromeric region. The TopoII density were 1.32-fold, 1.58-fold, and 1.36-fold at the terminal region, at the NORs, and the centromeric region, respectively. The findings of TopoII localization in this study support the multiple reported functions of TopoII in the barley metaphase chromosome.

Molecular mapping of virus-infected cells with immunogold and metal-tagging transmission electron microscopy

Transmission electron microscopy (TEM) has been essential to study virus-cell interactions. The architecture of viral replication factories, the principles of virus assembly and the components of virus egress pathways are known thanks to the contribution of TEM methods. Specially, when studying viruses in cells, methodologies for labeling proteins and other macromolecules are important tools to correlate morphology with function. In this review, we present the most widely used labeling method for TEM, immunogold, together with a lesser known technique, metal-tagging transmission electron microscopy (METTEM) and how they can contribute to study viral infections. Immunogold uses the power of antibodies and electron dense, colloidal gold particles while METTEM uses metallothionein (MT), a metal-binding protein as a clonable tag. MT molecules build gold nano-clusters inside cells when these are incubated with gold salts. We describe the necessary controls to confirm that signals are specific, the advantages and limitations of both methods, and show some examples of immunogold and METTEM of cells infected with viruses.

Lighting lantern above Psalteriomonadidae: Unveiling novel diversity within the genus Psalteriomonas (Discoba: Heterolobosea)

Psalteriomonadidae are a small family of anaerobic free-living protists belonging to Heterolobosea, Discoba. We cultured 74 new strains of mostly amoeboid Psalteriomonadidae obtained from mainly freshwater habitats and sequenced their 18S rRNA gene. Based on the phylogenetic analysis and genetic distances, we report multiple novel species, four of which we formally describe based on the light-microscopic morphology (Psalteriomonas minuta, P. australis, P. fimbriata, and P. parva). We also examined the ultrastructure of two Psalteriomonas species using transmission electron microscopy. We transfer Sawyeria marylandensis into the genus Psalteriomonas and synonymize Sawyeria with Psalteriomonas. In addition, we studied the flagellate stage of P. marylandensis comb. nov. for the first time, using light and scanning electron microscopy.

Square condenser apertures for square cameras in low-dose transmission electron microscopy

In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam-sensitive samples. We present condenser aperture plates with square and rectangular shapes that improve the efficiency of area usage by 70% and enhance montage imaging for beam-sensitive specimens. We demonstrate the compatibility of these condenser aperture plates with high-resolution cryogenic TEM by reconstructing a 1.8-Å map of equine apo-ferritin.

The application and development of electron microscopy for three-dimensional reconstruction in life science: a review

Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.

Square beams for optimal tiling in transmission electron microscopy

Imaging large fields of view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large area is either imperfect or results in uneven exposures, a problem for dose-sensitive samples. Here, we introduce a square electron beam that can easily be retrofitted in existing microscopes, and demonstrate its application, showing that it can tile nearly perfectly and deliver cryo-electron microscopy imaging with a resolution comparable to conventional set-ups.

Stimulation of microvesicle secretion in Trichomonas vaginalis

Trichomonas vaginalis is an extracellular flagellate protozoan and the etiological agent of human trichomoniasis, a sexually transmitted infection (STI) with a high incidence. Several reports have shown that this protozoan releases microvesicles into the culture medium, which show high potential in modulating cell-to-cell communication and the host response to infections. However, the biogenesis of these vesicles has not been analyzed in detail. In the present study, high-resolution ion scanning microscopy (SEM) and transmission electron microscopy (TEM) were used to analyze the surface of control cells and cells incubated in the presence of Ca2+ alone or with A 23187 calcium ionophore. Two different strains of T. vaginalis were analyzed. Most control cells displayed relatively smooth surfaces, whereas cells incubated with Ca2+ had many surface projections of variable shape and size (from 40 nm to around 1 μm). Quantitative analyses were performed directly in the scanning electron microscope and showed a significant increase in the number of cells with surface projections after incubation in the presence of calcium. TEM showed that treated cells presented several cytoplasmic multivesicular structures, suggesting membrane fusion and exosomes in the extracellular medium. The amount and size of the released vesicles were quantitatively analyzed using light scattering and TEM on negatively stained samples. The observations show that incubation of both parasite strains in the presence of Ca2+ significantly increased the release of microvesicles into the extracellular medium in a time-dependent process. Sequential incubation in the presence of Ca2+ and the calcium ionophore A23187 increases the presence of vesicles on the parasite surface only at a short incubation time (5 min). Transmission electron microscopy showed that at least part of the vesicles are originated from cytoplasmic multivesicular structures. This information contributes to a better understanding of the biogenesis of extracellular vesicles secreted by T. vaginalis.

Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling

Ultrastructure of human brain tissue has traditionally been examined using electron microscopy (EM) following fixation, staining, and sectioning, which limit resolution and introduce artifacts. Alternatively, cryo-electron tomography (cryo-ET) allows higher resolution imaging of unfixed cellular samples while preserving architecture, but it requires samples to be vitreous and thin enough for transmission EM. Due to these requirements, cryo-ET has yet to be employed to investigate unfixed, never previously frozen human brain tissue. Here we present a method for generating lamellae in human brain tissue obtained at time of autopsy that can be imaged via cryo-ET. We vitrify the tissue via plunge-freezing and use xenon plasma focused ion beam (FIB) milling to generate lamellae directly on-grid at variable depth inside the tissue. Lamellae generated in Alzheimer's disease brain tissue reveal intact subcellular structures including components of autophagy and potential pathologic tau fibrils. Furthermore, we reveal intact compact myelin and functional cytoplasmic expansions. These images indicate that plasma FIB milling with cryo-ET may be used to elucidate nanoscale structures within the human brain.

Morphological and biochemical characteristics associated with autophagy in gastrointestinal diseases

Autophagy is a cellular catabolic process characterized by the formation of double-membrane autophagosomes. Transmission electron microscopy is the most rigorous method to clearly visualize autophagic engulfment and degradation. A large number of studies have shown that autophagy is closely related to the digestion, secretion, and regeneration of gastrointestinal (GI) cells. However, the role of autophagy in GI diseases remains controversial. This article focuses on the morphological and biochemical characteristics of autophagy in GI diseases, in order to provide new ideas for their diagnosis and treatment.

[Automatic classification of immune-mediated glomerular diseases based on multi-modal multi-instance learning]

OBJECTIVE

To develop a multi-modal deep learning method for automatic classification of immune-mediated glomerular diseases based on images of optical microscopy (OM), immunofluorescence microscopy (IM), and transmission electron microscopy (TEM).

METHODS

We retrospectively collected the pathological images from 273 patients and constructed a multi-modal multi- instance model for classification of 3 immune-mediated glomerular diseases, namely immunoglobulin A nephropathy (IgAN), membranous nephropathy (MN), and lupus nephritis (LN). This model adopts an instance-level multi-instance learning (I-MIL) method to select the TEM images for multi-modal feature fusion with the OM images and IM images of the same patient. By comparing this model with unimodal and bimodal models, we explored different combinations of the 3 modalities and the optimal methods for modal feature fusion.

RESULTS

The multi-modal multi-instance model combining OM, IM, and TEM images had a disease classification accuracy of (88.34±2.12)%, superior to that of the optimal unimodal model [(87.08±4.25)%] and that of the optimal bimodal model [(87.92±3.06)%].

CONCLUSION

This multi- modal multi- instance model based on OM, IM, and TEM images can achieve automatic classification of immune-mediated glomerular diseases with a good classification accuracy.

In-section Click-iT detection and super-resolution CLEM analysis of nucleolar ultrastructure and replication in plants

Correlative light and electron microscopy (CLEM) is an important tool for the localisation of target molecule(s) and their spatial correlation with the ultrastructural map of subcellular features at the nanometre scale. Adoption of these advanced imaging methods has been limited in plant biology, due to challenges with plant tissue permeability, fluorescence labelling efficiency, indexing of features of interest throughout the complex 3D volume and their re-localization on micrographs of ultrathin cross-sections. Here, we demonstrate an imaging approach based on tissue processing and embedding into methacrylate resin followed by imaging of sections by both, single-molecule localization microscopy and transmission electron microscopy using consecutive CLEM and same-section CLEM correlative workflow. Importantly, we demonstrate that the use of a particular type of embedding resin is not only compatible with single-molecule localization microscopy but shows improvements in the fluorophore blinking behavior relative to the whole-mount approaches. Here, we use a commercially available Click-iT ethynyl-deoxyuridine cell proliferation kit to visualize the DNA replication sites of wild-type Arabidopsis thaliana seedlings, as well as fasciata1 and nucleolin1 plants and apply our in-section CLEM imaging workflow for the analysis of S-phase progression and nucleolar organization in mutant plants with aberrant nucleolar phenotypes.

Protocol for synthesis of spherical silver nanoparticles with stable optical properties and characterization by transmission electron microscopy

The synthesis of metallic plasmonic nanoparticles (NPs) faces challenges in stability and reproducibility, especially with silver. Here, we present a protocol for tunable synthesis of spherical silver NPs (AgNPs) with stable optical properties. We describe steps for preparing solutions, morphological characterization of AgNPs by transmission electron microscopy, and testing stability. AgNPs exhibit enduring stability and compatibility with various pH values. Moreover, they can be functionalized for optical biosensing applications, offering versatility in nanomaterial applications.

Sensitive detection of dextromethorphan hydrobromide based on portable Raman spectrometer and CuO@AgNPs nano composite SERS substrate

A highly sensitive surface-enhanced Raman spectroscopy approach was established for the detection of dextromethorphan hydrobromide (DXM) utilizing nano CuO modified silver nanoparticles (CuO@AgNPs) as substrate. Ultraviolet visible spectra (UV-vis), X-ray diffraction (XRD) and transmission electron microscopy (TEM) characterized the synthesized CuO@AgNPs. UV-vis and fourier transform infrared (FT-IR) were adopted to investigate the interaction between DXM and CuO@AgNPs. The optimal experimental conditions (the dosages of CuO@AgNPs and NaCl as well as mixing time) were explored. The enhancement factor (EF) was 1.71 × 106. The linear relationship between SERS intensity and the concentration of DXM in the range of 67 - 1000 nmol L-1 was obtained as ISERS = 25.81 c + 40398.77, and the limit of detection (LOD) was 2.12 nmol L-1 (S/N = 3). The interference of K+, Mg2+, Zn2+, Ca2+, Cu2+, Fe3+, glucose, HSA, L-tryptophan, soluble starch and ibuprofen were investigated. The method was successfully applied to test DXM in serum samples. The recovery was 99.06% - 101.51% with the relative standard deviation (RSD) of 0.74% - 3.87%.

Enhanced visible-light photocatalytic oxidative desulfurization of model fuel over Pt-decorated carbon-doped TiO2 nanoparticles

Modification of photocatalysts to improve their adsorption and photocatalytic activity in the oxidative desulfurization of liquid fuels has been reported by many investigators. In this study, Pt-decorated carbon-doped TiO2 nanoparticles were synthesized by hydrothermal and photo-deposition techniques and were subsequently used in photocatalytic oxidative desulfurization of dibenzothiophene (DBT) in n-heptane as a simulated liquid fuel with methanol as the extracting solvent. Carbon-doped TiO2 was first synthesized by a simple self-doping method. Pt was then loaded by a photo-deposition technique. The synthesized photocatalysts (labeled as YPt-CT where Y is percent Pt loading) were characterized by of X-ray diffraction (XRD), photoluminescence (PL), field emission scanning electron microscopy (FESEM), N2-physisorption, UV-Vis diffusive reflectance spectra (UV-Vis DRS), transmission electron microscopy (TEM), Fourier transform infrared spectra (FTIR), and nitrogen sorption measurements. The removal efficiency of DBT was 98% in the presence of 2 g/l of 0.5Pt-CT catalyst under visible-light irradiation (λ > 400 nm), ambient pressure, and reaction temperature of 40°C.

Transmission electron microscopic study of the surface layer of surgical resected disc specimens in human temporomandibular joint

In this study, we investigated specific and characteristic findings of the surface layer of surgical resected disc specimens in human temporomandibular joint osteoarthritis cases by transmission electron microscopy (TEM).Specimens were surgically removed from the TMJ of 5 cases (4 female patients: 5 cases) clinically osteoarthritis. Following findings were observed by TEM. Images were photographed on a JEM1400-Flash Electron microscope (JEOL, Japan) equipped with an EM-14661FLASH high-sensitivity digital complementary metal-oxide-semiconductor camera.Following findings were observed by TEM. 1) The surface is covered with plump fibroblastic and histiocytoid cells. 2) Collagen fiber bundles and collagenous matrix are exposed onto the eroded disc surface. 3) Fibrinous dense material is observed on the eroded disc surface. 4) Bundles of collagen fibers are densely observed. 5) Collagen bundles are rich around capillary vessels. 6) Synovial surface cells reveal features of activated macrophages with vacuole formation. Especially, plump fibroblastic and histiocytoid cells, and activated macrophages with vacuole, which were significant findings of the surface layer. These findings might have a significant effect on the regulation of synovial fluid.

Synthesis and characterization of TiO2-based supported materials for industrial application and recovery in a pilot photocatalytic plant using chemometric approach

In this contribution, the performance of powdered titanium dioxide (TiO2)-based photocatalysts was evaluated in a pilot photocatalytic plant for the degradation of different dyes, with an investigated volume of 1 L and solar simulated light as irradiation source. Five different samples, synthesized in our laboratories, were tested in the pilot plant, each consisting of TiO2 nanoparticles (NPs) coupled with a different material (persistent luminescent material and semiconductor material) and treated in different thermal conditions. All synthesized samples have been subjected to X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Brunauer-Emmett-Teller analysis (BET), and transmission electron microscopy (TEM) characterization, to shed light on the influence of introducing other materials on titania characteristics. To study and evaluate the significance of the parameters affecting the process in the pilot plant, a chemometric approach was applied, by selecting a mathematical model (D-Optimal) to simultaneously monitor a large number of variables (i.e., 7), both qualitative and quantitative, over a wide range of levels. At the same time, the recovery of the synthesized photocatalysts was studied following a novel promising recuperation method, i.e., annulling the surface charge of the suspended samples by reaching the isoelectric point (pHPZC) of each sample, for the quantitative precipitation of TiO2 nanoparticles.

Ultrastructural Examination of Glomerular Fibrillary Deposits in Diabetic Nephropathy

Glomerular fibrillary deposits have occasionally been reported in diabetic nephropathy, but no large-scale, ultrastructural evaluation of these deposits has been reported so far. Here, we report our study of glomerular non-Congophilic, DnaJ homolog subfamily B member 9 negative fibrillary deposits in diabetic nephropathy as characterized by transmission electron microscopy. Clinical data from 55 patients with biopsy-confirmed diabetic nephropathy and 18 healthy living donors were reviewed, and their biopsies were evaluated by light microscopy, immunofluorescence, and electron microscopy. Small fibrillary structures with a diameter of 10 ± 1 nm were present in all cases with diabetic nephropathy, regardless of the histologic class. In addition, glomerular fibrillary structures with a diameter of 23 ± 5 nm or 30 ± 7 nm were present in 35 cases. Interestingly, especially the small- and medium-sized fibrils, usually without apparent organization, were comparable with fibrils in fibrillary glomerulopathy. We conclude that glomerular fibrillary deposits occur far more commonly in renal biopsies of patients with diabetic nephropathy than generally considered. This is an important finding because their similarity to fibrils in fibrillary glomerulonephritis may complicate the histologic diagnostic process, especially in cases of overlapping clinical manifestations. Therefore, when encountering fibrillary deposits on electron microscopy, it is important to consider diabetic nephropathy as an alternative diagnosis.

Centriole and transition zone structures in photoreceptor cilia revealed by cryo-electron tomography

Primary cilia mediate sensory signaling in multiple organisms and cell types but have structures adapted for specific roles. Structural defects in them lead to devastating diseases known as ciliopathies in humans. Key to their functions are structures at their base: the basal body, the transition zone, the "Y-shaped links," and the "ciliary necklace." We have used cryo-electron tomography with subtomogram averaging and conventional transmission electron microscopy to elucidate the structures associated with the basal region of the "connecting cilia" of rod outer segments in mouse retina. The longitudinal variations in microtubule (MT) structures and the lumenal scaffold complexes connecting them have been determined, as well as membrane-associated transition zone structures: Y-shaped links connecting MT to the membrane, and ciliary beads connected to them that protrude from the cell surface and form a necklace-like structure. These results represent a clearer structural scaffold onto which molecules identified by genetics, proteomics, and superresolution fluorescence can be placed in our emerging model of photoreceptor sensory cilia.

Characterization of cleavage patterns and assembly of N-terminally modified GII.6 norovirus VP1 proteins

When expressed in vitro, the major capsid protein VP1 of a norovirus (NoV) can self-assemble into virus-like particles (VLPs), and its N-terminus can tolerate foreign sequences without the assembly being affected. We explored the effects of adding an N-terminal sequence to the VP1 of a GII.6 NoV strain on its cleavage and assembly. Sequences of varying lengths derived from the minor capsid protein VP2 were added to the VP1 N-terminus. Using a recombinant baculovirus expression system, the fusion proteins were expressed, and their cleavage patterns and assembly were analyzed using mass spectrometry and transmission electron microscopy, respectively. All of the fusion proteins were successfully expressed and exhibited varying degrees of enzyme cleavage, most probably at the N-terminus. LC-MS results revealed that similar fragments were obtained for wild-type VP1 and fusion proteins, indicating that the cleavage sites were conserved. EM analysis indicated that VLPs of different sizes were successfully assembled for certain fusion proteins. The study data demonstrate that NoV VP1 can tolerate foreign sequences of a certain length at its N-terminus and that a conserved cleavage pattern exists, which might facilitate further investigation of the assembly and cleavage mechanisms of NoV.

Characterization of Nanohybridosomes from Lipids and Spruce Homogenate Containing Extracellular Vesicles

Introduction

Lipid nanovesicles associated with bioactive phytochemicals from spruce needle homogenate (here called nano-sized hybridosomes or nanohybridosomes, NSHs) were considered.

Methods

We formed NSHs by mixing appropriate amounts of lecithin, glycerol and supernatant of isolation of extracellular vesicles from spruce needle homogenate. We visualized NSHs by light microscopy and cryogenic transmission electron microscopy and assessed them by flow cytometry, dynamic light scattering, ultraviolet-visual spectroscopy, interferometric light microscopy and liquid chromatography-mass spectrometry.

Results

We found that the particles consisted of a bilayer membrane and a fluid-like interior. Flow cytometry and interferometric light microscopy measurements showed that the majority of the particles were nano-sized. Dynamic light scattering and interferometric light microscopy measurements agreed well on the average hydrodynamic radius of the particles Rh (between 140 and 180 nm), while the concentrations of the particles were in the range between 1013 and 1014/mL indicating that NSHs present a considerable (more than 25%) of the sample which is much more than the yield of natural extracellular vesicles (EVs) from spruce needle homogenate (estimated less than 1%). Spruce specific lipids and proteins were found in hybridosomes.

Discussion

Simple and low-cost preparation method, non-demanding saving process and efficient formation procedure suggest that large-scale production of NSHs from lipids and spruce needle homogenate is feasible.

Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography

Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.

Amyloid Modifier SERF1a Accelerates Alzheimer's Amyloid-β Fibrillization and Exacerbates the Cytotoxicity

Alzheimer's disease (AD) is a devastating, progressive neurodegenerative disease affecting the elderly in the world. The pathological hallmark senile plaques are mainly composed of amyloid-β (Aβ), in which the main isoforms are Aβ40 and Aβ42. Aβ is prone to aggregate and ultimately forms amyloid fibrils in the brains of AD patients. Factors that alter the Aβ aggregation process have been considered to be potential targets for treatments of AD. Modifier of aggregation 4 (MOAG-4)/small EDRK-rich factor (SERF) was previously selected from a chemical mutagenesis screen and identified as an amyloid modifier that promotes amyloid aggregation for α-synuclein, huntingtin, and Aβ40. The interaction and effect of yeast ScSERF on Aβ40 were previously described. Here, we examined the human SERF1a effect on Aβ40 and Aβ42 fibrillization by the Thioflavin T assay and found that SERF1a accelerated Aβ fibrillization in a dose-dependent manner without changing the fibril amount and without incorporation. By Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM), we found that SERF1a altered the secondary structures and the morphology of Aβ fibrils. The electrospray ionization mass spectrometry (ESI-MS) and analytical ultracentrifugation (AUC) results showed that SERF1a binds to Aβ in a 1:1 stoichiometry. Moreover, the NMR study showed that SERF1a interacts with Aβ via its N-terminal region. Cytotoxicity assay demonstrated that SERF1a enhanced toxicity of Aβ intermediates, and the effect can be rescued by SERF1a antibody. Overall, our study provides the underlying molecular mechanism for the SERF1a effect on Aβ fibrillization and facilitates the therapeutic development of AD.

Synthesis of silver and copper nanoparticle using Spirulina platensis and evaluation of their anticancer activity

The present research displays the green synthesis of stable silver nanoparticles (Ag-NPs) and copper oxide nanoparticles (CuO-NPs). The aqueous solution of Spirulina platensis (blue green algae) source was used as a reducing and capping agent and this study assessed the cytotoxicity of Ag- and CuO-NPs on three cancer cell cultures: A549 (lung cancer), HCT (human colon cancer), Hep2 (laryngeal carcinoma cancer) and normal cell (WISH). For NPs characterization, the UV/Vis spectroscopy was used where their formation and crystallinity were proven with λ max values for Ag- and CuO-NPs of 425 and 234 nm, respectively. According to X-ray diffraction and transmission electron microscopy (TEM), Ag-NPs were spherical in shape (size 2.23-14.68 nm) and CuO-NPs were small (size 3.75-12.4 nm). Zeta potential analysis showed the particles potential, which was recorded by -14.95 ± 4.31 mV for Ag-NPs and -21.63 ± 4.90 mV for CuO-NPs. After that, Ag- and CuO-NPs were assessed for anticancer properties against A549, HCT, Hep2 and WISH. IC50 of Ag-NPs recorded 15.67, 12.94, 3.8 and 10.44 µg/ml for WISH, A549, HCT and Hep2, respectively. IC50 for CuO-NPs was recorded as 32.64, 54.59, 3.98 and 20.56 µg/ml for WISH, A549, HCT and Hep2 cells, respectively. Safety limits for WISH and A549 were achieved 98.64% by 2.44 µg/ml and 83.43% by 4.88 µg/ml of Ag-NPs, and it was found to be 97.94% by 2.44 µg/ml against HCT, while that for Hep2 is 95.9% by 2.44 µg/ml. Concerning the anticancer effect of CuO-NPs, the safety limit was recorded as 88.70% by 2.44 and 98.48% by 4.88 µg/ml against WISH and A549, while HCT reached 89.92% by 2.44 µg/ml and Hep2 was 83.33% by 4.88 µg/ml. Green nanotechnology applications such as Ag-NPs and CuO-NPs have numerous benefits of ecofriendliness and compatibility for biomedical applications such as anticancer effects against cancer cells.

Single-Molecule Graphene Liquid Cell Electron Microscopy for Instability of Intermediate Amyloid Fibrils

Single-molecule techniques are powerful microscopy methods that provide new insights into biological processes. Liquid-phase transmission electron microscopy (LP-TEM) is an ideal single-molecule technique for overcoming the poor spatiotemporal resolution of optical approaches. However, single-molecule LP-TEM is limited by several challenges such as electron-beam-induced molecular damage, difficulty in identifying biomolecular species, and a lack of analytical approaches for conformational dynamics. Herein, a single-molecule graphene liquid-cell TEM (GLC-TEM) technique that enables the investigation of real-time structural perturbations of intact amyloid fibrils is presented. It is demonstrated that graphene membranes significantly extend the observation period of native amyloid beta proteins without causing oxidative damage owing to electron beams, which is necessary for imaging. Stochastic and time-resolved investigations of single fibrils reveal that structural perturbations in the early fibrillar stage are responsible for the formation of various amyloid polymorphs. The advantage of observing structural behavior in real time with unprecedented resolution will potentially make GLC-TEM a complementary approach to other single-molecule techniques.

Characterization of the pancreas of common pheasant (Phasianus colchicus): A light and transmission electron microscope study

The present work was carried out to investigate the structure and ultra structure of the pancreas in the common pheasant (Phasianus colchicus). Totally, five healthy adult pheasant were used. The pancreas was assessed using histochemistry and transmission electron microscopy (TEM). The pancreas was composed of four lobes: dorsal, ventral, third, and splenic lobes. These lobes emptied into ascending duodenum through three excretory ducts as: ventral duct, splenic duct, and a common duct for dorsal and third lobes. The exocrine pancreas was constituted of pyramidal-shaped acinar cells with aggregation of zymogen granules at their apical cytoplasm. The endocrine pancreas was identified as large islet of Langerhans as α islets and small islets as β ones. No mixed islet was observed. At the level of TEM, two types of acinar cells were distinguished: Dark cells with electron dense cytoplasm, and indented nucleus, Light cells with electron lucent cytoplasm, and regular nucleus. The α islets were mainly constituted by A and D cells, whereas the β islets principally contained B cells and a few A cells. No D cells were identified in β islets. B cells were characterized by their polymorphic granules which were surrounded by a narrow halo zone. The granules of D cells were quite different. These cells contained large spherical granules with lower density as compared to the A or B granules surrounded by a limiting membrane. In conclusion, the pancreas of the common pheasant has a species-specific feature which must be considered in phylogenic studies. RESEARCH HIGHLIGHTS: The common pheasant's pancreas was composed of four lobes as dorsal, ventral, third, and splenic lobe. There were three excretory ducts. Ventral duct for ventral lobe, a common duct for both dorsal and third lobes, and a distinct splenic duct for splenic lobe. The exocrine acini were composed of two distinct types of cells: dark cells and light cells. The large alpha islets were composed of alpha cells and a few numbers of delta cells and small beta islets were composed of beta cells and a few numbers of alpha cells.

Visualisation of microalgal lipid bodies through electron microscopy

In this study, transmission electron microscopy (TEM) and cryo-scanning electron microscopy (cryo-SEM) were evaluated for their ability to detect lipid bodies in microalgae. To do so, Phaeodactylum tricornutum and Nannochloropsis oculata cells were harvested in both the mid-exponential and early stationary growth phase. Two different cryo-SEM cutting methods were compared: cryo-planing and freeze-fracturing. The results showed that, despite the longer preparation time, TEM visualisation preceded by cryo-immobilisation allows a clear detection of lipid bodies and is preferable to cryo-SEM. Using freeze-fracturing, lipid bodies were rarely detected. This was only feasible if crystalline layers in the internal structure, most likely related to sterol esters or di-saturated triacylglycerols, were revealed. Furthermore, lipid bodies could not be detected using cryo-planing. Cryo-SEM is also not the preferred technique to recognise other organelles besides lipid bodies, yet it did reveal chloroplasts in both species and filament-containing organelles in cryo-planed Nannochloropsis oculata samples.

Flower shaped Bi2O2.33/Bi2WO6 composite: An efficient photocatalyst for degradation of methylene blue from aqueous solution in direct solar light

Herein, we synthesized a Bi2O2.33/Bi2WO6 heterostructure as a platform for the degradation of methylene blue (MB) dye in an aqueous phase. The heterostructure was synthesized by facile ultrasonicated assisted solvothermal method. Various structural, morphological and other techniques such as XRD, FTIR, PL, EIS, UV-DRS, FESEM, HRTEM, XPS, EPR, TGA, BET surface area were used to analyze the characteristics of as-synthesized Bi2O2.33/Bi2WO6. The morphological studies revealed the deposition of Bi2O2.33 flowers in high density on Bi2WO6. Under solar irradiation, 98.6% degradation of MB was achieved in 190 min at optimal conditions (pH = 5, catalyst dose = 0.35 gL-1 and MB concentration = 10 mgL-1). The improved photocatalytic ability of composite in contrast to Bi2O2.33 and Bi2WO6 could be usually ascribed to the interface created between them, assisting the charge transfer. Based on the findings of radical trapping experiments, the charge transfer process over the photocatalyst was completely studied. Additionally, the present heterostructure demonstrated good recyclability over five runs. In nutshell, this study provided a facile approach for synthesizing solar light driven photocatalyst for degradation of methylene blue in aqueous phase and can further explored to be utilized for varied environmental remediation.

Antivesiculation and Complete Unbinding of Tail-Tethered Lipids

We report the effect of tail-tethering on vesiculation and complete unbinding of bilayered membranes. Amphiphilic molecules of a bolalipid, resembling the tail-tethered molecular structure of archaeal lipids, with two identical zwitterionic phosphatidylcholine headgroups self-assemble into a large flat lamellar membrane, in contrast to the multilamellar vesicles (MLVs) observed in its counterpart, monopolar nontethered zwitterionic lipids. The antivesiculation is confirmed by small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cyro-TEM). With the net charge of zero and higher bending rigidity of the membrane (confirmed by neutron spin echo (NSE) spectroscopy), the current membrane theory would predict that membranes should stack with each other (aka "bind") due to dominant van der Waals attraction, while the outcome of the nonstacking ("unbinding") membrane suggests that the theory needs to include entropic contribution for the nonvesicular structures. This report pioneers an understanding of how the tail-tethering of amphiphiles affects the structure, enabling better control over the final nanoscale morphology.

Immunophenotype profile by flow cytometry reveals different subtypes of extracellular vesicles in porcine seminal plasma

BACKGROUND

Porcine seminal plasma (SP) is endowed with a heterogeneous population of extracellular vesicles (sEVs). This study evaluated the immunophenotypic profile by high-sensitivity flow cytometry of eight sEV subpopulations isolated according to their size (small [S-sEVs] and large [L-sEVs]) from four different SP sources, namely three ejaculate fractions (the first 10 mL of the sperm rich fraction [SRF-P1], the remaining SRF [SRF-P2], and the post-SRF [PSRF]) and entire ejaculate (EE).

METHODS

Seminal EVs were isolated using a size exclusion chromatography-based protocol from six SP pools (five ejaculates/pool) of each SP source and characterized using complementary approaches including total protein (BCA™assay), particle size distribution (dynamic light scattering), morphology (transmission electron microscopy), and purity (albumin by Western blot). Expression of CD9, CD63, CD81, CD44 and HSP90β was analyzed in all sEV subpopulations by high-sensitivity flow cytometry according to MIFlowCyt-EV guidelines, including an accurate calibration, controls, and discrimination by CFSE-labelling.

RESULTS

Each sEV subpopulation exhibited a specific immunophenotypic profile. The percentage of sEVs positive for CD9, CD63, CD81 and HSP90β differed between S- and L-sEVs (P < 0.0001). Specifically, the percentage of sEVs positive for CD9 and CD63 was higher and that for CD81 was lower in S- than L-sEVs in the four SP sources. However, the percentage of HSP90β-positive sEVs was lower in S-sEVs than L-sEVs in the SRF-P1 and EE samples. The percentage of sEVs positive for CD9, CD63, and CD44 also differed among the four SP sources (P < 0.0001), being highest in PSRF samples. Notably, virtually all sEV subpopulations expressed CD44 (range: 88.04-98.50%).

CONCLUSIONS

This study demonstrated the utility of high-sensitivity flow cytometry for sEV immunophenotyping, allowing the identification of distinct sEV subpopulations that may have different cellular origin, cargo, functions, and target cells.

Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora

"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.1,2,3,4 Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.2Meteora sporadica5 is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.6 Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.

Modified toxic potential of multi-walled carbon nanotubes to zebrafish (Danio rerio) following a two-year incubation in water

Multi-walled carbon nanotubes (MWCNTs), widely used in several industrial fields, are not readily degradable thus, persist in environmental matrices, serving as a source of environmental toxicity to organisms. However, the effects of environmental weathering on nanomaterial toxicity remain unclear. Herein, we prepared aged-MWCNTs (a-CNTs) by incubating commercial pristine-MWCNTs (p-CNTs) for two years and compared their changes in physicochemical properties and toxic effects on zebrafish. The characterization of a-CNTs by transmission electron microscopy, X-ray photoelectron spectra, Raman spectroscopy, and Fourier-transform infrared spectroscopy showed an increased surface area, pore size, structural defects, and surface oxidation than those of p-CNTs. Zebrafish were exposed to 100 mg/L p-CNT and a-CNT for four days. Subsequently, the mRNA expression of antioxidant enzymes, including cat, gst, and sod, in a-CNT group increased by 1.5- to 1.7-fold, consistent with increased expression of genes associated with inflammation (interleukin-8) and apoptosis (p53) compared to control. The higher toxicity of a-CNTs to zebrafish than p-CNT might be due to the increased oxidative potential by altered physicochemical properties. These findings provide new insights into the risk assessment and environmental management of MWCNTs in the aquatic environment. However, further testing at environmentally relevant doses, different exposure durations, and diverse weathering parameters is warranted.

EMDB-the Electron Microscopy Data Bank

The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.

Recombinant Full-Length TDP-43 Oligomers Retain Their Ability to Bind RNAs, Are Not Toxic, and Do Not Seed TDP-43 Aggregation in Vitro

TAR DNA-binding protein with 43 kD (TDP-43) is a partially disordered protein that misfolds and accumulates in the brains of patients affected by several neurodegenerative diseases. TDP-43 oligomers have been reported to form due to aberrant misfolding or self-assembly of TDP-43 monomers. However, very little is known about the molecular and structural basis of TDP-43 oligomerization and the toxic properties of TDP-43 oligomers due to several reasons, including the lack of conditions available for isolating native TDP-43 oligomers or producing pure TDP-43 oligomers in sufficient quantities for biophysical, cellular, and in vivo studies. To address these challenges, we developed new protocols to generate different stable forms of unmodified and small-molecule-induced TDP-43 oligomers. Our results showed that co-incubation of TDP-43 with small molecules, such as epigallocatechin gallate (EGCG), dopamine, and 4-hydroxynonenal (4-HNE), increased the production yield of TDP-43 stable oligomers, which could be purified by size-exclusion chromatography. Interestingly, despite significant differences in the morphology and size distribution of the TDP-43 oligomer preparations revealed by transmission electron microscopy (TEM) and dynamic light scattering (DLS), they all retained the ability to bind to nucleotide DNA. Besides, circular dichroism (CD) analysis of these oligomers did not show much difference in the secondary structure composition. Surprisingly, none of these oligomer preparations could seed the aggregation of TDP-43 core peptide 279-360. Finally, we showed that all four types of TDP-43 oligomers exert very mild cytotoxicity to primary neurons. Collectively, our results suggest that functional TDP-43 oligomers can be selectively stabilized by small-molecule compounds. This strategy may offer a new approach to halt TDP-43 aggregation in various proteinopathies.

Myxoinflammatory fibroblastic sarcoma: ultrastructural study of 7 cases

Since first described, several studies about Myxoinflammatory fibroblastic sarcomas (MIFS) have been published stating the clinicopathological, morphological and immunohistochemical features. However, the ultrastructural findings of these MIFS are limited. Thus, the objective of the present paper is to describe the ultrastructural characteristics of these type of tumors by utilizing tissue that was embedded in paraffin and submitted for immunohistochemistry.The tissue of seven different cases was obtained for ultrastructural study with automatized staining devices, that were later observed by using transmission electron microscopy. Histologically all cases displayed conventional structures of Myxoinflammatory fibroblastic sarcoma (Reed-Sternberg like cells, pseudolipoblasts and emperipolesis). Conversely, two of them exhibited high-grade components, one rich in osteoclastic type giant cells and hypercellular areas, and another one rich in inflammation (Hodgkin-like).After immunohistochemistry, all the samples revealed positivity for CD68 with six cases CD163 and five being positive to CD34, Cyclin-D1, and D2-40. Ultrastructural findings indicated rough endoplasmic reticulum with dilatation of the cisterns that indented the nuclei ("soccer ball" cells), abundant lysosomes, phagolysosomes, and intermediate filaments evidencing this entity as a morphologic continuum that exhibited modified fibroblastic phenotype and variable proportion of macrophagic differentiation.

Functional morphology and ultrastructure of the mouth apparatus in the freshwater mite larvae Limnochares aquatica (L., 1758) (Acariformes, Limnocharidae)

The mouth apparatus in larvae of the freshwater mite Limnochares aquatica (L., 1758) (Acariformes, Limnocharidae), belonging to the lower Hydrachnidia, was studied with light microscopy, scanning (SEM) and transmission (TEM) electron microscopy, as well as with confocal laser scanning microscopy (CLSM) to reveal its main morphological and functional characteristics. The gnathosoma, functioning as a mouth organ takes a prognathous position, and inclines to the body axial line at the angle of around 30°. The gnathosoma is composed of segments of the two pairs of anterior appendages and their derivatives - two-segmented chelicerae lying above the infracapitulum - the compound medial portion of the palpal coxae, and five-segmented palps, articulated with the infracapitulum laterally. The palp tibia bears the bifid palpal claw facing downward nearly at right angle. The basal cheliceral segments are free, i.e., are not covered with the integumental fold posteriorly, and do not fuse with each other. Apically, they articulate with the relatively short movable digits composed of the basal portion (lever) and the distal portion (the cheliceral blades) curved upward by their ends. The flexible fixed digits protrude forward from the distal parts of the basal cheliceral segments. The ventral wall of the gnathosoma (mentum) transforms into a very specific papillary area (velum). A papillary area with long slim papillae is formed of a light cuticle and likely acts as a sucker but does not have contractile elements. The hypostome possesses the well developed lateral lips (galea) tightly embracing the distal portions of the chelicerae and hiding the movable digits. The roof of the infracapitulum (the cervix, or epistome) lying beneath the chelicerae, shows a compound structure. Anteriorly it connects with the inner hypostomal walls forming a particular pharyngeal ring framing the narrow mouth opening. We saw no evidence of a labrum. A characteristic valve projects forward from the dorsal surface of the cervix. A crescent-shaped pharynx runs along the bottom of the infracapitulum and is attached but not fused with the cuticle of the papillary area. The dorsal pharyngeal dilators originate on the cervix, sigmoid pieces and the lateral walls of the infracapitulum at their junction with the dorsal walls of the basal cheliceral segments. A pair of sigmoid pieces having small cavities inside serves for termination of the cheliceral elevators originated on the posterior portions of the dorsal walls of the basal cheliceral segments. The organizational pattern of the gnathosoma in larvae of L. aquatica is rather specific and is quite different from those of other aquatic or terrestrial parasitengonin larvae.

Expression dynamics of the aplysia abyssovirus

Two recent studies documented the genome of a novel, extremely large (35.9 kb), nidovirus in RNA sequence databases from the marine neural model Aplysia californica. The goal of the present study was to document the distribution and transcriptional dynamics of this virus, Aplysia abyssovirus 1 (AAbV), in maricultured and wild animals. We confirmed previous findings that AAbV RNA is widespread and reaches extraordinary levels in apparently healthy animals. Transmission electron microscopy identified viral replication factories in ciliated gill epithelial cells but not in neurons where viral RNA is most highly expressed. Viral transcripts do not exhibit evidence of discontinuous RNA synthesis as in coronaviruses but are consistent with production of a single leaderless subgenomic RNA, as in the Gill-associated virus of Penaeus monodon. Splicing patterns in chronically infected adults suggested high levels of defective genomes, possibly explaining the lack of obvious disease signs in high viral load animals.