237 results on '"Li, Chaolun"'
Search Results
202. Transcriptomic responses and evolutionary insights of deep-sea and shallow-water mussels under high hydrostatic pressure condition.
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Zhong, Zhaoshan, Guo, Yang, Zhou, Li, Chen, Hao, Lian, Chao, Wang, Hao, Zhang, Huan, Cao, Lei, Sun, Yan, Wang, Minxiao, and Li, Chaolun
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- 2024
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203. Integrated transcriptomic and metabolomic approaches reveal molecular response and potential biomarkers of the deep-sea mussel Gigantidas platifrons to copper exposure.
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He, Yameng, Zhou, Li, Wang, Minxiao, Zhong, Zhaoshan, Chen, Hao, Lian, Chao, Zhang, Huan, Wang, Hao, Cao, Lei, and Li, Chaolun
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COPPER , *METABOLOMICS , *OCEAN mining , *MUSSELS , *ANAEROBIC metabolism - Abstract
Metal pollution caused by deep-sea mining activities has potential detrimental effects on deep-sea ecosystems. However, our knowledge of how deep-sea organisms respond to this pollution is limited, given the challenges of remoteness and technology. To address this, we conducted a toxicity experiment by using deep-sea mussel Gigantidas platifrons as model animals and exposing them to different copper (Cu) concentrations (50 and 500 μg/L) for 7 days. Transcriptomics and LC-MS-based metabolomics methods were employed to characterize the profiles of transcription and metabolism in deep-sea mussels exposed to Cu. Transcriptomic results suggested that Cu toxicity significantly affected the immune response, apoptosis, and signaling processes in G. platifrons. Metabolomic results demonstrated that Cu exposure disrupted its carbohydrate metabolism, anaerobic metabolism and amino acid metabolism. By integrating both sets of results, transcriptomic and metabolomic, we find that Cu exposure significantly disrupts the metabolic pathway of protein digestion and absorption in G. platifrons. Furthermore, several key genes (e.g., heat shock protein 70 and baculoviral IAP repeat-containing protein 2/3) and metabolites (e.g., alanine and succinate) were identified as potential molecular biomarkers for deep-sea mussel's responses to Cu toxicity. This study contributes novel insight for assessing the potential effects of deep-sea mining activities on deep-sea organisms. [Display omitted] • Cu affected the immune response, apoptosis and signaling processes in G. mussels. • Cu disrupted the carbohydrate, anaerobic and amino acid metabolism in G. mussels. • Cu interfered with the pathway of protein digestion and absorption in G. mussels. • Potential biomarkers associated with Cu toxicity were identified in G. mussels. [ABSTRACT FROM AUTHOR]
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- 2024
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204. Toxicology assessment of deep-sea mining impacts on Gigantidas platifrons: A comparative in situ and laboratory metal exposure study.
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Zhou, Li, Lian, Chao, He, Yameng, Chi, Xupeng, Chen, Hao, Zhong, Zhaoshan, Wang, Minxiao, Cao, Lei, Wang, Hao, Zhang, Huan, and Li, Chaolun
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- 2024
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205. Geochemical origin of methane in hydrothermal fluid and its implication for the subseafloor hydrothermal circulation at the Middle Okinawa Trough.
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Cao, Lei, Lian, Chao, Zhang, Xin, Zhang, Huan, Wang, Hao, Zhou, Li, Chen, Hao, Wang, Minxiao, Li, Lianfu, Luan, Zhendong, and Li, Chaolun
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Hydrothermal systems are ubiquitous in various tectonic settings and are important in transferring internal mass and energy sources from the crust and mantle to the oceans. However, the biogeochemical processes involved in subseafloor hydrothermal circulation are not fully understood. This study investigated the compositional and isotopic properties of the high-temperature fluids collected from three hydrothermal vents of the Izena Hole in the middle Okinawa Trough in 2016 with Remotely Operated Vehicle (ROV) named Faxian. The results confirm that the latest geochemical parameters of the high-temperature hydrothermal fluids are similar to the previously reported parameters and indicate the origin of methane in the hydrothermal fluid. The nearly identical geochemistry of the three fluids indicate that they likely shared a common fluid reservoir. The endmember hydrothermal fluid contained isotopically 13C-moderate methane (− 30.4‰ to − 32.1‰), suggesting the predominance of thermogenic methane over biogenic methane incorporation in the hydrothermal fluids. The differences in the concentrations of ethane (C1/C2+ = 11,600, 5600, 970 for Faxian-1, Faxian-2, and Faxian-3, respectively) and molecular hydrogen (0.11, 0.67, and 2.4 mM for Faxian-1, Faxian-2, and Faxian-3, respectively) suggest significantly different thermal fluid-sediment interaction during the discharge stage between two hydrothermal fields. The relatively low contents of biogenic methane in all the fluids here indicated limited biogenic methane incorporation during the recharge stage due to the horizontal restriction of hydrothermal fluid circulation. The geochemical origins of methane in hydrothermal fluid and their relevance to hydrothermal fluid circulation revealed herein shed light on the different degrees of sediment influence in various geological/geographical settings in the Okinawa Trough. [ABSTRACT FROM AUTHOR]
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- 2021
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206. Toward a global reference database of COI barcodes for marine zooplankton.
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Bucklin, Ann, Peijnenburg, Katja T. C. A., Kosobokova, Ksenia N., O'Brien, Todd D., Blanco-Bercial, Leocadio, Cornils, Astrid, Falkenhaug, Tone, Hopcroft, Russell R., Hosia, Aino, Laakmann, Silke, Li, Chaolun, Martell, Luis, Questel, Jennifer M., Wall-Palmer, Deborah, Wang, Minxiao, Wiebe, Peter H., and Weydmann-Zwolicka, Agata
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MARINE zooplankton , *CLIMATE change detection , *MARINE species diversity , *BAR codes , *GENETIC barcoding , *DNA sequencing , *MARINE toxins - Abstract
Characterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change. [ABSTRACT FROM AUTHOR]
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- 2021
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207. Inductive effect of bioactive substances on strobilation of jellyfish Aurelia coerulea.
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Wang, Nan, Wang, Minxiao, Wang, Yantao, and Li, Chaolun
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AURELIA , *BIOACTIVE compounds , *TERRITORIAL waters , *OCEAN temperature , *TRETINOIN - Abstract
The moon jellyfish Aurelia spp. is a worldwide distributed scyphozoan species that seasonally blooms in coastal waters. Although the strobilation is directly responsible for the scale of jellyfish bloom, the underlying mechanisms remain largely unknown. We exposed Aurelia coerulea polyps to 18 bioactive substances to test their ability to induce strobilation at the natural typically non-strobilation temperature of 21°C. Results revealed that A. coerulea polyps responded in four types. Type I—no change for estradiol, folic acid, iodine, retinoic acid, serotonin hydrochloride, and vitamin A. We suggested that 5-aza-2-deoxycytidine and N-acetyl-L-glutamic acid could not induce strobilation, since the percent of strobilated polyps in these two substances treatments was 3.3% and 1%, respectively. Type II—polyp body elongation for 3,5-diiodo-L-tyrosine, indole-3-acetic acid, L-dopamine, and noradrenaline treatments. Type III—transverse constrictions for L-thyroxine, progesterone, and melatonin treatments. Finally, Type IV—complete strobilation for 5-methoxy-2-methylindole, acetylcholine chloride, and indomethacin treatments, where the pre-strobilation periods were 2, 4, and 2 days, and the mean numbers of ephyrae released per strobila were 4.7, 5.7, and 5.7, respectively. The results reveal that indole derivatives, which contained methoxy or methyl pharmacophore, were the common strobilation inducer in the genus Aurelia. Iodinated organic compounds, catecholamine, acetylcholine chloride, and retinoic acid are species-specific strobilation inducer. Therefore, A. coerulea strobilation is regulated by neuronal and endocrine processes. Our findings provide clues in understanding the mechanism of strobilation and contribute to developing specific strobilation antagonists in controlling moon jellyfish blooms. [ABSTRACT FROM AUTHOR]
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- 2020
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208. Assessment of Metastatic and Reactive Sentinel Lymph Nodes with B7-H3-Targeted Ultrasound Molecular Imaging: A Longitudinal Study in Mouse Models.
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Zheng, Fengyang, Li, Pan, Bachawal, Sunitha V., Wang, Huaijun, Li, Chaolun, Yuan, Wei, Huang, Beijian, and Paulmurugan, Ramasamy
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SENTINEL lymph nodes , *ULTRASONIC imaging , *DIAGNOSTIC imaging , *LONGITUDINAL method , *INTRAVENOUS injections , *MICE - Abstract
Purpose: To explore the potential of B7-H3-targeted ultrasound molecular imaging (USMI) for longitudinal assessment and differentiation of metastatic and reactive sentinel lymph nodes (SLNs) in mouse models.Procedures: Metastatic and reactive SLN models were established by injection of 4T1 breast cancer cells and complete Freund's adjuvant (CFA) respectively to the 4th mammary fat pad of female BALB/c mice. At day 21, 28, and 35 after inoculation, USMI was performed following intravenous injection of B7-H3-targeted microbubbles (MBB7-H3) or IgG-control microbubbles (MBcontrol). All SLNs were histopathologically examined after the last imaging session.Results: A total of 20 SLNs from tumor-bearing mice (T-SLNs) and five SLNs from CFA-injected mice (C-SLNs) were examined by USMI. Nine T-SLNs were histopathologically positive for metastasis (MT-SLNs). From day 21 to 35, T-SLNs showed a rising trend in MBB7-H3 signal with a steep increase in MT-SLNs at day 35 (213.5 ± 80.8 a.u.) as compared to day 28 (87.6 ± 77.2 a.u., P = 0.002) and day 21 (55.7 ± 35.5 a.u., P < 0.001). At day 35, MT-SLNs had significantly higher MBB7-H3 signal than non-metastatic T-SLNs (NMT-SLNs) (101.9 ± 48.0 a.u., P = 0.001) and C-SLNs (38.5 ± 34.0 a.u., P = 0.001); MBB7-H3 signal was significantly higher than MBcontrol in MT-SLNs (P = 0.001), but not in NMT-SLNs or C-SLNs (both P > 0.05). A significant correlation was detected between MBB7-H3 signal and volume fraction of metastasis in MT-SLNs (r = 0.76, P = 0.017).Conclusions: B7-H3-targeted USMI allows differentiation of MT-SLNs from NMT-SLNs and C-SLNs in mouse models and has great potential to evaluate tumor burden in SLNs of breast cancer. [ABSTRACT FROM AUTHOR]- Published
- 2020
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209. Identification and characterization of endosymbiosis-related immune genes in deep-sea mussels Gigantidas platifrons.
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Li, Mengna, Chen, Hao, Wang, Minxiao, Zhong, Zhaoshan, Zhou, Li, and Li, Chaolun
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MUSSELS , *HYDROTHERMAL vents , *ENDOSYMBIOSIS , *NATURAL immunity , *IMMUNE recognition , *MATRIX metalloproteinases , *TOLL-like receptors - Abstract
Deep-sea mussels of the subfamily Bathymodiolinae are common and numerically dominant species widely distributed in cold seeps and hydrothermal vents. During long-time evolution, deep-sea mussels have evolved to be well adapted to the local environment of cold seeps and hydrothermal vents by various ways, especially by establishing endosymbiosis with chemotrophic bacteria. However, biological processes underlying the establishment and maintenance of symbiosis between host mussels and symbionts are largely unclear. In the present study, Gigantidas platifrons genes possibly involved in the symbiosis with methane oxidation symbionts were identified and characterized by Lipopolysaccharide (LPS) pull-down and in situ hybridization. Five immune related proteins including Toll-like receptor 2 (TLR2), integrin, vacuolar sorting protein (VSP), matrix metalloproteinase 1 (MMP1), and leucine-rich repeat (LRR-1) were identified by LPS pull-down assay. These five proteins were all conserved in either molecular sequences or functional domains and known to be key molecules in host immune recognition, phagocytosis, and lysosome-mediated digestion. Furthermore, in situ hybridization of LRR-1, TLR2 and VSP genes was conducted to investigate their expression patterns in gill tissues of G. platifrons. Consequently, LRR-1, TLR2, and VSP genes were found expressed exclusively in the bacteriocytes of G. platifrons. Therefore, it was suggested that TLR2, integrin, VSP, MMP1, and LRR-1 might be crucial molecules in the symbiosis between G. platifrons and methane oxidation bacteria by participating in symbiosis-related immune processes. [ABSTRACT FROM AUTHOR]
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- 2020
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210. Experimental clearance rates of Aurelia coerulea ephyrae and medusae, and the predation impact on zooplankton in Jiaozhou Bay.
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Wang, Pengpeng, Zhang, Fang, Sun, Song, Wang, Weicheng, Wan, Aiyong, and Li, Chaolun
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JELLYFISHES , *AURELIA , *SCYPHOZOA , *MARINE species diversity , *ZOOPLANKTON - Abstract
The population explosion of jellyfish Aurelia coerulea occurred in Jiaozhou Bay, China in 2009. The potential predation impact of A. coerulea on zooplankton was investigated. Population clearance potential and residence time (t1/2) for copepods were calculated from laboratory clearance rates and measurements of jellyfish size and abundance from May to August 2009 in Jiaozhou Bay. Clearance rates varied widely with prey organisms, but they were not significantly different among various prey concentrations. Medusae captured rotifers, fish larvae and hydromedusae more efficiently than fish eggs, copepods and chaetognaths. Ephyrae captured rotifers and hydromedusae more efficiently than fish larvae and copepods. Clearance rate linearly increased with the cross sectional area of A. coerulea (size from 0.3 to 7.1 cm). Water temperature also had a marked effect on clearance rate and this was related to the increased beat frequency as water temperature increased. In early May 2009, A. coerulea potentially cleared the volume of water in the Bay less than 0.001 times a day, but this value was estimated to be more than 0.3 times a day in July. The t1/2 for copepods was less than 6 d in June and July. Abundances of copepods, hydromedusae and chaetognaths were extremely low in 2009 compared to 2008 and 2010 (jellyfish non-bloom years). Large predation pressure by the A. coerulea population occurred to control zooplankton communities in Jiaozhou Bay. A. coerulea, when present at a high population level, can be a keystone species in Jiaozhou Bay and control the trophic structure here. [ABSTRACT FROM AUTHOR]
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- 2020
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211. Contrast enhanced imaging features of liver metastasis from a meningeal solitary fibrous tumor: a case report.
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Beilei Lu, Qing Lu, Beijian Huang, Haixia Yuan, Chaolun Li, Lu, Beilei, Lu, Qing, Huang, Beijian, Yuan, Haixia, and Li, Chaolun
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LIVER metastasis , *ULTRASONIC imaging , *MAGNETIC resonance imaging , *DIAGNOSTIC imaging , *DIAGNOSIS , *THERAPEUTICS - Abstract
A solitary fibrous tumor seldom originates from the meninges, and the accuracy of imaging modalities in the diagnosis of meningeal SFT metastasisis is perlexing. Contrast enhanced imaging modalities, such as contrast enhanced ultrasound and contrast enhanced magnetic resonance imaging are valuable in the differential diagnosis of hepatic neoplasms. This case report demonstrated the contrast enhanced ultrasound and enhanced magnetic resonance imaging features of one case of liver metastasis from a menigeal solitary fibrous tumor. [ABSTRACT FROM AUTHOR]
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- 2018
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212. Effects of duration at low temperature on asexual reproduction in polyps of the scyphozoan Nemopilema nomurai (Scyphozoa: Rhizostomeae).
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Feng, Song, Zhang, Fang, Sun, Song, Wang, Shiwei, and Li, Chaolun
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JELLYFISHES , *SCYPHOZOA , *EFFECT of temperature on Cnidaria , *ASEXUAL reproduction , *BENTHIC ecology , *REPRODUCTION - Abstract
In recent decades, massive outbreaks of the giant jellyfish, Nemopilema nomurai have been appearing frequently in coastal seas of China. In the life cycle of N. nomurai, asexual reproduction by its benthic polyps may largely determine the jellyfish population size, and it was thought that asexual reproduction leading to medusae might be affected by differences in the duration at low winter temperature on different parts of the coast. To test this hypothesis, polyps were first stored at low temperature for two different durations, 5°C for either 40 or 117 days. They were then maintained at seven temperatures, (maintained at 5°C, and separately elevated to 10, 13, 16, 19, 22, 27°C) reached by raising the temperature 1°C every 2 days from 5°C, as well as a control temperature: 5°C. Polyps were fed with three frequencies (once per 5 days, once per 10 days, and unfed, prey concentration, 0.1 mgC l, being supplied once). The percentages of polyps strobilating, strobilation duration, ephyra and podocyst production were recorded. The results showed that longer duration at low temperature accelerated strobila formation at warmer temperature, as well as significantly enhancing podocyst production, but not for the strobilation percentage or ephyra production. Temperature had a marked influence on strobilation percentage, as well as on ephyra and podocyst production. The optimum temperature for strobilation by N. nomurai polyps ranged from 10 to 13°C. The maximum numbers of ephyrae appeared after polyps had been stored at longer low temperature then warmed to 10°C and fed once per 5 days, while the maximum production of podocysts occurred in polyps warmed to 27°C and fed once per 5 days. We conclude that longer duration at low temperature in winter, a continuous 10-13°C period in spring, and increasing food supply all accelerate the strobila formation, increase jellyfish production and are tend to increase blooms of N. nomurai medusae. [ABSTRACT FROM AUTHOR]
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- 2015
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213. Vertical occurrence of copepod carcasses in the Cosmonaut Sea during austral summer.
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Yang, Guang, Mou, Wenxiu, Chen, Xiaoli, Xu, Zhiqiang, Wang, Yanqing, and Li, Chaolun
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ASTRONAUTS , *MESOPELAGIC zone , *COLLOIDAL carbon , *FOOD chains , *COPEPODA , *SUMMER , *OCEAN - Abstract
Zooplankton carcasses and their contribution to carbon export are increasingly garnering attention in food web studies of polar oceans. We investigated the occurrence of carcasses of dominant copepod species at four depths (100–200 m, 200–500 m, 500–1000 m, 1000–1500 m) and their potential contribution to particulate organic carbon (POC) concentrations in the Cosmonaut Sea, Antarctica, during summer, 2019/2020. The abundance of small copepods (< 2 mm), either live or dead individuals, was 1-3 orders of magnitude higher than the four dominant large copepod species Calanoides acutus , Calanus propinquus , Metridia gerlachei and Rhincalanus gigas at each depth. Most carcasses were observed at the surface (100–200 m), while the proportions of dead individuals increased with depth, from 22% in the 100–200 m layer to 70% of the 500–1500 m layer. The total number of passive sinkers (carcasses and moults) was dominated by carcasses of small copepods in each depth layer, while the carbon biomass of passive sinkers was dominated by carcasses of large copepods. Both abundance and carbon biomass of passive sinkers decreased with depth. The average contribution of passive sinkers to the POC concentration decreased from 0.27% in the 100–200 m depth stratum to 0.10% in the 500–1500 m layer. This study provides the first report of occurrence and contribution of carcasses from the surface to the mesopelagic layer of the Southern Ocean. This information can improve understanding of the role zooplankton play in downward carbon flux within the ocean's twilight zone. [ABSTRACT FROM AUTHOR]
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- 2022
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214. Minimal Fat Renal Angiomyolipoma: The Initial Study with Contrast-Enhanced Ultrasonography
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Lu, Qing, Wang, Wenping, Huang, Beijian, Li, Chaolun, and Li, Cong
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RENAL cell carcinoma , *CONTRAST-enhanced ultrasound , *KIDNEY tumors , *RETROSPECTIVE studies , *TUMOR classification , *FAT , *KIDNEY blood-vessels , *DIAGNOSIS - Abstract
Abstract: We visualized minimal fat renal angiomyolipomas (AMLs) by contrast-enhanced ultrasonography (CEUS). Conventional ultrasound and CEUS images were retrospectively analyzed for solid minimal fat renal AML cases (n = 18) and solid renal cell carcinoma (RCC) cases (n = 105). We compared size, echogenicity and color flow signals with conventional ultrasound, and enhancement patterns with CEUS, in AMLs vs. RCCs. No significant differences in echogenicity and color flow signal existed between AMLs and RCCs using conventional ultrasound. With CEUS, slow centripetal enhancement in the cortical phase (83.3% of AMLs vs. 1.9% of RCCs) and homogeneous peak enhancement (100.0% of AMLs vs. 34.3% of RCCs) were valuable traits for differentiating these tumor types. These two CEUS-determined traits, combined, were differentiating criteria for minimal fat renal AMLs and RCCs; positive and negative predictive values were 100.0% and 97.2%, respectively. Slow centripetal enhancement in the cortical phase and homogeneous enhancement at peak are main features of CEUS-confirmed solid minimal fat renal AML. [Copyright &y& Elsevier]
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- 2012
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215. Biomass and estimated production properties of size-fractionated zooplankton in the Yellow Sea, China
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Huo, Yuanzi, Sun, Song, Zhang, Fang, Wang, Minxiao, Li, Chaolun, and Yang, Bo
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ZOOPLANKTON , *BIOMASS estimation , *BIOMASS production , *FRACTIONS , *ANIMAL classification , *FOOD chains , *PARAMETER estimation - Abstract
Abstract: The size-fractionated zooplankton biomass, taxonomic composition, and production calculated by formulas basing on Ikeda–Motoda''s physiological methods were studied on the basis of samples taken from six cruises in the Yellow Sea. Zooplankton was size-fractionated using sieves into ~2mm, 1–2mm, 0.5–1mm, 0.25–0.5mm and 0.16–0.25mm groups. The results showed that the average zooplankton biomass was 84.03mg DM m−3 in May, followed in order by September, June, March, August and December with 42.34, 38.36, 32.37, 27.17 and 21.83mg DM m−3, respectively. The contribution of ~2mm, 1–2mm, 0.5–1mm, 0.25–0.5mm and 0.16–0.25mm groups to the total biomass was in the range of 15.2–27.4%, 13.2–29.4%, 14.7–18.2%, 15.8–22.6% and 16.3–34.2%, respectively, during the investigating period. The biomass of all size groups was all highest in May, and except that the biomass of 0.16–0.25mm group was lowest in August, the biomass of other size groups was lowest in December. The dominant zooplankton species (or taxa) in each group were similar between six cruises. The estimated zooplankton production was highest in May with 1.97mg C m−3 d−1, and was lowest in December with 0.51mg C m−3 d−1, and was in the range of 0.67–1.44mg C m−3 d−1 in other investigating months. The estimated annual zooplankton production was 0.37g C m−3 y−1. The two smallest groups aggregately comprised 59–84% of the net-zooplankton production in the Yellow Sea. The geographical distribution of size-fractionated zooplankton biomass and production was significantly affected by the complex physical features of the Yellow Sea. When the Yellow Sea Cold Bottom Water appeared from June to September, the biomass and production of zooplankton larger than 1mm were higher inside the cold water mass area than outside it, while the zooplankton smaller than 1mm showed contrary results. The higher biomass and production of all zooplankton groups occurred in the southern part of the study area in December due to the intrusion of the Yellow Sea Warm Current. And in March, the higher zooplankton biomass and production, especially for small size zooplankton, occurred at the coastal waters resulting from complex physical properties. Results of the present paper showed the biomass and production properties of size-fractionated zooplankton, which is very important for “parameterization” of food web structure models of the Yellow Sea. [Copyright &y& Elsevier]
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- 2012
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216. Comparative transcriptomic analysis illuminates the host-symbiont interactions in the deep-sea mussel Bathymodiolus platifrons.
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Wang, Hao, Zhang, Huan, Wang, Minxiao, Chen, Hao, Lian, Chao, and Li, Chaolun
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SYMBIOSIS , *HYDROTHERMAL vents , *MUSSELS , *TOLL-like receptors , *COMPARATIVE studies , *ECOLOGICAL niche , *DEEP-sea animals , *ORGANIZATIONAL change , *UBIQUITINATION - Abstract
Bathymodiolus platifrons adapted the chemosynthetic ecosystems, both cold seeps and hydrothermal vents, by harbouring gill symbionts. To survive these extreme and volatile ecological niches, the host mussel must be able to strictly regulate the symbionts in response to the environmental fluctuations. However, despite the research efforts, the molecular mechanisms governing host-symbiont interaction in deep-sea mussels are still largely unknown. Here, using the model deep-sea mussel Bathymodiolus plantiforns , we profiled the transcriptomic dynamic of the mussel gill during the loss and re-contact with symbionts with RNA-seq technology. The analysis of DEGs between untreated and symbiont loss samples revealed that metabolic and cellular organizational changes in the gill were associated with increased ribosomal activities, ubiquitin-proteasome systems, and autophagy. Meanwhile, the DE immune genes suggest that the host recognizes and interacts with endosymbionts through the pattern recognizing receptors, especially the Toll-like receptors. In addition, the DEGs between symbionts treated and environmental bacteria treated samples shed light on the mechanism of symbiont recognition. The symbionts treatment not only partially reversed the transcriptomic changes caused by symbiont-loss, but also suppressed host immune system which might facilitate the symbionts' entrance and survival in the host bacteriocytes. All together, these results suggest that the host-symbiont system in B. platifrons is tightly regulated but also with plasticity to fit environmental fluctuations. • First transcriptomic dynamic analysis of the deep-sea mussel Bathymodiolus platifrons gill during the loss and re-contact with symbionts. • The differentially expressed genes analysis revealed metabolic and cellular organizational changes associated with symbiont-loss. • Identified pattern recognizing receptors that might be involved in host-symbiont interaction. • Symbionts treatment could partially reverse the transcriptomic changes caused by symbiont-loss and suppress expression of host immune genes. • Identified genes that might be involved in symbiont recognition. [ABSTRACT FROM AUTHOR]
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- 2019
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217. A novel ultrasound-based score for assessing carotid artery activity in Takayasu's arteritis.
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Ma L, Sun Y, Liu Y, Huang H, Chen R, Li C, Han H, and Jiang L
- Abstract
Objectives: The role of ultrasonography for evaluating vessel wall inflammation in Takayasu's arteritis (TAK) is well-recognised; however, an effective approach for the quantitative assessment of disease activity remains lacking. This study aimed to develop a novel ultrasound-based score for determining TAK activity., Methods: TAK patients with carotid artery involvement were prospectively followed-up for 6 months. Our proposed ultrasonographic activity score (ULTRAS, range between 0-12) consisted of wall thickness (TS, range between 0-8) and semi-quantitative echogenicity scores (ES, range between 0-4). The diagnostic performance of ULTRAS for disease activity was evaluated in terms of area under the receiver operating characteristic curve (AUC). Internal validation was subsequently performed., Results: The patients were divided into training and validation groups (n=136 and 30. respectively). In the training group, 83 (61.0%) had active disease. At an optimal cut-off of 7, ULTRAS showed good diagnostic accuracy for active TAK (AUC, 0.88; 95% CI, 82-94). Improved diagnostic performance was achieved when combined with ESR (AUC, 0.91; 95% CI, 86-96) or CRP (AUC, 0.90; 95%CI, 86-95). In the verification group, the AUCs were 0.88, 0.95, and 0.92 for ULTRAS, ESR plus ULTRAS, and CRP plus ULTRAS, respectively. At post-treatment follow-up, the TS, ES, and ULTRAS paralleled the patients' disease remission and symptom recovery. At 3-month follow-up, an improvement in wall thickness of ≥0.3 mm correlated with symptom recovery in 50% of the patients., Conclusions: Our proposed ultrasound-based score carries the potential in the detection of active disease among TAK patients.
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- 2024
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218. Insights into prokaryotic communities and their potential functions in biogeochemical cycles in cold seep.
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Quan Q, Liu J, Li C, Ke Z, and Tan Y
- Abstract
Microorganisms are significant drivers of organic matter mineralization and are essential in marine biogeochemical cycles. However, the variations and influencing factors in prokaryotic communities from cold-seep sediments to the water column and the specific role of these microorganisms in biogeochemical cycles in the water column above cold seep remain unclear. Here, we investigated prokaryotic communities and their roles in nitrogen/sulfur cycling processes and conducted in situ dissolved organic matter (DOM) enrichment experiments to explore the effects of diverse sources of DOM on prokaryotic communities. Field investigations showed that the prokaryotic communities in the near-bottom water were more similar to those in the deep layer of the euphotic zone (44.60%) and at a depth of 400 m (50.89%) than those in the sediment (18.00%). DOM enrichment experiments revealed that adding dissolved organic nitrogen (DON) and phosphorus DOP caused a notable increase in the relative abundances of Rhodobacterales and Vibrionales, respectively. A remarkable increase was observed in the relative abundance of Alteromonadales and Pseudomonadales after the addition of dissolved organic sulfur (DOS). The metagenomic results revealed that Proteobacteria served as the keystone taxa in mediating the biogeochemical cycles of nitrogen, phosphorus, and sulfur in the Haima cold seep. This study highlights the responses of prokaryotes to DOM with different components and the microbially driven elemental cycles in cold seeps, providing a foundational reference for further studies on material energy metabolism and the coupled cycling of essential elements mediated by deep-sea microorganisms., Importance: Deep-sea cold seeps are among the most productive ecosystems, sustaining unique fauna and microbial communities through the release of methane and other hydrocarbons. Our study revealed that the influence of seepage fluid on the prokaryotic community in the water column is surprisingly limited, which challenges conventional views regarding the impact of seepage fluids. In addition, we identified that different DOM compositions play a crucial role in shaping the prokaryotic community composition, providing new insights into the factors driving microbial diversity in cold seeps. Furthermore, the study highlighted Proteobacteria as key and multifaceted drivers of biogeochemical cycles in cold seeps, emphasizing their significant contribution to complex interactions and processes. These findings offer a fresh perspective on the dynamics of cold-seep environments and their microbial communities, advancing our understanding of the biogeochemical functions in deep-sea environments.
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- 2024
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219. Transcriptomic responses to shifts in light and nitrogen in two congeneric diatom species.
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Ma X, Qin Z, Johnson KB, Sweat LH, Dai S, Li G, and Li C
- Abstract
Light and nitrogen availability are basic requirements for photosynthesis. Changing in light intensity and nitrogen concentration may require adaptive physiological and life process changes in phytoplankton cells. Our previous study demonstrated that two Thalassiosira species exhibited, respectively, distinctive physiological responses to light and nitrogen stresses. Transcriptomic analyses were employed to investigate the mechanisms behind the different physiological responses observed in two diatom species of the genus Thalassiosira . The results indicate that the congeneric species are different in their cellular responses to the same shifting light and nitrogen conditions. When conditions changed to high light with low nitrate (HLLN), the large-celled T. punctigera was photodamaged. Thus, the photosynthesis pathway and carbon fixation related genes were significantly down-regulated. In contrast, the small-celled T. pseudonana sacrificed cellular processes, especially amino acid metabolisms, to overcome the photodamage. When changing to high light with high nitrate (HLHN) conditions, the additional nitrogen appeared to compensate for the photodamage in the large-celled T. punctigera , with the tricarboxylic acid cycle (TCA cycle) and carbon fixation significantly boosted. Consequently, the growth rate of T. punctigera increased, which suggest that the larger-celled species is adapted for forming post-storm algal blooms. The impact of high light stress on the small-celled T. pseudonana was not mitigated by elevated nitrate levels, and photodamage persisted., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Ma, Qin, Johnson, Sweat, Dai, Li and Li.)
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- 2024
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220. Deciphering deep-sea chemosynthetic symbiosis by single-nucleus RNA-sequencing.
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Wang H, He K, Zhang H, Zhang Q, Cao L, Li J, Zhong Z, Chen H, Zhou L, Lian C, Wang M, Chen K, Qian PY, and Li C
- Subjects
- Animals, Gills microbiology, Sequence Analysis, RNA methods, Bivalvia microbiology, Bivalvia genetics, Mytilidae genetics, Mytilidae microbiology, Bacteria genetics, Symbiosis
- Abstract
Bathymodioline mussels dominate deep-sea methane seep and hydrothermal vent habitats and obtain nutrients and energy primarily through chemosynthetic endosymbiotic bacteria in the bacteriocytes of their gill. However, the molecular mechanisms that orchestrate mussel host-symbiont interactions remain unclear. Here, we constructed a comprehensive cell atlas of the gill in the mussel Gigantidas platifrons from the South China Sea methane seeps (1100 m depth) using single-nucleus RNA-sequencing (snRNA-seq) and whole-mount in situ hybridisation. We identified 13 types of cells, including three previously unknown ones, and uncovered unknown tissue heterogeneity. Every cell type has a designated function in supporting the gill's structure and function, creating an optimal environment for chemosynthesis, and effectively acquiring nutrients from the endosymbiotic bacteria. Analysis of snRNA-seq of in situ transplanted mussels clearly showed the shifts in cell state in response to environmental oscillations. Our findings provide insight into the principles of host-symbiont interaction and the bivalves' environmental adaption mechanisms., Competing Interests: HW, KH, HZ, QZ, LC, JL, ZZ, HC, LZ, CL, MW, KC, PQ, CL No competing interests declared, (© 2023, Wang, He, Zhang et al.)
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- 2024
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221. Single-cell RNA-seq reveals distinct metabolic "microniches" and close host-symbiont interactions in deep-sea chemosynthetic tubeworm.
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Wang H, Xiao H, Feng B, Lan Y, Fung CW, Zhang H, Yan G, Lian C, Zhong Z, Li J, Wang M, Wu AR, Li C, and Qian PY
- Subjects
- Animals, Gammaproteobacteria metabolism, Gammaproteobacteria genetics, Single-Cell Gene Expression Analysis, Symbiosis, Single-Cell Analysis methods, Polychaeta metabolism, Polychaeta microbiology, Polychaeta genetics, RNA-Seq methods
- Abstract
Vestimentiferan tubeworms that thrive in deep-sea chemosynthetic ecosystems rely on a single species of sulfide-oxidizing gammaproteobacterial endosymbionts housed in a specialized symbiotic organ called trophosome as their primary carbon source. While this simple symbiosis is remarkably productive, the host-symbiont molecular interactions remain unelucidated. Here, we applied an approach for deep-sea in situ single-cell fixation in a cold-seep tubeworm, Paraescarpia echinospica . Single-cell RNA sequencing analysis and further molecular characterizations of both the trophosome and endosymbiont indicate that the tubeworm maintains two distinct metabolic "microniches" in the trophosome by controlling the availability of chemosynthetic gases and metabolites, resulting in oxygenated and hypoxic conditions. The endosymbionts in the oxygenated niche actively conduct autotrophic carbon fixation and are digested for nutrients, while those in the hypoxic niche conduct anaerobic denitrification, which helps the host remove ammonia waste. Our study provides insights into the molecular interactions between animals and their symbiotic microbes.
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- 2024
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222. Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses.
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Zhang Y, Chen H, Lian C, Cao L, Guo Y, Wang M, Zhong Z, Li M, Zhang H, and Li C
- Subjects
- Animals, Gene Expression Profiling, Transcriptome, Virome genetics, Bacteria genetics, Bacteria classification, Symbiosis genetics, Metagenome, Metagenomics methods, Bacteriophages genetics, Bacteriophages isolation & purification, Gills microbiology, Gills virology, Gills metabolism, Bivalvia microbiology, Bivalvia virology, Bivalvia genetics
- Abstract
Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea., (© 2024. The Author(s).)
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- 2024
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223. The diversification and potential function of microbiome in sediment-water interface of methane seeps in South China Sea.
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Fu L, Liu Y, Wang M, Lian C, Cao L, Wang W, Sun Y, Wang N, and Li C
- Abstract
The sediment-water interfaces of cold seeps play important roles in nutrient transportation between seafloor and deep-water column. Microorganisms are the key actors of biogeochemical processes in this interface. However, the knowledge of the microbiome in this interface are limited. Here we studied the microbial diversity and potential metabolic functions by 16S rRNA gene amplicon sequencing at sediment-water interface of two active cold seeps in the northern slope of South China Sea, Lingshui and Site F cold seeps. The microbial diversity and potential functions in the two cold seeps are obviously different. The microbial diversity of Lingshui interface areas, is found to be relatively low. Microbes associated with methane consumption are enriched, possibly due to the large and continuous eruptions of methane fluids. Methane consumption is mainly mediated by aerobic oxidation and denitrifying anaerobic methane oxidation (DAMO). The microbial diversity in Site F is higher than Lingshui. Fluids from seepage of Site F are mitigated by methanotrophic bacteria at the cyclical oxic-hypoxic fluctuating interface where intense redox cycling of carbon, sulfur, and nitrogen compounds occurs. The primary modes of microbial methane consumption are aerobic methane oxidation, along with DAMO, sulfate-dependent anaerobic methane oxidation (SAMO). To sum up, anaerobic oxidation of methane (AOM) may be underestimated in cold seep interface microenvironments. Our findings highlight the significance of AOM and interdependence between microorganisms and their environments in the interface microenvironments, providing insights into the biogeochemical processes that govern these unique ecological systems., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Fu, Liu, Wang, Lian, Cao, Wang, Sun, Wang and Li.)
- Published
- 2024
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224. Stem-cell based soft tissue substitutes: Engineering of crosslinked polylysine-hyaluronic acid microspheres ladened with gingival mesenchymal stem cells for collagen tissue regeneration and angiogenesis.
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Ni J, Li M, Li C, Zhong Z, Xi H, and Wu Y
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- Hyaluronic Acid pharmacology, Microspheres, Endothelial Cells, Angiogenesis, Cell Differentiation, Gingiva metabolism, Stem Cells, Collagen metabolism, Tissue Engineering, Polylysine metabolism, Polylysine pharmacology, Mesenchymal Stem Cells
- Abstract
Background: The aim of this study was to construct crosslinked polylysine-hyaluronic acid microspheres (pl-HAM) ladened with gingival mesenchymal stem cells (GMSCs) and explore its biologic behavior in soft tissue regeneration., Methods: The effects of the crosslinked pl-HAM on the biocompatibility and the recruitment of L-929 cells and GMSCs were detected in vitro. Moreover, the regeneration of subcutaneous collagen tissue, angiogenesis and the endogenous stem cells recruitment were investigated in vivo. We also detected the cell developing capability of pl-HAMs., Results: The crosslinked pl-HAMs appeared to be completely spherical-shaped particles and had good biocompatibility. L-929 cells and GMSCs grew around the pl-HAMs and increased gradually. Cell migration experiments showed that pl-HAMs combined with GMSCs could promote the migration of vascular endothelial cells significantly. Meanwhile, the green fluorescent protein-GMSCs in the pl-HAM group still remain in the soft tissue regeneration area 2 weeks after surgery. The results of in vivo studies showed that denser collagen deposition and more angiogenesis-related indicator CD31 expression in the pl-HAMs+ GMSCs + GeL group compared with the pl-HAMs + GeL group. Immunofluorescence showed that CD44, CD90, CD73 co-staining positive cells surrounded the microspheres in both pl-HAMs + GeL group and pl-HAM + GMSCs + GeL group., Conclusions: The crosslinked pl-HAM ladened with GMSCs system could provide a suitable microenvironment for collagen tissue regeneration, angiogenesis and endogenous stem cells recruitment, which may be an alternative to autogenous soft tissue grafts for minimally invasive treatments for periodontal soft tissue defects in the future., (© 2023 American Academy of Periodontology.)
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- 2023
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225. Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont.
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Sun Y, Wang M, Cao L, Seim I, Zhou L, Chen J, Wang H, Zhong Z, Chen H, Fu L, Li M, Li C, and Sun S
- Subjects
- Animals, Phylogeny, Bacteria, Ecosystem, Methane metabolism, Symbiosis, Mytilidae genetics, Mytilidae microbiology, Hydrothermal Vents
- Abstract
Background: The within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intraspecies variation has recently been detected in many deep-sea endosymbionts, their ecological role in environmental adaptation, their genome evolution pattern under heterogeneous geochemical environments, and the underlying molecular forces remain unclear., Results: Here, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep. Endosymbiont genomes were assembled using a pipeline that distinguishes within-species variation and revealed highly heterogeneous compositions in mussels from different habitats. Phylogenetic analysis separated the assemblies into three distinct environment-linked clades. Their functional differentiation follows a mosaic evolutionary pattern. Core genes, essential for central metabolic function and symbiosis, were conserved across all clades. Clade-specific genes associated with heavy metal resistance, pH homeostasis, and nitrate utilization exhibited signals of accelerated evolution. Notably, transposable elements and plasmids contributed to the genetic reshuffling of the symbiont genomes and likely accelerated adaptive evolution through pseudogenization and the introduction of new genes., Conclusions: The current study uncovers the environment-driven evolution of deep-sea symbionts mediated by mobile genetic elements. Its findings highlight a potentially common and critical role of within-species diversity in animal-microbiome symbioses. Video Abstract., (© 2023. The Author(s).)
- Published
- 2023
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226. Monthly dietary shifts in the jellyfish Nemopilema nomurai in Liaodong Bay, China.
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Wang J, Wang Y, Tao Z, and Li C
- Subjects
- Animals, Bays, Oceans and Seas, Diet, Cnidaria, Scyphozoa
- Abstract
Nemopilema nomurai is a frequently bloomed species in the China seas. Their feeding organ has an ontogenetic change when they grow up, but whether their diet changes along with it is unclear. A 5-month study on N. nomurai was conducted in Liaodong Bay, China to clarify the dietary shift and feeding effect of N. nomurai. Fatty acid biomarkers revealed the proportion of carnivorous food in the diet of N. nomurai decreased when their bell diameter increased. The isotope data revealed a similar story with δ
15 N dropping which indicated a decreased trophic level. The diet composition was dominated (74 %) by zooplankton >200 μm in May and then decreased to <32 % in July. In contrast, the proportion of particulate organic matter increased from <35 % to 68 %. This study revealed a monthly shift in the diet of N. nomurai and contributed to knowledge of trophic interactions between plankton and N. nomurai., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)- Published
- 2023
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227. Variation in epibiotic bacteria on two squat lobster species of Munidopsidae.
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Feng W, Wang M, Dong D, Hui M, Zhang H, Fu L, Zhong Z, Xu Z, and Li C
- Abstract
The relationships between epibiotic bacteria on deep-sea hosts and host lifestyle factors are of particular interest in the field of deep-sea chemoautotrophic environmental adaptations. The squat lobsters Shinkaia crosnieri and Munidopsis verrilli are both dominant species in cold-seep ecosystems, and they have different distributions and feeding behaviors. These species may have evolved to have distinct epibiotic microbiota. Here, we compared the epibiotic bacterial communities on the M. verrilli carapace (MV
carapace ), S. crosnieri carapace (SCcarapace ), and S. crosnieri ventral plumose setae (SCsetae ). The epibiotic bacteria on SCsetae were dense and diverse and had a multi-layer configuration, while those on MVcarapace and SCcarapace were sparse and had a monolayer configuration. Chemoautotrophic bacteria had the highest relative abundance in all epibiotic bacterial communities. The relative abundance of amplicon sequence variant 3 (ASV3; unknown species in order Thiotrichales ), which is associated with sulfide oxidation, was significantly higher in SCsetae than MVcarapace and SCcarapace . Thiotrichales species seemed to be specifically enriched on SCsetae , potentially due to the synthetic substrate supply, adhesion preference, and host behaviors. We hypothesize that the S. crosnieri episymbionts use chemical fluxes near cold seeps more efficiently, thereby supporting the host's nutrient strategies, resulting in a different distribution of the two species of squat lobster., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Feng, Wang, Dong, Hui, Zhang, Fu, Zhong, Xu and Li.)- Published
- 2023
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228. Effect of femtosecond laser ablate ultra-fine microgrooves on surface properties of dental zirconia materials.
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Li Q, Li C, and Wang Y
- Subjects
- Animals, Dental Materials, Lasers, Materials Testing, Mice, Microscopy, Electron, Scanning, Surface Properties, Osteogenesis, Zirconium chemistry
- Abstract
Objectives: Zirconia is an important dental implant material, yet it surfaces milling method is still under investigation. To explore the feasibility of laser etching in processing fine micro grooves on the surface of zirconia and to observe fine micro groove structure' influence on mouse embryonic osteoblasts, the survey was conducted., Methods: 31 zirconia discs were made and polished to mirror surface. Then, they were divided into 3 groups: the mirror group, the femtosecond laser ablated microgroove group and the air blasted + acid etched group. Then, the surface properties of zirconia discs were analyzed by Scanning Electron Microscope/Energy Dispersive Spectrometer (SEM/EDS), X-Ray Diffraction (XRD), Atomic Force Microscope (AFM), water contact angle test and micro-Vickers hardness test. The biocompatibility of each machined zirconia was tested by cell proliferation test and SEM analyze of cell morphology. Then, the effect of these surface treatment to MC-3T3-E1's osteogenic differentiation was evaluated by Q-PCR test., Results: SEM image showed that the femtosecond laser is a reliable method for forming regular-arranged microgrooves with pitch width of around 5 μm. EDS and XRD indicated that there were stable and purified tetragonal crystal system on the laser-roughened surface. AFM suggested that laser machining generated rougher surface (Ra) (271.7 ± 67.2 nm) than other groups. Furthermore, the contact angle showed laser ablated grooves induced anisotropic wetting. The micro-Vickers hardness test ascertained that laser-ablation strengthened zirconia surface. In vitro experiment showed that MC-3T3-E1 grown along the long axis of microgrooves on the first day. Besides, Real time PCR implied that osteogenesis-related gene expression OPN and ALP was much higher than the rest groups., Significance: Femtosecond laser is able to machine zirconia with ultra-fine microgrooves (around 2.5 μm). These structures promoted MC-3T3-E1 cell to line along the microstructure and differentiate into osteogenic cells. Thus, femtosecond laser might be a potential processing options for zirconia micro-texturing., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Yongyue Wang reports a relationship with Chengdu Science and Technology Bureau that includes: funding grants. Yongyue Wang has patent no pending to no. We look forward to the publication of this revised manuscript in Journal of the Mechanical Behavior of Biomedical Materials., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2022
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229. Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps.
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Xu Z, Wang M, Zhang H, He W, Cao L, Lian C, Zhong Z, Wang H, Fu L, Zhang X, and Li C
- Subjects
- Animals, Ecosystem, In Situ Hybridization, Fluorescence, Bacteria metabolism, Methane metabolism, Sulfur metabolism, Anomura metabolism, Decapoda metabolism
- Abstract
Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales , Nitrosococcales , Flavobacteriales , and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales . Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation. IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri , a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.
- Published
- 2022
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230. Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea.
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Zhang H, Wang M, Wang H, Chen H, Cao L, Zhong Z, Lian C, Zhou L, and Li C
- Subjects
- Archaea genetics, Bacteria genetics, Geologic Sediments microbiology, Phylogeny, RNA, Ribosomal, 16S genetics, Genome, Microbial, Metagenome, Microbiota
- Abstract
Cold seep microbial communities are fascinating ecosystems on Earth which provide unique models for understanding the living strategies in deep-sea distinct environments. In this study, 23 metagenomes were generated from samples collected in the Site-F cold seep field in South China Sea, including the sea water closely above the invertebrate communities, the cold seep fluids, the fluids under the invertebrate communities and the sediment column around the seep vent. By binning tools, we retrieved a total of 768 metagenome assembled genome (MAGs) that were estimated to be >60% complete. Of the MAGs, 61 were estimated to be >90% complete, while an additional 105 were >80% complete. Phylogenomic analysis revealed 597 bacterial and 171 archaeal MAGs, of which nearly all were distantly related to known cultivated isolates. In the 768 MAGs, the abundant Bacteria in phylum level included Proteobacteria, Desulfobacterota, Bacteroidota, Patescibacteria and Chloroflexota, while the abundant Archaea included Asgardarchaeota, Thermoplasmatota, and Thermoproteota. These results provide a dataset available for further interrogation of deep-sea microbial ecology., (© 2022. The Author(s).)
- Published
- 2022
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231. The complete mitochondrial genome of Asteroschema tubiferum (Ophiuroidea: Euryalida: Asteroschematidae).
- Author
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Zhong Z, Wang M, Wang H, and Li C
- Abstract
We describe the first mitochondrial genome of a brittle star Asteroschema tubiferum Matsumoto 1911 in family Asteroschematidae. The mitogenome was sequenced and assembled using next-generation sequencing technology, and were 16,361 bp in size with 37 genes containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. The phylogenetic tree was constructed based on 13 protein-coding mitochondrial genes of A. tubiferum and 26 species in the phylum Echinodermata by RAxML, which showed that it was mostly related to the species in Family Gorgonocephalidae. These results could provide a novel insight to the phylogeny of Ophiuroidea., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)
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- 2022
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232. Aequorivita iocasae sp. nov., a halophilic bacterium isolated from sediment collected at a cold seep field in the South China Sea.
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Zhang H, Wang H, Cao L, Chen H, Zhong Z, Wang M, Lian C, Liu R, Zhou L, and Li C
- Subjects
- Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae isolation & purification, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 chemistry, Flavobacteriaceae classification, Geologic Sediments microbiology, Phylogeny, Seawater microbiology
- Abstract
A moderately halophilic bacterium, designated strain KX20305
T , was isolated from sediment collected from a cold seep field in the South China Sea. Cells of strain KX20305T were Gram-stain-negative, rod-shaped, non-motile, facultatively anaerobic, oxidase- and catalase-positive, and grew optimally at 25-30 °C, pH 6.0-8.0 and with 3-6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KX20305T grouped with members of the genus Aequorivita , including Aequorivita aquimaris D-24T (98.3 % sequence similarity), Aequorivita vladivostokensis KMM 3516T (98.1 %) and Aequorivita echinoideorum CC-CZW007T (97.5 %). Genome sequencing of strain KX20305T revealed a genome size of 3.35 Mb and a DNA G+C content of 38.71 mol%. Genomic average nucleotide identity (orthoANI) values of strain KX20305T with A. aquimaris D-24T , A. vladivostokensis KMM 3516T and A. echinoideorum JCM 30378T were 83.8, 81.7 and 75.4 %, respectively, while in silico DNA-DNA hybridization (GGDC) values for strain KX20305T with these strains were 27.2, 25.0 and 19.6 %, respectively. The major fatty acids of strain KX20305T were iso-C15 : 0 , iso-C17 : 0 3-OH and 10-methyl C16 : 0 /iso-C17 : 1 ω 9 c . The predominant respiratory quinone was menaquinone-6 (MK-6). The polar lipids mainly comprised phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. Based on comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX20305T represents a novel species of the genus Aequorivita , for which the name Aequorivita iocasae sp. nov. is proposed. The type strain is KX20305T (=KCTC 82699T =MCCC 1K06238T =JCM 34635T ).- Published
- 2022
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233. Molecular analyses of the gill symbiosis of the bathymodiolin mussel Gigantidas platifrons .
- Author
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Wang H, Zhang H, Zhong Z, Sun Y, Wang M, Chen H, Zhou L, Cao L, Lian C, and Li C
- Abstract
Although the deep-sea bathymodiolin mussels have been intensively studied as a model of animal-bacteria symbiosis, it remains challenging to assess the host-symbiont interactions due to the complexity of the symbiotic tissue-the gill. Using cold-seep mussel Gigantidas platifrons as a model, we isolated the symbiont harboring bacteriocytes and profiled the transcriptomes of the three major parts of the symbiosis-the gill, the bacteriocyte, and the symbiont. This breakdown of the complex symbiotic tissue allowed us to characterize the host-symbiont interactions further. Our data showed that the gill's non-symbiotic parts play crucial roles in maintaining and protecting the symbiosis; the bacteriocytes supply the symbiont with metabolites, control symbiont population, and shelter the symbiont from phage infection; the symbiont dedicates to the methane oxidation and energy production. This study demonstrates that the bathymodiolin symbiosis interacts at the tissue, cellular, and molecular level, maintaining high efficiency and harmonic chemosynthetic micro niche., Competing Interests: The authors declare no competing interests., (© 2020 The Authors.)
- Published
- 2020
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234. [Computer-assisted quantitative analysis of contrast-enhanced ultrasonography in Takayasu arteritis carotid artery lesions].
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Hu Y, Zhang Q, and Li C
- Abstract
Takayasu arteritis (TA) is a chronic nonspecific inflammation that commonly occurs in the aorta and its main branches. Most patients with TA are lack of clinical manifestations, leading to misdiagnosis. When the TA is correctly diagnosed, the patients may already have stenosis or occlusion in the involved arteries, resulting in arterial ischemia and hypoxia symptoms, and in severe cases it will be life-threatening. Contrast-enhanced ultrasonography (CEUS) is an emerging method for assessing TA, but the assessment relies heavily on experiences of radiologists performing manual and qualitative analyses, so the diagnostic results are often not accurate. To overcome this limitation, this paper presents a computer-assisted quantitative analysis of TA carotid artery lesions based on CEUS. First, the TA lesion was outlined on the carotid wall, and one homogeneous rectangle and one polygon were selected as two reference regions in the carotid lumen. The temporal and spatial features of the lesion region and the reference regions were then calculated. Furthermore, the difference and ratio of the features between the lesion and the reference regions were computed as new features (to eliminate interference factors). Finally, the correlation was analyzed between the CEUS features and inflammation biomarkers consisting of erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP). The data in this paper were collected from 34 TA patients in Zhongshan Hospital undergoing CEUS examination with a total of thirty-seven carotid lesions, where two patients were with two lesions before and after treatment and one patient was with left and right bilateral lesions. Among these patients, 13 were untreated primary patients with a total of 14 lesions, where one patient was with bilateral lesions. The results showed that for all patients, the neovascularization area ratio in the 1/3 inner region of a lesion (ARi
1/3 ) achieved a correlation coefficient ( r ) of 0.56 ( P =0.001) with CRP, and for the primary patients, the neovascularization area ratio in the 1/2 inner region of a lesion (ARi1/2 ) had an r -value of 0.76 ( P =0.001) with CRP. This study indicates that the proposed computer-assisted method can objectively and semi-automatically extract quantitative features from CEUS images, so as to reduce the effect on diagnosis due to subjective experiences of the radiologists, and thus it is expected to be used for clinical diagnosis and severity evaluation of TA carotid lesions.- Published
- 2017
- Full Text
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235. Molecular identification of methane monooxygenase and quantitative analysis of methanotrophic endosymbionts under laboratory maintenance in Bathymodiolus platifrons from the South China Sea.
- Author
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Sun Y, Wang M, Li L, Zhou L, Wang X, Zheng P, Yu H, Li C, and Sun S
- Abstract
Deep-sea mussels of the genus Bathymodiolus are numerically dominant macrofauna in many cold seep and hydrothermal vent ecosystems worldwide, and they depend on organic carbon produced by symbionts present in the epithelial cells of the gills. Although Bathymodiolus platifrons represents typical methanotrophic endosymbiosis, our understanding of molecular mechanisms of methane oxidization and carbon fixation is still in its infancy. Moreover, the laboratory maintenance of B. platifrons and the symbiont abundance dynamics during maintenance has not been reported. In the present study, we report the first systematic identification and phylogenetic analysis of three subunits of methane monooxygenase (pmoA, pmoB, and pmoC) obtained from the endosymbiotic bacteria found in B. platifrons . The coding sequences (CDS) of the three genes in the B. platifrons endosymbiont were 750, 1,245, and 753 bp, encoding 249, 414, and 250 amino acids, respectively. Sequence alignment and phylogenetic analysis revealed that the symbiont of B. platifrons belongs to the type I methanotrophs. In order to clarify the impact of environmental methane on symbiont abundance, a 34-day laboratory maintenance experiment was conducted in which B. platifrons individuals were acclimatized to methane-present and methane-absent environments. Symbiont abundance was evaluated by calculating the relative DNA content of the methane monooxygenase gene using quantitative real-time PCR. We found that symbiont quantity immediately decreased from its initial level, then continued to gradually decline during maintenance. At 24 and 34 days of maintenance, symbiont abundance in the methane-absent environment had significantly decreased compared to that in the methane-present environment, indicating that the maintenance of symbionts relies on a continuous supply of methane. Our electron microscopy results validated the qPCR analysis. This study enriches our knowledge of the molecular basis and the dynamic changes of the methanotrophic endosymbiosis in B. platifrons , and provides a feasible model biosystem for further investigation of methane oxidization, the carbon fixation process, and environmental adaptations of deep-sea mussels., Competing Interests: The authors declare there are no competing interests.
- Published
- 2017
- Full Text
- View/download PDF
236. Quantification of carotid plaque elasticity and intraplaque neovascularization using contrast-enhanced ultrasound and image registration-based elastography.
- Author
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Zhang Q, Li C, Zhou M, Liao Y, Huang C, Shi J, Wang Y, and Wang W
- Abstract
It is valuable for evaluation of carotid plaque vulnerability to investigate the relation between intraplaque neovascularization (IPN) and plaque elasticity. The contrast-enhanced ultrasound (CEUS) has been used in IPN measurement, but it cannot assess plaque elasticity. The aim of this study was to develop an ultrasound elastography technique based on registration of CEUS sequential images and to use this technique for direct comparison between IPN and plaque elasticity. We employed a nonrigid image registration method using the free-form deformation model to register a pair of clinical CEUS images at systole and diastole. The 2D displacement field of the plaque was estimated and then utilized to calculate the axial and lateral strain distributions within the plaque, from which quantitative strain parameters were obtained. The IPN was measured semiquantitatively with visual assessment and quantitatively with the time-intensity curve analysis and the analysis of contrast agent spatial distributions. Histopathology with CD34 staining for quantification of microvessel density (MVD) was performed on plaques excised by carotid endarterectomy. Simulation experiments showed that the mean absolute error and the root mean squared error of the displacement estimation were 0.325±0.180 pixel (7.2%±3.8%) and 0.556±0.284 pixel (12.3%±6.1%), respectively, demonstrating high accuracy of the elastography technique. Thirty-eight plaques in 29 patients met the inclusion criteria for the elastography and image analysis, where ten plaques underwent endarterectomy. The 95th percentile (A95) and standard deviation (Asd) of the axial strains exhibited significant differences between the low and high grades of IPN visually assessed (p<0.01). A95 (R=0.579; p<0.001) and Asd (R=0.609; p<0.001) were correlated with the enhanced intensity of plaque, and also correlated with the MVD (R=0.793 and 0.817, respectively; p<0.01), suggesting that plaque became softer and more elastically heterogeneous as IPN increased. These findings provide direct and quantitative evidence for the associations between plaque strains and IPN and might be helpful for evaluation of carotid plaque vulnerability and for plaque risk stratification., (Copyright © 2015 Elsevier B.V. All rights reserved.)
- Published
- 2015
- Full Text
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237. Quantification of carotid plaque neovascularization using contrast-enhanced ultrasound with histopathologic validation.
- Author
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Li C, He W, Guo D, Chen L, Jin X, Wang W, Huang B, and Wang W
- Subjects
- Aged, Aged, 80 and over, Carotid Arteries surgery, Endarterectomy, Carotid methods, Female, Humans, Male, Middle Aged, Plaque, Atherosclerotic surgery, Reproducibility of Results, Retrospective Studies, Ultrasonography, Carotid Arteries diagnostic imaging, Contrast Media, Image Enhancement methods, Neovascularization, Pathologic diagnostic imaging, Phospholipids, Plaque, Atherosclerotic diagnostic imaging, Sulfur Hexafluoride
- Abstract
We sought to evaluate contrast-enhanced ultrasound (CEUS) imaging for the quantification of carotid plaque neovascularization. Seventeen patients underwent carotid endarterectomy after standard ultrasound and CEUS. Semiquantitative and quantitative analyses of contrast enhancement within the plaque were performed using a visual interpretation scale and quantitative analysis software, respectively. Enhancement intensity (dB) was measured at the plaque (EI(plaque)). Each specimen was stained with CD34 and CD68 to assess for microvessels and macrophages, respectively. Semiquantitative CEUS analyses were correlated with neovascularization at histology (r = 0.70, p = 0.002). Quantitative analysis was also correlated with neovascularization at histology (EI(plaque)r = 0.81, p < 0.001). EI(plaque) (r = 0.64, p = 0.01) was correlated with the degree of enhancement as assessed visually. Semiquantitative and quantitative analyses were not correlated with macrophage infiltration at the plaque. Contrast enhancement in the carotid plaque was correlated with neovascularity at the histopathologic exam. Furthermore, semiquantitative and quantitative measurements were highly correlated with each other, suggesting that either can be used to detect intraplaque neovascularization., (Copyright © 2014 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
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