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Muraoka A, Yokoi A, Yoshida K, Kitagawa M, Asano-Inami E, Murakami M, Bayasula, Miyake N, Nakanishi N, Nakamura T, Osuka S, Iwase A, Kajiyama H. Small extracellular vesicles in follicular fluids for predicting reproductive outcomes in assisted reproductive technology. COMMUNICATIONS MEDICINE 2024; 4:33. [PMID: 38418565 PMCID: PMC10902298 DOI: 10.1038/s43856-024-00460-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Assisted reproductive technology accounts for an increasing proportion of infertility treatments, and assessments to predict clinical pregnancy outcomes are desired. Extracellular vesicles exist in follicular fluid, and small non coding RNAs in extracellular vesicles underline the possibility of reflecting pregnancy potential. METHODS Follicular fluid samples are collected from 20 ovarian follicles of 15 infertile patients undergoing assisted reproductive technology. Extracellular vesicles are isolated by serial centrifugation and small RNA sequencing is performed to investigate the profiles of microRNAs and P-element-induced wimpy testis-interacting RNAs. RESULTS Small extracellular vesicles with a size range of approximately 100 nm are successfully isolated, and the small non coding RNA profiles of pregnant samples (n = 8) are different from those of non-pregnant samples (n = 12). Fourteen dysregulated small non coding RNAs are selected to identify the independent candidates [mean read count >100, area under the curve >0.8]. Among them, we find that a specific combination of small non coding RNAs (miR-16-2-3p, miR-378a-3p, and miR-483-5p) can predict the pregnant samples more precisely using a receiver operating characteristics curves analysis (area under the curve: 0.96). Furthermore, even in the same patients, the three microRNAs are differentially expressed between pregnant and non-pregnant samples. CONCLUSIONS Our results demonstrate that small non coding RNAs derived from small extracellular vesicles in follicular fluid can be potential non-invasive biomarkers for predicting pregnancy, leading to their probable application in assisted reproductive technology. Further large-scale studies are required to validate the clinical usefulness of these small non coding RNAs.
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Affiliation(s)
- Ayako Muraoka
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Akira Yokoi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
- Nagoya University Institute for Advanced Research, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
- Japan Science and Technology Agency (JST), FOREST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Kosuke Yoshida
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
- Nagoya University Institute for Advanced Research, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Masami Kitagawa
- Bell Research Center for Reproductive Health and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Eri Asano-Inami
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Mayuko Murakami
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Bayasula
- Bell Research Center for Reproductive Health and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Natsuki Miyake
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Natsuki Nakanishi
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tomoko Nakamura
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Satoko Osuka
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Akira Iwase
- Department of Obstetrics and Gynecology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
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Axelrod JJ, Petrov PN, Zhang JT, Remis J, Buijsse B, Glaeser RM, Mȕller H. Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy. Ultramicroscopy 2023; 249:113730. [PMID: 37011498 PMCID: PMC11229668 DOI: 10.1016/j.ultramic.2023.113730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
We identify thermal magnetic field fluctuations, caused by thermal electron motion ("Johnson noise") in electrically conductive materials, as a potential resolution limit in transmission electron microscopy with a phase plate. Specifically, resolution loss can occur if the electron diffraction pattern is magnified to extend phase contrast to lower spatial frequencies, and if conductive materials are placed too close to the electron beam. While our initial implementation of a laser phase plate (LPP) was significantly affected by these factors, a redesign eliminated the problem and brought the performance close to the expected level. The resolution now appears to be limited by residual Johnson noise arising from the electron beam liner tube in the region of the LPP, together with the chromatic aberration of the relay optics. These two factors can be addressed during future development of the LPP.
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Affiliation(s)
- Jeremy J Axelrod
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.
| | - Petar N Petrov
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jessie T Zhang
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathan Remis
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Bart Buijsse
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, the Netherlands
| | - Robert M Glaeser
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Holger Mȕller
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
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Axelrod JJ, Petrov PN, Zhang JT, Remis J, Buijsse B, Glaeser RM, Mȕller H. Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.12.528160. [PMID: 36824829 PMCID: PMC9949102 DOI: 10.1101/2023.02.12.528160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We identify thermal magnetic field fluctuations, caused by thermal electron motion ("Johnson noise") in electrically conductive materials, as a potential resolution limit in transmission electron microscopy with a phase plate. Specifically, resolution loss can occur if the electron diffraction pattern is magnified to extend phase contrast to lower spatial frequencies, and if conductive materials are placed too close to the electron beam. While our initial implementation of a laser phase plate (LPP) was significantly affected by these factors, a redesign eliminated the problem and brought the performance close to the expected level. The resolution now appears to be limited by residual Johnson noise arising from the electron beam liner tube in the region of the LPP, together with the chromatic aberration of the relay optics. These two factors can be addressed during future development of the LPP.
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Affiliation(s)
- Jeremy J. Axelrod
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Petar N. Petrov
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jessie T. Zhang
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathan Remis
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Bart Buijsse
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, the Netherlands
| | - Robert M. Glaeser
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Holger Mȕller
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
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Harder OF, Voss JM, Olshin PK, Drabbels M, Lorenz UJ. Microsecond melting and revitrification of cryo samples: protein structure and beam-induced motion. Acta Crystallogr D Struct Biol 2022; 78:883-889. [PMID: 35775987 PMCID: PMC9248841 DOI: 10.1107/s205979832200554x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/21/2022] [Indexed: 11/10/2022] Open
Abstract
A novel approach to time-resolved cryo-electron microscopy (cryo-EM) has recently been introduced that involves melting a cryo sample with a laser beam to allow protein dynamics to briefly occur in the liquid, before trapping the particles in their transient configurations by rapidly revitrifying the sample. With a time resolution of just a few microseconds, this approach is notably fast enough to study the domain motions that are typically associated with the activity of proteins but which have previously remained inaccessible. Here, crucial details are added to the characterization of the method. It is shown that single-particle reconstructions of apoferritin and Cowpea chlorotic mottle virus from revitrified samples are indistinguishable from those from conventional samples, demonstrating that melting and revitrification leaves the particles intact and that they do not undergo structural changes within the spatial resolution afforded by the instrument. How rapid revitrification affects the properties of the ice is also characterized, showing that revitrified samples exhibit comparable amounts of beam-induced motion. The results pave the way for microsecond time-resolved studies of the conformational dynamics of proteins and open up new avenues to study the vitrification process and to address beam-induced specimen movement.
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Burton-Smith RN, Murata K. Cryo-Electron Microscopy of the Giant Viruses. Microscopy (Oxf) 2021; 70:477-486. [PMID: 34490462 DOI: 10.1093/jmicro/dfab036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/12/2022] Open
Abstract
High resolution study of the giant viruses presents one of the latest challenges in cryo-electron microscopy of viruses. Too small for light microscopy, but too large for easy study at high resolution by electron microscopy, they range in size from ~0.2-2 μm, from high symmetry icosahedral viruses such as Paramecium burseria Chlorella virus 1 to asymmetric forms like Tupanvirus or Pithovirus. To attain high resolution, two strategies exist to study these large viruses by cryo-EM: firstly, increasing the acceleration voltage of the electron microscope to improve sample penetration and overcome the limitations imposed by electro-optical physics at lower voltages, and secondly the method of "block-based reconstruction" pioneered by Michael G. Rossmann and his collaborators, which resolves the latter limitation through an elegant leveraging of high symmetry, but cannot overcome sample penetration limitations. In addition, more recent advances in both computational capacity and image processing also yield assistance in studying the giant viruses. Especially, the inclusion of Ewald sphere correction can provide large improvements in attainable resolutions for 300 kV electron microscopes. Despite this, the study of giant viruses remains a significant challenge.
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Affiliation(s)
- Raymond N Burton-Smith
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
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Sub-3 Å Cryo-EM Structures of Necrosis Virus Particles via the Use of Multipurpose TEM with Electron Counting Camera. Int J Mol Sci 2021; 22:ijms22136859. [PMID: 34202259 PMCID: PMC8268952 DOI: 10.3390/ijms22136859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
During this global pandemic, cryo-EM has made a great impact on the structure determination of COVID-19 proteins. However, nearly all high-resolution results are based on data acquired on state-of-the-art microscopes where their availability is restricted to a number of centers across the globe with the studies on infectious viruses being further regulated or forbidden. One potential remedy is to employ multipurpose microscopes. Here, we investigated the capability of 200 kV multipurpose microscopes equipped with a direct electron camera in determining the structures of infectious particles. We used 30 nm particles of the grouper nerve necrosis virus as a test sample and obtained the cryo-EM structure with a resolution as high as ∼2.7 Å from a setting that used electron counting. For comparison, we tested a high-end cryo-EM (Talos Arctica) using a similar virus (Macrobrachium rosenbergii nodavirus) to obtain virtually the same resolution. Those results revealed that the resolution is ultimately limited by the depth of field. Our work updates the density maps of these viruses at the sub-3Å level to allow for building accurate atomic models from de novo to provide structural insights into the assembly of the capsids. Importantly, this study demonstrated that multipurpose TEMs are capable of the high-resolution cryo-EM structure determination of infectious particles and is thus germane to the research on pandemics.
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