| 1. |
- Fang, Qinghua, et al.
(författare)
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Comparative Analysis on Abnormal Methylome of Differentially Expressed Genes and Disease Pathways in the Immune Cells of RA and SLE
- 2021
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Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- We identified abnormally methylated, differentially expressed genes (DEGs) and pathogenic mechanisms in different immune cells of RA and SLE by comprehensive bioinformatics analysis. Six microarray data sets of each immune cell (CD19+ B cells, CD4+ T cells and CD14+ monocytes) were integrated to screen DEGs and differentially methylated genes by using R package "limma." Gene ontology annotations and KEGG analysis of aberrant methylome of DEGs were done using DAVID online database. Protein-protein interaction (PPI) network was generated to detect the hub genes and their methylation levels were compared using DiseaseMeth 2.0 database. Aberrantly methylated DEGs in CD19+ B cells (173 and 180), CD4+ T cells (184 and 417) and CD14+ monocytes (193 and 392) of RA and SLE patients were identified. We detected 30 hub genes in different immune cells of RA and SLE and confirmed their expression using FACS sorted immune cells by qPCR. Among them, 12 genes (BPTF, PHC2, JUN, KRAS, PTEN, FGFR2, ALB, SERB-1, SKP2, TUBA1A, IMP3, and SMAD4) of RA and 12 genes (OAS1, RSAD2, OASL, IFIT3, OAS2, IFIH1, CENPE, TOP2A, PBK, KIF11, IFIT1, and ISG15) of SLE are proposed as potential biomarker genes based on receiver operating curve analysis. Our study suggests that MAPK signaling pathway could potentially differentiate the mechanisms affecting T- and B- cells in RA, whereas PI3K pathway may be used for exploring common disease pathways between RA and SLE. Compared to individual data analyses, more dependable and precise filtering of results can be achieved by integrating several relevant data sets.
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| 2. |
- Gao, Hongkai, et al.
(författare)
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Assessing glacier retreat and its impact on water resources in a headwater of Yangtze River based on CMIP6 projections
- 2021
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 765
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Tidskriftsartikel (refereegranskat)abstract
- Glacier retreat caused by global warming alters the hydrological regime and poses far-reaching challenges to water resources and nature conservation of the headwater of Yangtze River, and its vast downstream regions with dense population. However, there is still lack of a robust modeling framework of the “climate-glacier-streamflow” in this water tower region, to project the future changes of glacier mass balance, glacier geometry, and the consequent impacts on runoff. Moreover, it is imperative to use the state-of-the-art sixth phase Coupled Model Intercomparison Project (CMIP6) to assess glacio-hydrology variations in future. In this study, we coupled a glacio-hydrological model (FLEXG) with a glacier retreat method (Δh-parameterization) to simulate glacio-hydrological processes in the Dongkemadi Glacier (over 5155 m.a.s.l), which has the longest continuous glacio-hydrology observation on the headwater of Yangtze River. The FLEXG-Δh model was forced with in-situ observed meteorological data, radar ice thickness, remote sensing topography and land cover data, and validated by measured runoff. The results showed that the model was capable to simulate hydrological processes in this glacierized basin, with Kling-Gupta efficiency (IKGE) of daily runoff simulation 0.88 in calibration and 0.70 in validation. Then, forcing by the bias-corrected meteorological forcing from the eight latest CMIP6 Earth system models under two climate scenarios (RCP2.6 and RCP8.5), we assessed the impact of future climate change on glacier response and its hydrological effects. The results showed that, to the end of simulation in 2100, the volume of the Dongkemadi Glacier would continuously retreat. For the RCP2.6 and RCP8.5 scenarios, the glacier volume will decrease by 8.7 × 108 m3 (74%) and 10.8 × 108 m3 (92%) respectively in 2100. The glacier runoff will increase and reach to peak water around 2060 to 2085, after this tipping point water resources will likely decrease.
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| 3. |
- Guo, Ying, et al.
(författare)
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Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history
- 2021
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Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571.
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Tidskriftsartikel (refereegranskat)abstract
- Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current com-mercial stocks bred for efficient meat and egg production. In-depth characteriza-tions of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.
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| 4. |
- Li, Jinxiu, et al.
(författare)
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A Discovery of a Genetic Mutation Causing Reduction of Atrogin-1 Expression in Broiler Chicken Muscle
- 2019
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Ingår i: Frontiers in Genetics. - : FRONTIERS MEDIA SA. - 1664-8021. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Chickens are bred all over the world and have significant economic value as one of the major agricultural animals. The growth rate of commercial broiler chickens is several times higher than its Red Jungle fowl (RJF) ancestor. To further improve the meat production of commercial chickens, it is quite important to decipher the genetic mechanism of chicken growth traits. In this study, we found that broiler chickens exhibited lower levels of E3 ubiquitin ligase muscle atrophy F-box (MAFbx or Atrogin-1) relative to its RJF ancestor. As a ubiquitin ligase, Atrogin-1 plays a crucial role in muscle development in which its up-regulation often indicates the activation of muscle atrophic pathways. Here, we showed that the Atrogin-1 expression variance partly affects chicken muscle growth rates among different breeds. Furthermore, we demonstrated that the reduced expression of Atrogin-1 in broiler chickens was ascribed to a single nucleotide polymorphism (SNP), which inhibited the binding of transcription regulators and attenuated the enhancer activity. The decreased Atrogin-1 in broiler chickens suppresses the catabolism of muscle protein and preserves muscle mass. Our study facilitates the understanding of the molecular mechanism of chicken muscle development and has a high translational impact in chicken breeding.
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| 5. |
- Wang, Tingting, et al.
(författare)
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Proteus mirabilis Vesicles Induce Mitochondrial Apoptosis by Regulating miR96-5p/Abca1 to Inhibit Osteoclastogenesis and Bone Loss
- 2022
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Ingår i: Frontiers in Immunology. - Lausanne : Frontiers Media S.A.. - 1664-3224. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Bone loss due to an increased osteoclast activity is common in osteoporosis and rheumatoid arthritis. For the first time, we observed an inhibition of osteoclast formation and bone resorption by outer-membrane vesicles (OMVs) from a Gram-negative, pathogenic bacterium, Proteus mirabilis (P.M). Gene ontogeny and KEGG enrichment analyses of miRNA and mRNA sequencing data demonstrated a significant effect of P.M OMVs on mitochondrial functions and apoptotic pathways. OMVs induced mitochondrial dysfunction through an increased level of intracellular ROS, collapse of mitochondrial membrane potential (ΔΨm), and modulation of Bax, Bcl-2, caspase-3, and cytochrome c expression. In addition, P.M OMVs strongly inhibited miR-96-5p expression, which caused an upregulation of ATP binding cassette subfamily A member 1 (Abca1) in osteoclasts leading to an increased level of mitochondria-dependent apoptosis. Moreover, treatment with P.M but not Escherichia coli OMVs attenuated bone loss in experimental osteoporosis and collagen-induced arthritis. Collectively, we demonstrated osteoprotective functions of OMVs from Proteus mirabilis, which downregulated miR-96-5p causing an increased Abca1 expression and mitochondria-dependent apoptosis. © 2022 Wang, Mo, Ou, Fang, Wu, Wu and Nandakumar.
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| 6. |
- Wang, Yuzhe, et al.
(författare)
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Multiple ancestral haplotypes harboring regulatory mutations cumulatively contribute to a QTL affecting chicken growth traits
- 2020
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Ingår i: Communications Biology. - : NATURE PUBLISHING GROUP. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- In depth studies of quantitative trait loci (QTL) can provide insights to the genetic architectures of complex traits. A major effect QTL at the distal end of chicken chromosome 1 has been associated with growth traits in multiple populations. This locus was fine-mapped in a fifteen-generation chicken advanced intercross population including 1119 birds and explored in further detail using 222 sequenced genomes from 10 high/low body weight chicken stocks. We detected this QTL that, in total, contributed 14.4% of the genetic variance for growth. Further, nine mosaic precise intervals (Kb level) which contain ancestral regulatory variants were fine-mapped and we chose one of them to demonstrate the key regulatory role in the duodenum. This is the first study to break down the detail genetic architectures for the well-known QTL in chicken and provides a good example of the fine-mapping of various of quantitative traits in any species. Yuzhe Wang, Xuemin Cao et al. report the fine-mapping of a major growth trait QTL in chicken using genome-wide association and haplotype association analyses. They discover multiple mutations cumulatively contribute to the previously-reported QTL and identify one of a regulatory mutation that contributes to the variation in the measured traits.
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| 7. |
- Xu, Yuzhe, 1982-, et al.
(författare)
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Distributed spectrum leasing via vertical cooperation in cognitive radio networks
- 2015
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Ingår i: IEEE Transactions on Wireless Communications. - : IEEE conference proceedings. - 1536-1276 .- 1558-2248. ; , s. 185-190
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Tidskriftsartikel (refereegranskat)abstract
- In hierarchical cognitive radio networks, unlicensed secondary users can increase their achievable rates by assisting licensed primary user transmissions via cooperation. In this paper, a novel approach to maximize the transmission rates in the secondary network by optimizing the relay selection, the secondary transmit powers, and the cooperative relaying power splitting parameters is proposed. The resulting optimization problem is mixed integer and non-convex, which makes it NP hard to find the optimal solutions. Therefore, centralized and distributed solution methods to find near-to-optimal solutions of this challenging problem are proposed. The methods are based on iteratively solving the secondary relay selection by a greedy approach, and the optimal power allocation problem by a fixed-point approach together with alternating direction method of multipliers. It is established that both centralized and distributed solution methods always converge. The numerical results illustrate how the performance of the proposed solution methods depend on the primary performance margins, and show that they give a near-to-optimal solution in few iterations.
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| 8. |
- Xu, Yuzhe, 1982-, et al.
(författare)
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Distributed spectrum leasing via vertical cooperation in spectrum sharing networks
- 2014
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Ingår i: Cognitive Radio Oriented Wireless Networks and Communications (CROWNCOM), 2014 9th International Conference on. - : IEEE conference proceedings. ; , s. 185-190
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Konferensbidrag (refereegranskat)abstract
- In hierarchical cognitive radio networks, unlicensedsecondary users can increase their achievable rates by assistinglicensed primary user transmissions via cooperation. In thispaper, a novel approach to maximize the transmission rates inthe secondary network by optimizing the relay selection, thesecondary transmit powers, and the cooperative relaying powersplitting parameters is proposed. The resulting optimizationproblem is mixed integer and non-convex, which makes it NPhard to find the optimal solutions. Therefore, centralized anddistributed solution methods to find near-to-optimal solutions ofthis challenging problem are proposed. The methods are basedon iteratively solving the secondary relay selection by a greedyapproach, and the optimal power allocation problem by a fixed-point approach together with alternating direction method ofmultipliers. It is established that both centralized and distributedsolution methods always converge. The numerical results illus-trate the performance of the proposed solution methods, andshow that they give a near-to-optimal solution. Moreover, theperformance margins of the primary transmitters that permitthe accommodation of relaying secondary users, still having highachievable transmit rates, are characterized.
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| 9. |
- Zhang, Pengyang, et al.
(författare)
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Generation Pathway of Hydroxyl Radical in Fe/N/C-Based Oxygen Reduction Electrocatalysts under Acidic Media
- 2021
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 12:32, s. 7797-7803
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Tidskriftsartikel (refereegranskat)abstract
- The identification of the generation pathway of •OH radical during the oxygen reduction reaction (ORR) is critical because it determines which strategy should be adopted to minimize these corrosive species. In this way, researchers can develop a more stable Fe/N/C ORR catalyst or a catalyst layer in the proton exchange membrane fuel cells (PEMFCs). To date, this critical problem has still been unresolved. Herein, the generation of the •OH radical during the acidic ORR was mimicked by using two known pathways, that is, the Fenton (and Fenton-like) and the electrochemical reduction of H2O2(H2O2-ECR) process. The latter was determined as the main generation pathway of •OH radical below 30 °C. As the temperature surpassed 30 °C, the H2O2-ECR process began to lose its dominance because of the appearance of a third so-far unknown generation pathway. This work lays a basis for future development of radical elimination strategies to stabilize a Fe/N/C ORR catalyst or a catalyst layer in PEMFCs.
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