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Dent JE, Devescovi V, Li H, Di Lena P, Lu Y, Liu Y, Nardini C. Mechanotransduction map: simulation model, molecular pathway, gene set. ACTA ACUST UNITED AC 2014; 31:1053-9. [PMID: 25429059 DOI: 10.1093/bioinformatics/btu776] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/17/2014] [Indexed: 01/07/2023]
Abstract
MOTIVATION Mechanotransduction--the ability to output a biochemical signal from a mechanical input--is related to the initiation and progression of a broad spectrum of molecular events. Yet, the characterization of mechanotransduction lacks some of the most basic tools as, for instance, it can hardly be recognized by enrichment analysis tools, nor could we find any pathway representation. This greatly limits computational testing and hypothesis generation on mechanotransduction biological relevance and involvement in disease or physiological mechanisms. RESULTS We here present a molecular map of mechanotransduction, built in CellDesigner to warrant that maximum information is embedded in a compact network format. To validate the map's necessity we tested its redundancy in comparison with existing pathways, and to estimate its sufficiency, we quantified its ability to reproduce biological events with dynamic simulations, using Signaling Petri Networks. AVAILABILITY AND IMPLEMENTATION SMBL language map is available in the Supplementary Data: core_map.xml, basic_map.xml. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jennifer E Dent
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Valentina Devescovi
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Han Li
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Pietro Di Lena
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Youtao Lu
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Yuanhua Liu
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Christine Nardini
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
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Nishitani K, Kobayashi M, Kuroki H, Mori K, Shirai T, Satake T, Nakamura S, Arai R, Nakagawa Y, Nakamura T, Matsuda S. Ultrasound can detect macroscopically undetectable changes in osteoarthritis reflecting the superficial histological and biochemical degeneration: ex vivo study of rabbit and human cartilage. PLoS One 2014; 9:e89484. [PMID: 24586815 PMCID: PMC3931779 DOI: 10.1371/journal.pone.0089484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/21/2014] [Indexed: 01/12/2023] Open
Abstract
Recognizing subtle cartilage changes in the preclinical stage of osteoarthritis (OA) is essential for early diagnosis. To this end, the ability of the ultrasound signal intensity to detect macroscopically undetectable cartilage change was investigated. In this study, cartilage of rabbit OA model and human OA samples was examined by macroscopic evaluation, ultrasound signal intensity, histology with Mankin scores, and Fourier transform infrared imaging (FTIRI) analysis. Rabbit OA was induced by anterior cruciate ligament transection and evaluated at 1, 2, 4 and 12 weeks. Twenty human samples were harvested during total knee arthroplasty from OA patients who had macroscopically normal human cartilage (ICRS grade 0) on the lateral femoral condyle. In the animal study, there was no macroscopic OA change at 2 weeks, but histology detected degenerative changes at this time point. Ultrasound signal intensity also detected degeneration at 2 weeks. In human samples, all samples were obtained from macroscopically intact site, however nearly normal (0≤ Mankin score <2), early OA (2≤ Mankin score <6), and moderate OA (6≤ Mankin score <10) samples were actually intermixed. Ultrasound signal intensity was significantly different among these 3 stages and was well correlated with Mankin scores (R = −0.80) and FTIR parameters related to collagen and proteoglycan content in superficial zone. In conclusion, ultrasound can detect microscopic cartilage deterioration when such changes do not exist macroscopically, reflecting superficial histological and biochemical changes.
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Affiliation(s)
- Kohei Nishitani
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- * E-mail:
| | - Masahiko Kobayashi
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Kuroki
- Department of Physical Therapy, Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Mori
- Department of Applied Medical Engineering Science, Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Takaaki Shirai
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Satake
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinnichiro Nakamura
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryuzo Arai
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuaki Nakagawa
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Orthopaedic surgery, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Takashi Nakamura
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Orthopaedic surgery, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Shuichi Matsuda
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Wang Q, Yang YY, Niu HJ, Zhang WJ, Feng QJ, Chen WF. An ultrasound study of altered hydration behaviour of proteoglycan-degraded articular cartilage. BMC Musculoskelet Disord 2013; 14:289. [PMID: 24119051 PMCID: PMC3819513 DOI: 10.1186/1471-2474-14-289] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Articular cartilage is a solid-fluid biphasic material covering the bony ends of articulating joints. Hydration of articular cartilage is important to joint lubrication and weight-wearing. The aims of this study are to measure the altered hydration behaviour of the proteoglycan-degraded articular cartilage using high-frequency ultrasound and then to investigate the effect of proteoglycan (PG) degradation on cartilage hydration. METHODS Twelve porcine patellae with smooth cartilage surface were prepared and evenly divided into two groups: normal group without any enzyme treatment and trypsin group treated with 0.25% trypsin solution for 4 h to digest PG in the tissue. After 40-minute exposure to air at room temperature, the specimens were immerged into the physiological saline solution. The dehydration induced hydration behaviour of the specimen was monitored by the high-frequency (25 MHz) ultrasound pulser/receiver (P/R) system. Dynamic strain and equilibrium strain were extracted to quantitatively evaluate the hydration behaviour of the dehydrated cartilage tissues. RESULTS The hydration progress of the dehydrated cartilage tissue was observed in M-mode ultrasound image indicating that the hydration behaviour of the PG-degraded specimens decreased. The percentage value of the equilibrium strain (1.84 ± 0.21%) of the PG-degraded cartilage significantly (p < 0.01) decreased in comparison with healthy cartilage (3.46 ± 0.49%). The histological sections demonstrated that almost PG content in the entire cartilage layer was digested by trypsin. CONCLUSION Using high-frequency ultrasound, this study found a reduction in the hydration behaviour of the PG-degraded cartilage. The results indicated that the degradation of PG decreased the hydration capability of the dehydrated tissue. This study may provide useful information for further study on changes in the biomechanical property of articular cartilage in osteoarthritis.
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Affiliation(s)
- Qing Wang
- Institute of Medical Information, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
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Wang Q, Zheng YP. Ultrasound assessment of boundary effect on osmosis-induced shrinkage and swelling of articular cartilage in vitro. Connect Tissue Res 2013; 54:153-8. [PMID: 23216088 DOI: 10.3109/03008207.2012.756872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study aims to use ultrasound to investigate the boundary effect of the cut edge on the osmosis-induced shrinkage and swelling of articular cartilage while the distance from the scanning site to the edge decreases with the reduction of specimen size. Sixteen cartilage-bone specimens (of diameter 6.35 mm) were prepared from normal bovine patellae. The cartilage width was gradually reduced to 4.35 mm and to 2.35 mm. Shrinkage and swelling were induced by changing the concentration of the saline solution and monitored using nominal 50 MHz focused ultrasound. The parameters including shrinkage and swelling peak strains (ϵ(P1) and ϵ(P2), respectively), shrinkage and swelling equilibrium strains (ϵ(E1) and ϵ(E2), respectively), and shrinkage and swelling slopes (k(1) and k(2), respectively) were extracted. The ϵ(P1), ϵ(E1), ϵ(E2), k(1), and k(2) of the 2.35 mm specimens were significantly different (p < 0.05) from those of the 6.35 mm specimens. For the 4.35 mm specimens, ϵ(E1) and ϵ(P1) were, respectively, significantly different (p < 0.05) from ϵ(E1) of the 6.35 mm specimens and ϵ(P1) of the 2.35 mm specimens. The percentage of coefficient of variation (18.5% for shrinkage and 16.3% for swelling) of the 2.35 mm specimens was much higher than that (<8.5%) of the 6.35 mm specimens. The relative root mean square difference (rRMSD%, 12.0% for shrinkage and 10.6% for swelling) of the 2.35 mm specimens was also much higher than that (<5.5%) of the 6.35 mm specimens. The results indicated that the boundary effect of the cut edge on the osmosis-induced shrinkage and swelling of articular cartilage increases with the reduction of specimen size.
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Affiliation(s)
- Qing Wang
- Institute of Medical Information, School of Biomedical Engineering, Southern Medical University, Guangzhou, China.
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