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Maxa J, Neděla V, Šabacká P, Binar T. Impact of Supersonic Flow in Scintillator Detector Apertures on the Resulting Pumping Effect of the Vacuum Chambers. SENSORS (BASEL, SWITZERLAND) 2023; 23:4861. [PMID: 37430777 DOI: 10.3390/s23104861] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/26/2023] [Accepted: 05/16/2023] [Indexed: 07/12/2023]
Abstract
The article describes the combination of experimental measurements with mathematical-physics analyses in flow investigation in the chambers of the scintillator detector, which is a part of the environmental scanning electron microscope. The chambers are divided with apertures by small openings that keep the desirable pressure differences between three chambers: The specimen chamber, the differentially pumped intermediate chamber, and the scintillator chamber. There are conflicting demands on these apertures. On the one hand, the diameter of the apertures must be as big as possible so that they incur minimal losses of the passing secondary electrons. On the other hand, it is possible to magnify the apertures only to a certain extent so the rotary and turbomolecular vacuum pump can maintain the required operating pressures in separate chambers. The article describes the combination of experimental measurement using an absolute pressure sensor and mathematical physics analysis to map all the specifics of the emerging critical supersonic flow in apertures between the chambers. Based on the experiments and their tuned analyses, the most effective variant of combining the sizes of each aperture concerning different operating pressures in the detector is determined. The situation is made more difficult by the described fact that each aperture separates a different pressure gradient, so the gas flow through each aperture has its own characteristics with a different type of critical flow, and they influence each other, thereby influencing the final passage of secondary electrons detected by the scintillator and thus affecting the resulting displayed image.
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Affiliation(s)
- Jiří Maxa
- Institute of Scientific Instruments of the CAS, Královopolská 147, 612 64 Brno, Czech Republic
- Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 10, 616 00 Brno, Czech Republic
| | - Vilém Neděla
- Institute of Scientific Instruments of the CAS, Královopolská 147, 612 64 Brno, Czech Republic
| | - Pavla Šabacká
- Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 10, 616 00 Brno, Czech Republic
| | - Tomáš Binar
- Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 10, 616 00 Brno, Czech Republic
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Šabacká P, Maxa J, Bayer R, Vyroubal P, Binar T. Slip Flow Analysis in an Experimental Chamber Simulating Differential Pumping in an Environmental Scanning Electron Microscope. SENSORS (BASEL, SWITZERLAND) 2022; 22:9033. [PMID: 36501735 PMCID: PMC9740474 DOI: 10.3390/s22239033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
This paper describes the combination of experimental measurements with mathematical-physical analysis during the investigation of flow in an aperture at low pressures in a prepared experimental chamber. In the first step, experimental measurements of the pressure in the specimen chamber and at its outlet were taken during the pumping of the chamber. This process converted the atmospheric pressure into the operating pressure typical for the current AQUASEM II environmental electron microscope at the ISI of the CAS in Brno. Based on these results, a mathematical-physical model was tuned in the Ansys Fluent system and subsequently used for mathematical-physical analysis in a slip flow regime on a nozzle wall at low pressure. These analyses will be used to fine-tune the experimental chamber. Once the chamber is operational, it will be possible to compare the results obtained from the experimental measurements of the nozzle wall pressure, static pressure, total pressure and temperature from the nozzle axis region in supersonic flow with the results obtained from the mathematical-physical analyses. Based on the above comparative analyses, we will be able to determine the realistic slip flow at the nozzle wall under different conditions at the continuum mechanics boundary.
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Affiliation(s)
- Pavla Šabacká
- Institute of Scientific Instruments of the CAS, Královopolská 147, 61200 Brno, Czech Republic
- Department of Electrical and Electronic Technology, Brno University of Technology, 61600 Brno, Czech Republic
| | - Jiří Maxa
- Institute of Scientific Instruments of the CAS, Královopolská 147, 61200 Brno, Czech Republic
- Department of Electrical and Electronic Technology, Brno University of Technology, 61600 Brno, Czech Republic
| | - Robert Bayer
- Department of Electrical and Electronic Technology, Brno University of Technology, 61600 Brno, Czech Republic
| | - Petr Vyroubal
- Department of Electrical and Electronic Technology, Brno University of Technology, 61600 Brno, Czech Republic
| | - Tomáš Binar
- Department of Electrical and Electronic Technology, Brno University of Technology, 61600 Brno, Czech Republic
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Bačovský V, Čegan R, Tihlaříková E, Neděla V, Hudzieczek V, Smrža L, Janíček T, Beneš V, Hobza R. Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2354-2368. [PMID: 35045170 DOI: 10.1093/jxb/erab538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. In Silene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia, induced by rapid demethylation in the parental generation. Eight candidates were found to have a positive role in gynoecium promotion, floral organ size, and whorl boundary, and affect the expression of class B MADS-box flower genes. To complement our transcriptome analysis, we closely examined the floral organs in their native state using field emission environmental scanning electron microscopy, and examined the differences between females and androhermaphrodites in their placenta and ovule organization. Our results reveal the regulatory pathways potentially involved in sex-specific flower development in the classical model of dioecy, S. latifolia. These pathways include previously hypothesized and unknown female-regulator genes that act on the factors that determine the flower boundaries, and a negative regulator of anther development, SUPERMAN-like (SlSUP).
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Eva Tihlaříková
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vilém Neděla
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Lubomír Smrža
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Vladimír Beneš
- EMBL Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, D-69117 Heidelberg, Germany
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
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Neděla V, Tihlaříková E, Maxa J, Imrichová K, Bučko M, Gemeiner P. Simulation-based optimisation of thermodynamic conditions in the ESEM for dynamical in-situ study of spherical polyelectrolyte complex particles in their native state. Ultramicroscopy 2020; 211:112954. [PMID: 32018072 DOI: 10.1016/j.ultramic.2020.112954] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 11/18/2022]
Abstract
We present a complex analysis and optimisation of dynamic conditions in the environmental scanning electron microscope (ESEM) to allow in-situ observation of extremely delicate wet bio-polymeric spherical particles in their native state. According to the results of gas flow and heat transfer simulations, we were able to develop an improved procedure leading to thermodynamic equilibrium between the sample and chamber environment. To quantify and hence minimise the extent of any sample deformation during specimen chamber pumping, a strength-stress analysis is used. Monte Carlo simulations of beam-gas, -water, and -sample interactions describe beam scattering, absorbed energy, interaction volume and the emission of signal electrons in the ESEM. Finally, we discuss sample damage as a result of drying and the production of beam-induced free radicals. Based on all experimental and simulation results we introduce a Delicate Sample Observation Strategy for the ESEM. We show how this strategy can be applied to the characterization of polyelectrolyte complex spherical particles containing immobilized recombinant cells E. coli overexpressing cyclohexanone monooxygenase, used as a model biocatalyst. We present the first native-state electron microscopy images of the viscous core of a halved polyelectrolyte complex capsule containing living cells.
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Affiliation(s)
- Vilém Neděla
- Environmental electron microscopy group, Institute of Scientific Instruments of ASCR, Královopolská 147, 61264 Brno, Czech Republic.
| | - Eva Tihlaříková
- Environmental electron microscopy group, Institute of Scientific Instruments of ASCR, Královopolská 147, 61264 Brno, Czech Republic
| | - Jiří Maxa
- Environmental electron microscopy group, Institute of Scientific Instruments of ASCR, Královopolská 147, 61264 Brno, Czech Republic
| | - Kamila Imrichová
- Environmental electron microscopy group, Institute of Scientific Instruments of ASCR, Královopolská 147, 61264 Brno, Czech Republic
| | - Marek Bučko
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Peter Gemeiner
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
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Tihlaříková E, Neděla V, Đorđević B. In-situ preparation of plant samples in ESEM for energy dispersive x-ray microanalysis and repetitive observation in SEM and ESEM. Sci Rep 2019; 9:2300. [PMID: 30783188 PMCID: PMC6381206 DOI: 10.1038/s41598-019-38835-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/07/2019] [Indexed: 11/25/2022] Open
Abstract
The Extended Low Temperature Method (ELTM) for the in-situ preparation of plant samples in an environmental scanning electron microscope enables carrying out repetitive topographical and material analysis at a higher resolution in the vacuum conditions of a scanning electron microscope or in the low gas pressure conditions of an environmental scanning electron microscope. The method does not require any chemical intervention and is thus suitable for imaging delicate structures rarely observable with common treatment methods. The method enables both sample stabilization as close to their native state as possible, as well as the transfer of the same sample from a low vacuum to an atmospheric condition for sample storage or later study. It is impossible for wet samples in the environmental scanning electron microscope. Our studies illustrate the high applicability of the ELTM for different types of plant tissue, from imaging of plant waxes at higher resolution, the morphological study of highly susceptible early somatic embryos to the elemental microanalysis of root cells. The method established here provides a very fast, universal and inexpensive solution for plant sample treatment usable in a commercial environmental scanning electron microscope equipped with a cooling Peltier stage.
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Affiliation(s)
- Eva Tihlaříková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, 612 00, Czech Republic.
| | - Vilém Neděla
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, 612 00, Czech Republic
| | - Biljana Đorđević
- Department of Plant Biology, Mendel University in Brno, Brno, 613 00, Czech Republic
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Đorđević B, Neděla V, Tihlaříková E, Trojan V, Havel L. Effects of copper and arsenic stress on the development of Norway spruce somatic embryos and their visualization with the environmental scanning electron microscope. N Biotechnol 2018; 48:35-43. [PMID: 29782934 DOI: 10.1016/j.nbt.2018.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 11/17/2022]
Abstract
Somatic embryogenesis is an important biotechnological technique which can be used in studies associated with environmental stress. Four embryogenic cell lines of Norway spruce were grown on media enriched with copper and arsenic in concentration ranges 50-500 μM and 10-50 μM, respectively. The effects were observed during subsequent stages of somatic embryogenesis, the characteristics evaluated being proliferation potential, average number of somatic embryos obtained per g/fresh weight, morphology of developed somatic embryos, metal uptake, and microanalysis of macro- and micronutrients uptake. Copper and arsenic at higher concentrations significantly reduced the growth of early somatic embryos. In almost all treatments, the cell line V-1-3 showed the best performance compared with the other lines tested. Environmental scanning electron microscopy was used to visualize and identify morphological abnormalities in the development of somatic embryos. Abnormalities observed were classified into several categories: meristemless somatic embryos, somatic embryos with disrupted meristem, reduced number of cotyledons, single cotyledon and fused cotyledons. With the application of a low temperature method for the environmental scanning electron microscope, samples were stabilized and whole meristems could be investigated in their native state. As far as we are aware, this is the first report of the effect of copper and arsenic during the process of somatic embryogenesis and the first to evaluate the content of macro and micronutrients uptake in Norway spruce.
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Affiliation(s)
- Biljana Đorđević
- Department of Plant Biology, Mendel University in Brno, Zemědělská 1, Brno 613 00, Czech Republic.
| | - Vilém Neděla
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno 612 64, Czech Republic
| | - Eva Tihlaříková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno 612 64, Czech Republic
| | - Václav Trojan
- Department of Plant Biology, Mendel University in Brno, Zemědělská 1, Brno 613 00, Czech Republic
| | - Ladislav Havel
- Department of Plant Biology, Mendel University in Brno, Zemědělská 1, Brno 613 00, Czech Republic
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Vlašínová H, Neděla V, Đorđević B, Havel L. Bottlenecks in bog pine multiplication by somatic embryogenesis and their visualization with the environmental scanning electron microscope. PROTOPLASMA 2017; 254:1487-1497. [PMID: 27783182 DOI: 10.1007/s00709-016-1036-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 10/17/2016] [Indexed: 05/03/2023]
Abstract
Somatic embryogenesis (SE) is an important biotechnological technique used for the propagation of many pine species in vitro. However, in bog pine, one of the most endangered tree species in the Czech Republic, limitations were observed, which negatively influenced the development and further germination of somatic embryos. Although initiation frequency was very low-0.95 %, all obtained cell lines were subjected to maturation. The best responding cell line (BC1) was used and subjected to six different variants of the maturation media. The media on which the highest number of early-precotyledonary/cotyledonary somatic embryos was formed was supplemented with 121 μM abscisic acid (ABA) and with 6 % maltose. In the end of maturation experiments, different abnormalities in formation of somatic embryos were observed. For visualization and identification of abnormalities in meristem development during proliferation and maturation processes, the environmental scanning electron microscope was used. In comparison to the classical light microscope, the non-commercial environmental scanning electron microscope AQUASEM II has been found as a very useful tool for the quick recognition of apical meristem disruption and abnormal development. To our knowledge, this is the first report discussing somatic embryogenesis in bog pine. Based on this observation, the cultivation procedure could be enhanced and the method for SE of bog pine optimized.
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Affiliation(s)
- Helena Vlašínová
- Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic
| | - Vilem Neděla
- Institute of Scientific Instruments, Academy of Sciences of the Czech Republic, Královopolská 147, Brno, 61264, Czech Republic
| | - Biljana Đorđević
- Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic.
| | - Ladislav Havel
- Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic
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Wang C, Oh S, Lee HA, Kang J, Jeong KJ, Kang SW, Hwang DY, Lee J. In vivo feasibility test using transparent carbon nanotube-coated polydimethylsiloxane sheet at brain tissue and sciatic nerve. J Biomed Mater Res A 2017; 105:1736-1745. [PMID: 28076883 DOI: 10.1002/jbm.a.36001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/22/2016] [Accepted: 01/06/2017] [Indexed: 12/26/2022]
Abstract
Carbon nanotubes, with their unique and outstanding properties, such as strong mechanical strength and high electrical conductivity, have become very popular for the repair of tissues, particularly for those requiring electrical stimuli. Polydimethylsiloxane (PDMS)-based elastomers have been used in a wide range of biomedical applications because of their optical transparency, physiological inertness, blood compatibility, non-toxicity, and gas permeability. In present study, most of artificial nerve guidance conduits (ANGCs) are not transparent. It is hard to confirm the position of two stumps of damaged nerve during nerve surgery and the conduits must be cut open again to observe regenerative nerves after surgery. Thus, a novel preparation method was utilized to produce a transparent sheet using PDMS and multiwalled carbon nanotubes (MWNTs) via printing transfer method. Characterization of the PDMS/MWNT (PM) sheets revealed their unique physicochemical properties, such as superior mechanical strength, a certain degree of electrical conductivity, and high transparency. Characterization of the in vitro and in vivo usability was evaluated. PM sheets showed high biocompatibility and adhesive ability. In vivo feasibility tests of rat brain tissue and sciatic nerve revealed the high transparency of PM sheets, suggesting that it can be used in the further development of ANGCs. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1736-1745, 2017.
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Affiliation(s)
- Caifeng Wang
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Sangjin Oh
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Hyun Ah Lee
- Department of Biomaterials Science, College of Natural Resources and Life Science/Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
| | - Jieun Kang
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Ki-Jae Jeong
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Seon Woo Kang
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Dae Youn Hwang
- Department of Biomaterials Science, College of Natural Resources and Life Science/Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea
| | - Jaebeom Lee
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan, 46241, Republic of Korea
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