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Pu Y, Zhou Y, Liu J, Zhang H. A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation. Gigascience 2024; 13:giad107. [PMID: 38171490 PMCID: PMC10764150 DOI: 10.1093/gigascience/giad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/05/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Chiridota heheva is a cosmopolitan holothurian well adapted to diverse deep-sea ecosystems, especially chemosynthetic environments. Besides high hydrostatic pressure and limited light, high concentrations of metal ions also represent harsh conditions in hydrothermal environments. Few holothurian species can live in such extreme conditions. Therefore, it is valuable to elucidate the adaptive genetic mechanisms of C. heheva in hydrothermal environments. FINDINGS Herein, we report a high-quality reference genome assembly of C. heheva from the Kairei vent, which is the first chromosome-level genome of Apodida. The chromosome-level genome size was 1.43 Gb, with a scaffold N50 of 53.24 Mb and BUSCO completeness score of 94.5%. Contig sequences were clustered, ordered, and assembled into 19 natural chromosomes. Comparative genome analysis found that the expanded gene families and positively selected genes of C. heheva were involved in the DNA damage repair process. The expanded gene families and the unique genes contributed to maintaining iron homeostasis in an iron-enriched environment. The positively selected gene RFC2 with 10 positively selected sites played an essential role in DNA repair under extreme environments. CONCLUSIONS This first chromosome-level genome assembly of C. heheva reveals the hydrothermal adaptation of holothurians. As the first chromosome-level genome of order Apodida, this genome will provide the resource for investigating the evolution of class Holothuroidea.
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Affiliation(s)
- Yujin Pu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zhou
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
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2
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Kourouklis AP, Wahlsten A, Stracuzzi A, Martyts A, Paganella LG, Labouesse C, Al-Nuaimi D, Giampietro C, Ehret AE, Tibbitt MW, Mazza E. Control of hydrostatic pressure and osmotic stress in 3D cell culture for mechanobiological studies. BIOMATERIALS ADVANCES 2023; 145:213241. [PMID: 36529095 DOI: 10.1016/j.bioadv.2022.213241] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/25/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Hydrostatic pressure (HP) and osmotic stress (OS) play an important role in various biological processes, such as cell proliferation and differentiation. In contrast to canonical mechanical signals transmitted through the anchoring points of the cells with the extracellular matrix, the physical and molecular mechanisms that transduce HP and OS into cellular functions remain elusive. Three-dimensional cell cultures show great promise to replicate physiologically relevant signals in well-defined host bioreactors with the goal of shedding light on hidden aspects of the mechanobiology of HP and OS. This review starts by introducing prevalent mechanisms for the generation of HP and OS signals in biological tissues that are subject to pathophysiological mechanical loading. We then revisit various mechanisms in the mechanotransduction of HP and OS, and describe the current state of the art in bioreactors and biomaterials for the control of the corresponding physical signals.
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Affiliation(s)
- Andreas P Kourouklis
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland.
| | - Adam Wahlsten
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland
| | - Alberto Stracuzzi
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland; Empa, Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Anastasiya Martyts
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland
| | - Lorenza Garau Paganella
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland; Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Celine Labouesse
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Dunja Al-Nuaimi
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland
| | - Costanza Giampietro
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland; Empa, Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Alexander E Ehret
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland; Empa, Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Mark W Tibbitt
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Edoardo Mazza
- Institute for Mechanical Systems, Department of Mechanical and Process Engineering, ETH Zurich, Leonhardstrasse 21, 8092 Zurich, Switzerland; Empa, Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
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3
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Yan S, Liu K, Mu L, Liu J, Tang W, Liu B. Research and application of hydrostatic high pressure in tumor vaccines (Review). Oncol Rep 2021; 45:75. [PMID: 33760193 PMCID: PMC8020208 DOI: 10.3892/or.2021.8026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/05/2021] [Indexed: 11/29/2022] Open
Abstract
It is well known that hydrostatic pressure (HP) is a physical parameter that is now regarded as an important variable for life. High hydrostatic pressure (HHP) technology has influenced biological systems for more than 100 years. Food and bioscience researchers have shown great interest in HHP technology over the past few decades. The development of knowledge related to this area can better facilitate the application of HHP in the life sciences. Furthermore, new applications for HHP may come from these current studies, particularly in tumor vaccines. Currently, cancer recurrence and metastasis continue to pose a serious threat to human health. The limited efficacy of conventional treatments has led to the need for breakthroughs in immunotherapy and other related areas. Research into tumor vaccines is providing new insights for cancer treatment. The purpose of this review is to present the main findings reported thus far in the relevant scientific literature, focusing on knowledge related to HHP technology and tumor vaccines, and to demonstrate the potential of applying HHP technology to tumor vaccine development.
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Affiliation(s)
- Shuai Yan
- Department of Operating Room, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Kai Liu
- Department of Hand and Foot Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Lin Mu
- Department of Radiology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Jianfeng Liu
- Department of Hand and Foot Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wan Tang
- Department of Operating Room, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Bin Liu
- Department of Hand and Foot Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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Yan Q, Cai M, Zhou L, Xu H, Shi Y, Sun J, Jiang J, Gao J, Wang H. Using an RNA aptamer probe for super-resolution imaging of native EGFR. NANOSCALE ADVANCES 2019; 1:291-298. [PMID: 36132464 PMCID: PMC9473275 DOI: 10.1039/c8na00143j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 01/08/2019] [Accepted: 08/16/2018] [Indexed: 05/06/2023]
Abstract
Aptamers, referred to as "chemical antibodies", are short single-stranded oligonucleotides that bind to targets with high affinity and specificity. Compared with antibodies, aptamers can be designed, developed and modified easily. Since their discovery, aptamers have been widely used in in vitro diagnostics and molecular imaging. However, they are relatively less studied and applied in advanced microscopy. Here we used an RNA aptamer in dSTORM imaging and obtained a high-quality image of EGFR nanoscale clusters on live cell membranes. The results showed that the cluster number and size with aptamer labeling were almost the same as those with labeling with the natural ligand EGF, but the morphology of the clusters was smaller and more regular than that with cetuximab labeling. Meanwhile, dual-color imaging demonstrated sufficient fluorophore labeling, highly specific recognition and greatly accurate clustering information provided by aptamers. Furthermore, the aptamer labeling method indicated that active EGFR formed larger clusters containing more molecules than resting EGFR, which was hidden under the antibody labeling. Our work suggested that aptamers can be used as versatile probes in super-resolution imaging with small steric hindrance, opening a new avenue for detailed and precise morphological analysis of membrane proteins.
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Affiliation(s)
- Qiuyan Yan
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Lulu Zhou
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Haijiao Xu
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yan Shi
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Jiayin Sun
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Junguang Jiang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology Wenhai Road, Aoshanwei, Jimo, Qingdao Shandong 266237 P. R. China
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Kim J, Montagne K, Nemoto H, Ushida T, Furukawa KS. Hypergravity down-regulates c-fos gene expression via ROCK/Rho-GTP and the PI3K signaling pathway in murine ATDC5 chondroprogenitor cells. PLoS One 2017; 12:e0185394. [PMID: 28953959 PMCID: PMC5617206 DOI: 10.1371/journal.pone.0185394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 09/12/2017] [Indexed: 11/19/2022] Open
Abstract
Chondrocytes are known to be physiologically loaded with diverse physical factors such as compressive stress, shear stress and hydrostatic pressure. Although the effects of those mechanical stimuli onto various cell models have been widely studied, those of hypergravity have not yet been revealed clearly. Hereby, we hypothesized that the hypergravity affects relative positions of intracellular elements including nucleus and cytoskeletons due to their density differences, triggering mechanotransduction in the cell. The aim of this study was to investigate the effect of hypergravity on c-fos expression in the murine ATDC5 chondroprogenitor cells, as c-fos is a well known key regulator of cell proliferation and differentiation, including in chondrocytes. We first found that hypergravity down-regulated c-fos expression transiently via ROCK/Rho-GTP and PI3K signaling, and the down-regulation was suppressed by inhibition of actin polymerization.
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Affiliation(s)
- Jeonghyun Kim
- Department of Mechanical Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kevin Montagne
- Department of Mechanical Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Hidetoshi Nemoto
- Division of Regenerative Medical Engineering, Center for Disease Biology and Integrative Medicine, School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takashi Ushida
- Department of Mechanical Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Katsuko S. Furukawa
- Department of Mechanical Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Department of Bioengineering, Graduate school of engineering, University of Tokyo, Tokyo, Japan
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6
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Montagne K, Onuma Y, Ito Y, Aiki Y, Furukawa KS, Ushida T. High hydrostatic pressure induces pro-osteoarthritic changes in cartilage precursor cells: A transcriptome analysis. PLoS One 2017; 12:e0183226. [PMID: 28813497 PMCID: PMC5558982 DOI: 10.1371/journal.pone.0183226] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 08/01/2017] [Indexed: 01/22/2023] Open
Abstract
Due to the high water content of cartilage, hydrostatic pressure is likely one of the main physical stimuli sensed by chondrocytes. Whereas, in the physiological range (0 to around 10 MPa), hydrostatic pressure exerts mostly pro-chondrogenic effects in chondrocyte models, excessive pressures have been reported to induce detrimental effects on cartilage, such as increased apoptosis and inflammation, and decreased cartilage marker expression. Though some genes modulated by high pressure have been identified, the effects of high pressure on the global gene expression pattern have still not been investigated. In this study, using microarray technology and real-time PCR validation, we analyzed the transcriptome of ATDC5 chondrocyte progenitors submitted to a continuous pressure of 25 MPa for up to 24 h. Several hundreds of genes were found to be modulated by pressure, including some not previously known to be mechano-sensitive. High pressure markedly increased the expression of stress-related genes, apoptosis-related genes and decreased that of cartilage matrix genes. Furthermore, a large set of genes involved in the progression of osteoarthritis were also induced by high pressure, suggesting that hydrostatic pressure could partly mimic in vitro some of the genetic alterations occurring in osteoarthritis.
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Affiliation(s)
- Kevin Montagne
- Department of Mechanical Engineering, University of Tokyo, Tokyo, Japan
- * E-mail: (TU); (KM)
| | - Yasuko Onuma
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yasuhiko Aiki
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Katsuko S. Furukawa
- Department of Mechanical Engineering, University of Tokyo, Tokyo, Japan
- Department of Bioengineering, University of Tokyo, Tokyo, Japan
| | - Takashi Ushida
- Department of Mechanical Engineering, University of Tokyo, Tokyo, Japan
- Department of Bioengineering, University of Tokyo, Tokyo, Japan
- * E-mail: (TU); (KM)
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7
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Guevara JM, Moncayo MA, Vaca-González JJ, Gutiérrez ML, Barrera LA, Garzón-Alvarado DA. Growth plate stress distribution implications during bone development: a simple framework computational approach. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2015; 118:59-68. [PMID: 25453383 DOI: 10.1016/j.cmpb.2014.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/22/2014] [Accepted: 10/08/2014] [Indexed: 06/04/2023]
Abstract
Mechanical stimuli play a significant role in the process of long bone development as evidenced by clinical observations and in vivo studies. Up to now approaches to understand stimuli characteristics have been limited to the first stages of epiphyseal development. Furthermore, growth plate mechanical behavior has not been widely studied. In order to better understand mechanical influences on bone growth, we used Carter and Wong biomechanical approximation to analyze growth plate mechanical behavior, and explore stress patterns for different morphological stages of the growth plate. To the best of our knowledge this work is the first attempt to study stress distribution on growth plate during different possible stages of bone development, from gestation to adolescence. Stress distribution analysis on the epiphysis and growth plate was performed using axisymmetric (3D) finite element analysis in a simplified generic epiphyseal geometry using a linear elastic model as the first approximation. We took into account different growth plate locations, morphologies and widths, as well as different epiphyseal developmental stages. We found stress distribution during bone development established osteogenic index patterns that seem to influence locally epiphyseal structures growth and coincide with growth plate histological arrangement.
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Affiliation(s)
- J M Guevara
- Institute for the Study of Inborn Errors of Metabolism, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - M A Moncayo
- Biomimetics Laboratory and Numerical Methods and Modeling Research Group (GNUM), Instituto de Biotecnología (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia
| | - J J Vaca-González
- Biomimetics Laboratory and Numerical Methods and Modeling Research Group (GNUM), Instituto de Biotecnología (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia
| | - M L Gutiérrez
- Biomimetics Laboratory and Numerical Methods and Modeling Research Group (GNUM), Instituto de Biotecnología (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia
| | - L A Barrera
- Institute for the Study of Inborn Errors of Metabolism, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - D A Garzón-Alvarado
- Biomimetics Laboratory and Numerical Methods and Modeling Research Group (GNUM), Instituto de Biotecnología (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia.
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