| 1. |
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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Yang, Bao, et al.
(author)
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Long-term decrease in Asian monsoon rainfall and abrupt climate change events over the past 6,700 years
- 2021
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In: Proceedings of the National Academy of Sciences of the United States of America. - Washington : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:30
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Journal article (peer-reviewed)abstract
- Asian summer monsoon (ASM) variability and its long-term ecological and societal impacts extending back to Neolithic times are poorly understood due to a lack of high-resolution climate proxy data. Here, we present a precisely dated and well-calibrated treering stable isotope chronology from the Tibetan Plateau with 1- to 5-y resolution that reflects high- to low-frequency ASM variability from 4680 BCE to 2011 CE. Superimposed on a persistent drying trend since the mid-Holocene, a rapid decrease in moisture availability between similar to 2000 and similar to 1500 BCE caused a dry hydroclimatic regime from similar to 1675 to similar to 1185 BCE, with mean precipitation estimated at 42 +/- 4% and 5 +/- 2% lower than during themid-Holocene and the instrumental period, respectively. This second-millennium-BCE megadrought marks the mid-to late Holocene transition, during which regional forests declined and enhanced aeolian activity affected northern Chinese ecosystems. We argue that this abrupt aridification starting similar to 2000 BCE contributed to the shift of Neolithic cultures in northern China and likely triggered human migration and societal transformation.
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| 5. |
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| 6. |
- Lei, Yang, et al.
(author)
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Cellular responses to T-2 toxin and/or deoxynivalenol that induce cartilage damage are not specific to chondrocytes
- 2017
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In: Scientific Reports. - London : Nature Publishing Group. - 2045-2322. ; 7:1, s. 2231-
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Journal article (peer-reviewed)abstract
- The relationship between T-2 toxin and deoxynivalenol (DON) and the risk of Kashin-Beck disease is still controversial since it is poorly known about their selectivity in cartilage damage. We aimed to compare the cytotoxicity of T-2 toxin and DON on cell lines representative of cell types encountered in vivo, including human chondrocytes (C28/I2), human hepatic epithelial cells (L-02) and human tubular epithelial cells (HK-2). In addition, we determined the distribution of T-2 toxin and DON in Sprague-Dawley (SD) rats after a single dose exposure. T-2 toxin or DON decreased proliferation in a time- and concentration-dependent manner and their combination showed a similar antagonistic effect in C28/I2, L-02 and HK-2 cells. Moreover, we observed cell cycle arrest and apoptosis, associated with increased oxidative stress and decline in mitochondrial membrane potential induced by T-2 toxin and/or DON. In vivo study showed that T-2 toxin and DON did not accumulate preferentially in the knee joint compared to liver and kidney after an acute exposure in SD rats. These results suggest that T-2 toxin and/or DON inhibit proliferation and induce apoptosis through a possible mechanism involving reactive oxygen species-mediated mitochondrial pathway that is not specific for chondrocytes in vitro or joint tissues in vivo.
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| 7. |
- Liu, Huan, et al.
(author)
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The first human induced pluripotent stem cell line of Kashin–Beck disease reveals involvement of heparan sulfate proteoglycan biosynthesis and PPAR pathway
- 2022
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In: The FEBS Journal. - : John Wiley & Sons. - 1742-464X .- 1742-4658. ; 289:1, s. 279-293
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Journal article (peer-reviewed)abstract
- OBJECTIVE: Kashin-Beck disease (KBD) is an endemic osteochondropathy. Due to a lack of suitable animal or cellular disease models, the research progress on KBD has been limited. Our goal was to establish the first disease-specific human induced pluripotent stem cells (hiPSCs) cellular disease model of KBD, and to explore its etiology and pathogenesis exploiting transcriptome sequencing.METHODS: HiPSCs were reprogrammed from dermal fibroblasts of two KBD and one healthy control donors via integration-free vectors. Subsequently, hiPSCs were differentiated into chondrocytes through three-week culture. Gene expression profiles in KBD, normal primary chondrocytes and hiPSC-derived chondrocytes were defined by RNA sequencing. A Venn diagram was constructed to show the number of shared differentially expressed genes (DEGs) between KBD and normal. Gene oncology and Kyoto Encyclopedia of Genes and Genomes annotations were performed, and six DEGs were further validated in other individuals by real-time quantitative reverse transcription PCR (RT-qPCR).RESULTS: KBD cellular disease models were successfully established by generation of hiPSC lines. Seventeen consistent and significant DEGs present in all compared groups (KBD and normal) were identified. RT-qPCR validation gave consistent results with the sequencing data. Glycosaminoglycan biosynthesis-heparan sulfate/heparin, PPAR signaling pathway and cell adhesion molecules (CAMs) pathways were identified to be significantly altered in KBD.CONCLUSION: Differentiated chondrocytes deriving from KBD-origin hiPSCs provide the first cellular disease model for etiological studies of KBD. This study also provides new sights into the pathogenesis and etiology of KBD and is likely to inform the development of targeted therapeutics for its treatment.
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| 8. |
- Wang, Sen, et al.
(author)
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The importance of Se-related genes in the chondrocyte of Kashin-Beck disease revealed by whole genomic microarray and network analysis
- 2019
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In: Biological Trace Element Research. - : Springer. - 0163-4984 .- 1559-0720. ; 187:2, s. 367-375
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Journal article (peer-reviewed)abstract
- Kashin-Beck disease (KBD) is an endemic, chronic, and degenerative osteoarthropathy. Selenium (Se) deficiency plays important role in the pathogenesis of KBD. We aimed to screen Se-related gene from chondrocytes of patients with KBD. Whole-genome oligonucleotide microarrays were used to detect differentially expressed genes. qRT-PCR was used to confirm the microarray results. Comparative Toxicogenomics Database (CTD) was used to screen Se-related genes from differentially expressed genes. Gene Ontology (GO) classifications and network analysis of Se-related genes were constituted by STRING online system. Three hundred ninety-nine differentially expressed genes were obtained from microarray. Among them, 54 Se-related genes were identified by CTD. The qRT-PCR validation showed that four genes expressed similarly with the ones in the microarray transcriptional profiles. The Se-related genes were categorized into 6 cellular components, 8 molecular functions, 44 biological processes, 10 pathways, and 1 network by STRING. The Se-related gene insulin-like growth factor binding protein 2 (IGFBP2), insulin-like growth factor binding protein 3 (IGFBP3), interleukin 6 (IL6), BCL2, apoptosis regulator (BCL2), and BCL2-associated X, apoptosis regulator (BAX), which involved in many molecular functions, biological processes, and apoptosis pathway may play important roles in the pathogenesis of KBD.
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| 9. |
- Zhang, Xiangwei, et al.
(author)
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The prognostic value of tumor length to resectable esophageal squamous cell carcinoma : a retrospective study
- 2017
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In: PeerJ. - : PeerJ. - 2167-8359. ; 5
-
Journal article (peer-reviewed)abstract
- Background: The current TNM classification system does not consider tumor length for patients with esophageal carcinoma (EC). This study explored the effect of tumor length, in addition to tumor depth and lymph node involvement, on survival in patients with esophageal squamous cell carcinoma (ESCC).Methods: A total of 498 ESCC patients who underwent surgical resection as the primary treatment were selected in the retrospective study. Pathological details were collected, which included tumor type, TNM stage, differentiation. Other collected information were: the types of esophageal resection, ABO blood group, family history and demographic and lifestyle factors. A time-dependent receiver operating characteristic (ROC) curve and a regression tree for survival were used to identify the cut-off point of tumor length, which was 3 cm. Univariate and multivariate Cox proportional hazard regression models were used to identify the prognostic factors to ESCC.Results & Discussion: The 1-, 3-, 5-year overall survival rates were found to be 82.5%, 55.6%, and 35.1%, respectively. Patients who had larger tumor length (>3 cm) had a higher risk for death than the rest patients. From the univariate Cox proportional hazards regression model, the overall survival rate was significantly influenced by the depth of the tumor and lymph node involvement (either as dummy or continuous variables), Sex, and tumor length. Using these four variables in the multivariate Cox proportional hazard regression model, we found that the overall survival was significantly influenced by all variables except Sex. Therefore, in addition to the depth of the tumor and lymph node involvement (as either dummy or continuous variables), the tumor length is also an independent prognostic factor for ESCC. The overall survival rate was higher in a group with smaller tumor length (≤3 cm) than those patients with larger tumor length (>3 cm), no matter what the tumor stage was.Conclusion: The tumor length was found to be an important prognostic factor for ESCC patients without receiving neoadjuvant therapy. The modification of EC staging system may consider tumor length to better predict ESCC survival and identify higher risk patients for postoperative therapy.
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| 10. |
- Ding, Huaiyi, et al.
(author)
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Maximizing Integrated Optical and Electrical Properties of a Single ZnO Nanowire through Native Interfacial Doping
- 2014
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In: Advanced Materials. - : Wiley. - 0935-9648 .- 1521-4095. ; 26:19, s. 3035-3041
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Journal article (peer-reviewed)abstract
- A native interfacial doping layer introduced in core-shell type ZnO nanowires by a simple vapor phase re-growth procedure endows the produced nanowires with both excellent electrical and optical performances compared to conventional homogeneous ZnO nanowires. The unique Zn-rich interfacial structure in the core-shell nanowires plays a crucial role in the outstanding performances.
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| 11. |
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| 12. |
- Liu, Linan, et al.
(author)
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Silicon Effects on Biomass Carbon and Phytolith-Occluded Carbon in Grasslands Under High-Salinity Conditions
- 2020
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In: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 11, s. 1-13
-
Journal article (peer-reviewed)abstract
- Changes in climate and land use are causing grasslands to suffer increasingly fromabiotic stresses, including soil salinization. Silicon (Si) amendment has been frequentlyproposed to improve plant resistance to multiple biotic and abiotic stresses and increaseecosystem productivity while controlling the biogeochemical carbon (C) cycle. However,the effects of Si on plant C distribution and accumulation in salt-suffering grasslandsare still unclear. In this study, we investigated how salt ions affected major elementalcomposition in plants and whether Si enhanced biomass C accumulation in grasslandspecies in situ. In samples from the margins of salt lakes, our results showed that thediffering distance away from the shore resulted in distinctive phytocoenosis, includinghalophytes and moderately salt-tolerant grasses, which are closely related to changingsoil properties. Different salinity (NaC/KC, ranging from 0.02 to 11.8) in plants causednegative effects on plant C content that decreased from 53.9 to 29.2% with theincrease in salinity. Plant Si storage [0.02–2.29 g Si m?2 dry weight (dw)] and plantSi content (0.53 to 2.58%) were positively correlated with bioavailable Si in soils(ranging from 94.4 to 192 mg kg?1). Although C contents in plants and phytoliths werenegatively correlated with plant Si content, biomass C accumulation (1.90–83.5 g Cm?2 dw) increased due to the increase of Si storage in plants. Plant phytolith-occludedcarbon (PhytOC) increased from 0.07 to 0.28h of dry mass with the increase of Sicontent in moderately salt-tolerant grasses. This study demonstrates the potential ofSi in mediating plant salinity and C assimilation, providing a reference for potentialmanipulation of long-term C sequestration via PhytOC production and biomass Caccumulation in Si-accumulator dominated grasslands.
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| 13. |
- Ning, Yujie, et al.
(author)
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Comparative analysis of the gut microbiota composition between knee osteoarthritis and Kashin-Beck disease in Northwest China
- 2022
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In: Arthritis Research & Therapy. - : BioMed Central. - 1478-6362. ; 24:1
-
Journal article (peer-reviewed)abstract
- Background: Osteoarthritis (OA) and Kashin-Beck disease (KBD) both are two severe osteochondral disorders. In this study, we aimed to compare the gut microbiota structure between OA and KBD patients.Methods: Fecal samples collected from OA and KBD patients were used to characterize the gut microbiota using 16S rDNA gene sequencing. To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria between OA and KBD groups, metagenomic sequencing of fecal samples from OA and KBD subjects was performed.Results: The OA group was characterized by elevated Epsilonbacteraeota and Firmicutes levels. A total of 52 genera were identified to be significantly differentially abundant between the two groups. The genera Raoultella, Citrobacter, Flavonifractor, g__Lachnospiraceae_UCG-004, and Burkholderia-Caballeronia-Paraburkholderia were more abundant in the OA group. The KBD group was characterized by higher Prevotella_9, Lactobacillus, Coprococcus_2, Senegalimassilia, and Holdemanella. The metagenomic sequencing showed that the Subdoligranulum_sp._APC924/74, Streptococcus_parasanguinis, and Streptococcus_salivarius were significantly increased in abundance in the OA group compared to those in the KBD group, and the species Prevotella_copri, Prevotella_sp._CAG:386, and Prevotella_stercorea were significantly decreased in abundance in the OA group compared to those in the KBD group by using metagenomic sequencing.Conclusion: Our study provides a comprehensive landscape of the gut microbiota between OA and KBD patients and provides clues for better understanding the mechanisms underlying the pathogenesis of OA and KBD.
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| 14. |
- Ning, Yujie, et al.
(author)
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Genetic Variants and Protein Alterations of Selenium- and T-2 Toxin-Responsive Genes Are Associated With Chondrocytic Damage in Endemic Osteoarthropathy
- 2022
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In: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 12
-
Journal article (peer-reviewed)abstract
- The mechanism of environmental factors in Kashin-Beck disease (KBD) remains unknown. We aimed to identify single nucleotide polymorphisms (SNPs) and protein alterations of selenium- and T-2 toxin-responsive genes to provide new evidence of chondrocytic damage in KBD. This study sampled the cubital venous blood of 258 subjects including 129 sex-matched KBD patients and 129 healthy controls for SNP detection. We applied an additive model, a dominant model, and a recessive model to identify significant SNPs. We then used the Comparative Toxicogenomics Database (CTD) to select selenium- and T-2 toxin-responsive genes with the candidate SNP loci. Finally, immunohistochemistry was applied to verify the protein expression of candidate genes in knee cartilage obtained from 15 subjects including 5 KBD, 5 osteoarthritis (OA), and 5 healthy controls. Forty-nine SNPs were genotyped in the current study. The C allele of rs6494629 was less frequent in KBD than in the controls (OR = 0.63, p = 0.011). Based on the CTD database, PPARG, ADAM12, IL6, SMAD3, and TIMP2 were identified to interact with selenium, sodium selenite, and T-2 toxin. KBD was found to be significantly associated with rs12629751 of PPARG (additive model: OR = 0.46, p = 0.012; dominant model: OR = 0.45, p = 0.049; recessive model: OR = 0.18, p = 0.018), rs1871054 of ADAM12 (dominant model: OR = 2.19, p = 0.022), rs1800796 of IL6 (dominant model: OR = 0.30, p = 0.003), rs6494629 of SMAD3 (additive model: OR = 0.65, p = 0.019; dominant model: OR = 0.52, p = 0.012), and rs4789936 of TIMP2 (recessive model: OR = 5.90, p = 0.024). Immunohistochemistry verified significantly upregulated PPARG, ADAM12, SMAD3, and TIMP2 in KBD compared with OA and normal controls (p < 0.05). Genetic polymorphisms of PPARG, ADAM12, SMAD3, and TIMP2 may contribute to the risk of KBD. These genes could promote the pathogenesis of KBD by disturbing ECM homeostasis.
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| 15. |
- Wang, Faming, et al.
(author)
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Coastal blue carbon in China as a nature-based solution toward carbon neutrality
- 2023
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In: INNOVATION. - 2666-6758. ; 4:5
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Research review (peer-reviewed)abstract
- To achieve the Paris Agreement, China pledged to become "Carbon Neutral" by the 2060s. In addition to massive decarbonization, this would require significant changes in ecosystems toward negative CO2 emissions. The ability of coastal blue carbon ecosystems (BCEs), including mangrove, salt marsh, and seagrass meadows, to sequester large amounts of CO2 makes their conservation and restoration an important "nature-based solution (NbS)" for climate adaptation and mitigation. In this review, we examine how BCEs in China can contribute to climate mitigation. On the national scale, the BCEs in China store up to 118 Tg C across a total area of 1,440,377 ha, including over 75% as unvegetated tidal flats. The annual sedimental C burial of these BCEs reaches up to 2.06 Tg C year(-1) , of which most occurs in salt marshes and tidal flats. The lateral C flux of mangroves and salt marshes contributes to 1.17 Tg C year(-1) along the Chinese coastline. Conservation and restoration of BCEs benefit climate change mitigation and provide other ecological services with a value of $32,000 ha(-1) year(-1). The potential practices and technologies that can be implemented in China to improve BCE C sequestration, including their constraints and feasibility, are also outlined. Future directions are suggested to improve blue carbon estimates on aerial extent, carbon stocks, sequestration, and mitigation potential. Restoring and preserving BCEs would be a cost-effective step to achieve Carbon Neutral by 2060 in China despite various barriers that should be removed.
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| 16. |
- Wang, Mojin, et al.
(author)
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The quantitative analysis by stem-loop real-time PCR revealed the microRNA-34a, microRNA-155 and microRNA-200c overexpression in human colorectal cancer
- 2012
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In: Medical Oncology. - : Humana Press (Springer Imprint). - 1357-0560 .- 1559-131X. ; 29:5, s. 3113-3118
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Journal article (peer-reviewed)abstract
- The recently identified class of microRNAs (miRNAs) provided a new insight in cancer research. As the member of miRNAs family, miR-34a, miR-155 and miR-200c abnormalities have been found in various types of cancer. However, the relationship between these three miRNAs (miR-34a, miR-155 and miR-200c) and colorectal cancer is unclear. In this study, we applied stem-loop real-time PCR to quantitatively detect miR-34a, miR-155 and miR-200c expression in 109 pair-matched human colorectal cancers and the corresponding normal mucosa. MiR-34a (2.2-fold), miR-155 (2.3-fold) and miR-200c (3.1-fold) were all expressed at higher levels in colorectal cancer (P = 0.001, 0.005 and 0.001, respectively). In rectum, miR-34a and miR-200c were significantly upregulated (P = 0.006 and 0.007), while the miR-155 overexpression was not statistically significant (P = 0.083). In colon, the higher expression of three miRNAs was seen, however, without significant difference (P andgt; 0.05). We also found that the miR-34a expression was higher in rectal cancer having more advanced TNM stage (III + IV, P = 0.03). Then miR-200c expression was positively correlated with and sera CEA level of rectal cancer patients (P = 0.04). In conclusion, our results thus suggest that the overexpression of miR-34a, miR-155 and miR-200c be associated with the development of colorectal cancer, meanwhile miR-34a may be involved in the development and progression of rectal cancer. The more deeply and larger scale research are required to prove the correlation.
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| 17. |
- Wang, Xi, et al.
(author)
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Alterations in the gut microbiota and metabolite profiles of patients with Kashin-Beck disease, an endemic osteoarthritis in China
- 2021
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In: Cell Death and Disease. - : Nature Publishing Group. - 2041-4889. ; 12:11
-
Journal article (peer-reviewed)abstract
- Kashin-Beck disease (KBD) is a severe osteochondral disorder that may be driven by the interaction between genetic and environmental factors. We aimed to improve our understanding of the gut microbiota structure in KBD patients of different grades and the relationship between the gut microbiota and serum metabolites. Fecal and serum samples collected from KBD patients and normal controls (NCs) were used to characterize the gut microbiota using 16S rDNA gene and metabolomic sequencing via liquid chromatography-mass spectrometry (LC/MS). To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria in the KBD patients, metagenomic sequencing of fecal samples from grade I KBD, grade II KBD and NC subjects was performed. The KBD group was characterized by elevated levels of Fusobacteria and Bacteroidetes. A total of 56 genera were identified to be significantly differentially abundant between the two groups. The genera Alloprevotella, Robinsoniella, Megamonas, and Escherichia_Shigella were more abundant in the KBD group. Consistent with the 16S rDNA analysis at the genus level, most of the differentially abundant species in KBD subjects belonged to the genus Prevotella according to metagenomic sequencing. Serum metabolomic analysis identified some differentially abundant metabolites among the grade I and II KBD and NC groups that were involved in lipid metabolism metabolic networks, such as that for unsaturated fatty acids and glycerophospholipids. Furthermore, we found that these differences in metabolite levels were associated with altered abundances of specific species. Our study provides a comprehensive landscape of the gut microbiota and metabolites in KBD patients and provides substantial evidence of a novel interplay between the gut microbiome and metabolome in KBD pathogenesis.
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| 18. |
- Wu, Cuiyan, et al.
(author)
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Long noncoding RNA expression profile reveals lncRNAs signature associated with extracellular matrix degradation in kashin-beck disease
- 2017
-
In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7
-
Journal article (peer-reviewed)abstract
- Kashin-Beck disease (KBD) is a deformative, endemic osteochondropathy involving degeneration and necrosis of growth plates and articular cartilage. The pathogenesis of KBD is related to gene expression and regulation mechanisms, but long noncoding RNAs (lncRNAs) in KBD have not been investigated. In this study, we identified 316 up-regulated and 631 down-regulated lncRNAs (≥ 2-fold change) in KBD chondrocytes using microarray analysis, of which more than three-quarters were intergenic lncRNAs and antisense lncRNAs. We also identified 232 up-regulated and 427 down-regulated mRNAs (≥ 2-fold change). A lncRNA-mRNA correlation analysis combined 343 lncRNAs and 292 mRNAs to form 509 coding-noncoding gene co-expression networks (CNC networks). Eleven lncRNAs were predicted to have cis-regulated target genes, including NAV2 (neuron navigator 2), TOX (thymocyte selection-associated high mobility group box), LAMA4 (laminin, alpha 4), and DEPTOR (DEP domain containing mTOR-interacting protein). The differentially expressed mRNAs in KBD significantly contribute to biological events associated with the extracellular matrix. Meanwhile, 34 mRNAs and 55 co-expressed lncRNAs constituted a network that influences the extracellular matrix. In the network, FBLN1 and LAMA 4 were the core genes with the highest significance. These novel findings indicate that lncRNAs may play a role in extracellular matrix destruction in KBD.
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| 19. |
- Yang, Lei, et al.
(author)
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Gene expression profiles and molecular mechanism of cultured human chondrocytes' exposure to T-2 toxin and deoxynivalenol
- 2017
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In: Toxicon. - Amsterdam : Elsevier. - 0041-0101 .- 1879-3150. ; 140, s. 38-44
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Journal article (peer-reviewed)abstract
- T-2 toxin and deoxynivalenol (DON) are secondary metabolites produced by Fusarium fungi and are commonly found on food and feed. Although T-2 toxin and DON have been suggested as the etiology of Kashin-Beck disease (KBD), an endemic osteochondropathy, little is known about the mechanism when human chondrocytes are exposed to T-2 toxin and DON. The purpose of this study is to identify the gene expression differences and underlying molecular changes modulated by T-2 toxin and DON in vitro in human chondrocytes. After the experiments of cell viability, the gene expression profiles were analyzed in cells that were treated with 0.01 μg/ml T-2 toxin and 1.0 μg/ml DON for 72 h by Affymetrix Human Gene Chip. The array results showed that 882 and 2118 genes were differentially expressed for T-2 toxin and DON exposure, respectively. Enrichment analysis revealed that diverse cellular processes including DNA damage, cell cycle regulation and metabolism of extracellular matrix were affected when human chondrocytes were exposed to T-2 toxin and DON. These results demonstrate the gene expression differences and molecular mechanism of cultured human chondrocytes exposure to T-2 toxin and DON, and provide a new insight into future research in the etiology of KBD.
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| 20. |
- Ye, Lei, et al.
(author)
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Preparation of Metallized Pellets from Blast Furnace Dust and Electric Arc Furnace Dust Based on Microwave Impedance Matching
- 2020
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In: 11th International Symposium on High-Temperature Metallurgical Processing. - Cham : Springer Nature. - 9783030365400 - 9783030365394 ; , s. 569-579
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Conference paper (peer-reviewed)abstract
- Blast furnace dust and electric arc furnace dust are two typical solid wastes in iron and steel industry. In order to overcome the shortcomings of traditional processes, such as low metal recovery efficiency and high secondary pollution, microwave energy was applied in this study to intensify the self-reduction of core-shell BF dust-EAF dust composite pellets based on impedance matching for realizing highly efficient migration and separation of iron, zinc, and lead. By reducing the composite pellets in microwave field, it was found that under the optimal conditions of proportion of EAF dust in shell to all EAF dust in the pellet of 20%, reduction temperature of 1000 degrees C, and dwell time of 15 min, metallized pellets with the total iron content of 68.73 wt %, iron metallization degree of 95.87%, zinc removal percentage of 88.78%, lead removal percentage of 94.38%, and compressive strength of 190.4 N/p were obtained.
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| 21. |
- Ye, Lei, et al.
(author)
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Toward environmentally friendly direct reduced iron production : A novel route of comprehensive utilization of blast furnace dust and electric arc furnace dust
- 2021
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In: Waste Management. - : Elsevier. - 0956-053X .- 1879-2456. ; 135, s. 389-396
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Journal article (peer-reviewed)abstract
- In this study, a novel method for producing direct reduced iron (DRI) powders based on microwave-assisted self reduction of core-shell composite pellets composed of blast furnace (BF) dust and hazardous electric arc furnace (EAF) dust followed by magnetic separation was reported. The proper core-shell structure of the composite pellets was designed according to the rule of impedance matching and properties of BF dust and EAF dust by adjusting the thickness of shell (i.e., thickness of impedance matching layer) via controlling the C/O molar ratio of the raw materials from 0.55 to 0.70. The results showed that the EAF dust with high content of CaO was beneficial to the mechanical strength of green, dried, and metallized pellets (collected after reduction), while the BF dust with high content of carbon enabled sufficient microwave-assisted reduction of the pellets, facilitating subsequent magnetic separation and also the removal of zinc from EAF dust. By reduction of the core-shell BF dust-EAF dust composite pellets with the C/O molar ratio of 0.65 at 1050 degrees C for 15 min, the resulting metallized pellets showed superior reduction and magnetic separation indexes with higher removal percentages of zinc and lead, in comparison with conventional metallized pellets. The DRI powders obtained after magnetic separation had total iron content of 91.2 wt%, iron metallization degree of 95.8%, yield of 68.1%, and iron recovery of 88.0%. This study provided a good example for efficient and environmentally friendly comprehensive utilization of typical and hazardous wastes in the iron and steel industry.
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| 22. |
- Ye, Qing, et al.
(author)
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Thermodynamic Analysis of Carbothermic Reduction of Electric Arc Furnace Dust
- 2019
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In: 10th International Symposium On High-Temperature Metallurgical Processing. - Cham : Springer International Publishing. - 9783030059552 - 9783030059545 ; , s. 117-124
-
Conference paper (peer-reviewed)abstract
- Electric arc furnace (EAF) dust is a kind of secondary resource which contains multiple metallic elements, including Fe, Mn and Cr. Pyrometallurgical processes for recovering metal elements from EAF dust have been investigated for many years although they are suffered from high energy consumption due to the spinel-structured components of EAF dust. In this study, the thermodynamic analysis of carbothermic reduction of EAF dust was performed. The main components of EAF dust were magnetite (Fe3O4), hausmannite (Mn3O4) and chromate spinel (FeCr2O4). The gangue minerals were mainly composed of magnesium silicates. The thermodynamic analysis indicated that magnetite and hausmannite can be reduced to metallic iron and MnO, respectively. Meanwhile, the chromate spinel will be reduced to chromium oxide and then to form CaCr2O4. The results also demonstrated that the gangue components can promote the separation of Fe and Cr, agreeing well with the experimental results.
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| 23. |
- Yuan, Xiaotian, et al.
(author)
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GABPA inhibits invasion/metastasis in papillary thyroid carcinoma by regulating DICER1 expression
- 2019
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In: Oncogene. - : Springer Science and Business Media LLC. - 0950-9232 .- 1476-5594. ; 38:7, s. 965-979
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Journal article (peer-reviewed)abstract
- The ETS family transcription factor GABPA is suggested as an oncogenic element, which is further supported by the recent reporting of it as the sole ETS member to activate the mutant TERT promoter in thyroid carcinomas (TC). However, it remains unclear how GABPA contributes to TC pathogenesis. The present study is designed to address this issue. TERT expression was significantly diminished in TERT promoter-mutated TC cells upon GABPA inhibition. Surprisingly, GABPA depletion led to robustly increased cellular invasion independently of TERT promoter mutations and TERT expression. DICER1, a component of the microRNA machinery, was identified as a downstream effector of GABPA. GABPA facilitated Dicer1 transcription while its depletion reduced Dicer1 expression. The mutation of the GABPA binding site in the DICER1 promoter led to diminished basal levels of DICER1 promoter activity and abolishment of GABPA-stimulated promoter activity as well. The forced DICER1 expression abrogated the invasiveness of GABPA-depleted TC cells. Consistently, the analyses of 93 patients with papillary thyroid carcinoma (PTC) revealed a positive correlation between GABPA and DICER1 expression. GABPA expression was negatively associated with TERT expression and promoter mutations, in contrast to published observations in cancer cell lines. Lower GABPA expression was associated with distant metastasis and shorter overall/disease-free survival in PTC patients. Similar results were obtained for PTC cases in the TCGA dataset. In addition, a positive correlation between GABPA and DICER1 expression was seen in multiple types of malignancies. Taken together, despite its stimulatory effect on the mutant TERT promoter and telomerase activation, GABPA may itself act as a tumor suppressor rather than an oncogenic factor to inhibit invasion/metastasis in TCs and be a useful predictor for patient outcomes.
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| 24. |
- Zhai, Panlong, et al.
(author)
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Engineering single-atomic ruthenium catalytic sites on defective nickel-iron layered double hydroxide for overall water splitting
- 2021
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Journal article (peer-reviewed)abstract
- Rational design of single atom catalyst is critical for efficient sustainable energy conversion. However, the atomic-level control of active sites is essential for electrocatalytic materials in alkaline electrolyte. Moreover, well-defined surface structures lead to in-depth understanding of catalytic mechanisms. Herein, we report a single-atomic-site ruthenium stabilized on defective nickel-iron layered double hydroxide nanosheets (Ru-1/D-NiFe LDH). Under precise regulation of local coordination environments of catalytically active sites and the existence of the defects, Ru-1/D-NiFe LDH delivers an ultralow overpotential of 18mV at 10mAcm(-2) for hydrogen evolution reaction, surpassing the commercial Pt/C catalyst. Density functional theory calculations reveal that Ru-1/D-NiFe LDH optimizes the adsorption energies of intermediates for hydrogen evolution reaction and promotes the O-O coupling at a Ru-O active site for oxygen evolution reaction. The Ru-1/D-NiFe LDH as an ideal model reveals superior water splitting performance with potential for the development of promising water-alkali electrocatalysts. Rational design of single atom catalyst is critical for efficient sustainable energy conversion. Single-atomic-site ruthenium stabilized on defective nickel-iron layered double hydroxide nanosheets achieve superior HER and OER performance in alkaline media.
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