In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750×, uses 33× less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/.
Úvod: Lymfangiómy patria do skupiny benígnych vaskulárnych tumorov, ktoré majú svoj pôvod v lymfatickom tkanive. Až 90 % prípadov sa manifestuje u detí pred dovŕšením druhého roku života. U dospelých je ich prítomnosť veľmi zriedkavá. Vo väčšine prípadov sa nachádzajú v oblasti hlavy, krku a axily. Intraabodminálne lymfangiómy sú veľmi zriedkavé a predstavujú menej ako 1 % všetkých prípadov. Kazuistika: Autori prezentujú prípad 64-ročnej pacientky, ktorej bola v rámci preventívnej prehliadky diagnostikovaná intraabdominálna cystická lézia. CT vyšetrenie brucha potvrdilo cystickú léziu lokalizovanú v malom omente medzi ľavým lalokom pečene a malým zakrivením žalúdka. Pacientka bola indikovaná na laparoskopickú exstirpáciu ložiska. Histologické vyšetrenie potvrdilo klinickú diagnózu cystického lymfangiómu malého omenta. Záver: Etiopatogenéza lymfangiómov ostáva nejasná. Napriek tomu, že ide o benígne tumory, lymfangiómy majú tendenciu správať sa lokálne infiltratívne a invadujú do okolitých štruktúr. Väčšina prípadov je asymptomatická a diagnostika býva náhodná. Zlatým štandardom v liečbe ostáva kompletná chirurgická exstirpácia s mikroskopicky negatívnymi okrajmi.
Introduction: Lymphangiomas belong to the group of benign vascular tumors that originate in the lymphatic tissue. Up to 90% of cases manifest in children before the second year of life. In adults, their presence is very rare. In most cases, they are located in the head, neck and axilla. Intra-abdominal lymphangiomas are very rare and represent less than 1% of all cases. Case report: The authors present the case of a 64-year-old female patient diagnosed with an intra-abdominal cystic lesion following a routine examination. A CT scan of the abdomen confirmed a cystic lesion located in the lesser omentum between the left lobe of the liver and the lesser curvature of the stomach. The patient was scheduled for laparoscopic exstirpation of the lesion. Histological examination confirmed the clinical diagnosis of cystic lymphangioma of the lesser omentum. Conclusion: The etiopathogenesis of lymphangiomas remains unclear. Despite the fact that they are benign tumors, lymphangiomas tend to have an infiltrative pattern of growth, invading surrounding structures. The majority of cases are asymptomatic and the diagnosis is incidental. The gold standard in treatment remains complete surgical extirpation with microscopically negative margins.
- MeSH
- Diagnosis, Differential MeSH
- Immunohistochemistry methods MeSH
- Humans MeSH
- Lymphangioma, Cystic * surgery diagnostic imaging pathology MeSH
- Minimally Invasive Surgical Procedures methods MeSH
- Incidental Findings MeSH
- Omentum surgery diagnostic imaging pathology MeSH
- Peritoneal Neoplasms surgery diagnostic imaging pathology MeSH
- Tomography, X-Ray Computed MeSH
- Aged MeSH
- Check Tag
- Humans MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Case Reports MeSH
V této kazuistice popisujeme případ 53leté ženy, u které se objevil pomalu rostoucí útvar v oblasti dolního víčka pravého oka. Při zevrubném vyšetření bylo pozorováno nápadné vyklenutí dolního víčka. Palpačně byl zjištěn pod kůží útvar oválného tvaru, tuhé konsistence, velikosti přibližně 2 cm. Nekorigovaná zraková ostrost pacientky byla bilaterálně 20/20 (dle Snellenových optotypů), vyšetření předního a zadního segmentu obou očí bylo v normě. Na snímku z počítačové tomografie orbity pacientky byl patrný solitérní a homogenní pevný kulovitý útvar o hustotě odpovídající hustotě mozkové tkáně. Pacientka podstoupila chirurgickou excizi. Mikroskopické vyšetření léze odhalilo přítomnost dvojí struktury: dvoufázovou hypercelulární oblast (Antoni A) a myxomatózní hypocelulární oblast (Antoni B), obsahující štíhlé podlouhlé buňky se zúženými konci protkané kolagenními vlákny, což odpovídá diagnóze schwannomu. Kromě toho bylo možné pozorovat četné oblasti palisádovitého uspořádání jader kolem fibrilárního výběžku (Verocay tělíska) v oblastech s hustou buněčnou strukturou. Schwannomy se v očním víčku vyskytují jen zřídka, ale jsou doprovázeny klinickými a paraklinickými ukazateli, které svědčí o pravděpodobnosti této diagnózy. Závěrem navrhujeme, aby byl schwannom očního víčka zahrnut do seznamu diferenciálních diagnóz podkožních lézí očního víčka.
In this case report, we describe a 53-year-old woman who presented with a slow-growing lower lid mass in her right eye. On gross examination, a remarkable lower lid bulging was noted. On palpation, a subcutaneous oval-shaped mass with a firm consistency, measuring about 2cm, was noted. The uncorrected visual acuities of the patient were 20/20 (by Snellen chart) bilaterally, and the examinations of the anterior and posterior segments of both eyes were unremarkable. On the orbital Computed Tomography scan of the patient, a solitary and homogenous solid globular mass with the same density of the brain tissue was obvious. The patient underwent surgical excision. Microscopic assessment of the lesion revealed a biphasic hypercellular area (Antoni A) and myxoid hypocellular areas (Antoni B), containing slender cells with tapered ends, interspersed with collagen fibers, consistent with a diagnosis of schwannoma. In addition, some foci of nuclear palisading around the fibrillary process (Verocay bodies) could frequently be found throughout the highly cellular regions. Schwannomas rarely occur in the eyelids, but have clinical and paraclinical indicators which indicate the probable diagnosis. In conclusion, we suggest that eyelid schwannoma be considered as an element of the differential diagnoses list for subcutaneous lesions of the eyelid.
- MeSH
- Middle Aged MeSH
- Humans MeSH
- Neurilemmoma * surgery diagnosis pathology MeSH
- Eyelids surgery pathology MeSH
- Tomography, X-Ray Computed methods MeSH
- Check Tag
- Middle Aged MeSH
- Humans MeSH
- Female MeSH
- Publication type
- Case Reports MeSH
Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.
Although the cat flea, Ctenocephalides felis, has been identified as the primary vector of Rickettsia felis, additional flea, tick, mite, and louse species have also been associated with this bacterium by molecular means; however, the role of these arthropods in the transmission of R. felis has not been clarified. Here, we succeeded in culture isolation of R. felis from a host-seeking castor bean tick, Ixodes ricinus, the most common tick in Slovakia. The bacterial isolation was performed on XTC-2 cells at 28 °C using the shell-vial technique. An evaluation of the growth properties was performed for both the XTC-2 and Vero cell lines. We observed R. felis in the infected host cells microscopically by Gimenez staining and immunofluorescence assay. The R. felis isolate was purified by gradient ultracentrifugation and visualized by electron microscopy. Fragments of the genes gltA, ompA, ompB, htrA, rpoB, sca4, rffE, and rrs were amplified and compared with the corresponding sequences of the type strain URRWXCal2 and other R. felis culture -isolated strains. We did not detect any nucleotide polymorphisms; however, plasmid pRFδ, characteristic of the standard strain, was absent in our isolate. Herein, we describe the first successful isolation and characterization of a tick-derived R. felis strain "Danube", obtained from an I. ricinus nymph.
- MeSH
- Cell Line MeSH
- Arthropods * MeSH
- Ixodes * microbiology MeSH
- Rickettsia felis * genetics MeSH
- Rickettsia * genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The advances in electron cryo-microscopy have enabled high-resolution structural studies of vitrified macromolecular complexes in situ by cryo-electron tomography (cryo-ET). Since utilization of cryo-ET is generally limited to the specimens with thickness < 500 nm, a complex sample preparation protocol to study larger samples such as single eukaryotic cells by cryo-ET was developed and optimized over the last decade. The workflow is based on the preparation of a thin cellular lamella by cryo-focused ion beam milling (cryo-FIBM) from the vitrified cells. The sample preparation protocol is a multi-step process which includes utilization of several high-end instruments and comprises sample manipulation prone to sample deterioration. Here, we present a workflow for preparation of three different model specimens that was optimized to provide high-quality lamellae for cryo-ET or electron diffraction tomography with high reproducibility. Preparation of lamellae from large adherent mammalian cells, small suspension eukaryotic cell line, and protein crystals of intermediate size is described which represents examples of the most frequently studied samples used for cryo-FIBM in life sciences.
- MeSH
- Cells ultrastructure MeSH
- Cryoelectron Microscopy methods MeSH
- Ions MeSH
- Macromolecular Substances ultrastructure MeSH
- Molecular Biology methods MeSH
- Specimen Handling methods MeSH
- Proteins ultrastructure MeSH
- Workflow MeSH
- Reproducibility of Results MeSH
- Saccharomyces cerevisiae ultrastructure MeSH
- Electron Microscope Tomography methods MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Cobalt oxide nanoparticles were prepared via green chemistry route and fully characterized by Field Emission Scanning Electron Microscope (FESEM), Energy-dispersive X-ray spectroscopy (EDAX), X-ray diffraction (XRD), High-resolution transmission electron microscopy (HRTEM) and Transmission electron microscopy (TEM) analyses; the CoO and Co3O4 nanoparticles, in sheet-shaped cobalt oxide form, ensued simultaneously in one step. The varying concentrations of NPs were analyzed via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test on the cancer cell line (U87) which revealed that with increasing concentration of cobalt oxide nanoparticles, the survival rate of U87 tumor cells decreases; IC50 of nanoparticles being ~ 55 µg/ml-1.
- MeSH
- Anti-Bacterial Agents chemistry MeSH
- X-Ray Diffraction MeSH
- Inhibitory Concentration 50 MeSH
- Cobalt chemistry MeSH
- Hydrogen-Ion Concentration MeSH
- Metal Nanoparticles chemistry MeSH
- Humans MeSH
- Magnetics MeSH
- Microbial Sensitivity Tests MeSH
- Cell Line, Tumor MeSH
- Nanomedicine methods MeSH
- Nanotechnology methods MeSH
- Oxides chemistry MeSH
- Surface-Active Agents MeSH
- Antineoplastic Agents pharmacology MeSH
- Plant Extracts MeSH
- Rosmarinus MeSH
- Solubility MeSH
- Spectroscopy, Fourier Transform Infrared MeSH
- Green Chemistry Technology methods MeSH
- Temperature MeSH
- Tetrazolium Salts chemistry MeSH
- Thiazoles chemistry MeSH
- Microscopy, Electron, Transmission MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
The aim of this study was to observe the influence of electromagnetic radiation (EMR) on the structure and ultrastructure of the rat's liver. The pregnant rats used in the experiment were exposed to a pulsed microwave radiation (frequency of 2.45 GHz; mean power density of 2.8 mW/cm2) daily for 2 h, throughout their pregnancy. After delivery, the offspring was not exposed to EMR. Samples of the liver of 5-week-old offspring were subjected to histopathological evaluation. They were processed for light and transmission electron microscopy. Our results indicated that EMR did not cause pronounced changes in the structure of the liver of the investigated offspring. The size and shape of liver lobuli was preserved and the amount of connective tissue in the liver parenchyma did not increase. However, electron microscopy revealed changes in the shape and number of microvilli at the vascular pole of hepatocytes, and formation of vesicles of various shapes and sizes. The endothelial cells were swollen with larger fenestrations compared to the control group. The spaces of Disse were irregular and dilated. Even though these changes were only mild, further studies are needed to determine the effect of EMR and clarify its potential risk during pregnancy.
Melting summer snow in the Austrian Alps exhibited a yellowish bloom that was mainly comprised of an unidentified unicellular chrysophyte. Molecular data (18S rRNA and rbcL genes) showed a close relationship to published sequences from an American pond alga formerly identified as Kremastochrysis sp. The genera Kremastochrysis and Kremastochrysopsis are morphologically distinguished by the number of flagella observed with the light microscope, and therefore we assigned the Austrian snow alga and an American pond alga to the genus Kremastochrysopsis. Transmission and scanning electron microscopy revealed that swimming cells had two flagella oriented in opposite directions, typical for the Hibberdiales. Molecular phylogenetic analyses showed that both new species were closely related to Hibberdia. Kremastochrysopsis ocellata, the type species and only known species, has two chloroplasts per cell and the zoospores have red eyespots. Our two organisms had only a single chloroplast and no zoospore eyespot, but their gene sequences differed substantially. Therefore, we described two new species, Kremastochrysopsis austriaca sp. nov and Kremstochrysopsis americana sp. nov. When grown in culture, both taxa showed a characteristic hyponeustonic growth (hanging below the water surface), whereas older immotile cells grew at the bottom of the culture vessel. Ecologically, Kremastochrysopsis austriaca sp. nov., which caused snow discolorations, had no close phylogenetic relationships to other psychrophilic chrysophytes, for example, Chromulina chionophilia, Hydrurus sp., and Ochromonas-like flagellates.
- MeSH
- Chloroplasts * MeSH
- Chrysophyta * MeSH
- Phylogeny MeSH
- RNA, Ribosomal, 16S MeSH
- RNA, Ribosomal, 18S MeSH
- Sequence Analysis, DNA MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Austria MeSH
Primary cilia are microtubule-based organelles that are important for signaling and sensing in eukaryotic cells. Unlike the thoroughly studied motile cilia, the three-dimensional architecture and molecular composition of primary cilia are largely unexplored. Yet, studying these aspects is necessary to understand how primary cilia function in health and disease. We developed an enabling method for investigating the structure of primary cilia isolated from MDCK-II cells at molecular resolution by cryo-electron tomography. We show that the textbook '9 + 0' arrangement of microtubule doublets is only present at the primary cilium base. A few microns out, the architecture changes into an unstructured bundle of EB1-decorated microtubules and actin filaments, putting an end to a long debate on the presence or absence of actin filaments in primary cilia. Our work provides a plethora of insights into the molecular structure of primary cilia and offers a methodological framework to study these important organelles.
- MeSH
- Cell Culture Techniques MeSH
- Madin Darby Canine Kidney Cells MeSH
- Chlamydomonas metabolism ultrastructure MeSH
- Cilia metabolism ultrastructure MeSH
- Cryoelectron Microscopy MeSH
- Gene Expression MeSH
- Humans MeSH
- Actin Cytoskeleton metabolism ultrastructure MeSH
- Microtubules metabolism ultrastructure MeSH
- Microtubule-Associated Proteins genetics metabolism MeSH
- Dogs MeSH
- Electron Microscope Tomography MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Dogs MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
