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  • 1
    Online Resource
    Online Resource
    International expert consensus on diagnosis and treatment of lung cancer complicated by chronic obstructive pulmonary disease
    AME Publishing Company ; 2023
    In:  Translational Lung Cancer Research Vol. 12, No. 8 ( 2023-8), p. 1661-1701
    Details
    In: Translational Lung Cancer Research, AME Publishing Company, Vol. 12, No. 8 ( 2023-8), p. 1661-1701
    Type of Medium: Online Resource
    ISSN: 2218-6751 , 2226-4477
    URL: Journal
    URL: Article
    DOI: 10.21037/tlcr
    DOI: 10.21037/tlcr-23-339
    Language: Unknown
    Publisher: AME Publishing Company
    Publication Date: 2023
    detail.hit.zdb_id: 2754335-3
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  • 2
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    Resource availability affects how underground microbes band together to support plant life
    Springer Science and Business Media LLC ; 2023
    In:  Microbiome Vol. 11, No. 1 ( 2023-05-01)
    Details
    In: Microbiome, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2023-05-01)
    Abstract: For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability. Results We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass. Conclusions Our results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification.
    Type of Medium: Online Resource
    ISSN: 2049-2618
    URL: Article
    URL: Article
    DOI: 10.1186/s40168-023-01539-5
    DOI: 10.21203/rs.3.rs-2908960/v1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2697425-3
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  • 3
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    Community assembly of organisms regulates soil microbial functional potential through dual mechanisms
    Wiley ; 2024
    In:  Global Change Biology Vol. 30, No. 2 ( 2024-02)
    Details
    In: Global Change Biology, Wiley, Vol. 30, No. 2 ( 2024-02)
    Abstract: Unraveling the influence of community assembly processes on soil ecosystem functioning presents a major challenge in the field of theoretical ecology, as it has received limited attention. Here, we used a series of long‐term experiments spanning over 25 years to explore the assembly processes of bacterial, fungal, protist, and nematode communities using high‐throughput sequencing. We characterized the soil microbial functional potential by the abundance of microbial genes associated with carbon, nitrogen, phosphorus, and sulfur cycling using GeoChip‐based functional gene profiling, and determined how the assembly processes of organism groups regulate soil microbial functional potential through community diversity and network stability. Our results indicated that balanced fertilization (NPK) treatment improved the stochastic assembly of bacterial, fungal, and protist communities compared to phosphorus‐deficient fertilization (NK) treatment. However, there was a nonsignificant increase in the normalized stochasticity ratio of the nematode community in response to fertilization across sites. Our findings emphasized that soil environmental factors influenced the assembly processes of the biotic community, which regulated soil microbial functional potential through dual mechanisms. One mechanism indicated that the high phosphorus levels and low soil nutrient stoichiometry may increase the stochasticity of bacterial, fungal, and protist communities and the determinism of the nematode community under NPK treatment, ultimately enhancing soil microbial functional potential by reinforcing the network stability of the biotic community. The other mechanism indicated that the low phosphorus levels and high soil nutrient stoichiometry may increase the stochastic process of the bacterial community and the determinism of the fungal, protist, and nematode communities under NK treatment, thereby enhancing soil microbial functional potential by improving the β‐diversity of the biotic community. Taken together, these results provide valuable insights into the mechanisms underlying the assembly processes of the biotic community that regulate ecosystem functioning.
    Type of Medium: Online Resource
    ISSN: 1354-1013 , 1365-2486
    URL: Issue
    URL: Article
    DOI: 10.1111/gcb.v30.2
    DOI: 10.1111/gcb.17160
    Language: English
    Publisher: Wiley
    Publication Date: 2024
    detail.hit.zdb_id: 2020313-5
    SSG: 12
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  • 4
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    Genomic prediction of carcass traits using different haplotype block partitioning methods in beef cattle
    Wiley ; 2022
    In:  Evolutionary Applications Vol. 15, No. 12 ( 2022-12), p. 2028-2042
    Details
    In: Evolutionary Applications, Wiley, Vol. 15, No. 12 ( 2022-12), p. 2028-2042
    Abstract: Genomic prediction (GP) based on haplotype alleles can capture quantitative trait loci (QTL) effects and increase predictive ability because the haplotypes are expected to be in linkage disequilibrium (LD) with QTL. In this study, we constructed haploblocks using LD‐based and the fixed number of single nucleotide polymorphisms (fixed‐SNP) methods with Illumina BovineHD chip in beef cattle. To evaluate the performance of different haplotype block partitioning methods, we constructed haploblocks based on LD thresholds (from r 2   〉  0.2 to r 2   〉  0.8) and the number of fixed‐SNPs (5, 10, 20). The performance of predictive methods for three carcass traits including liveweight (LW), dressing percentage (DP), and longissimus dorsi muscle weight (LDMW) was evaluated using three approaches (GBLUP and BayesB model based on the SNP, G H BLUP, and BayesBH models based on the haploblock, and G H BLUP+GBLUP and BayesBH+BayesB models based on the combined haploblock and the nonblocked SNPs, which were located between blocks). In this study, we found the accuracies of LD‐based and fixed‐SNP haplotype Bayesian methods outperformed the Bayesian models (up to 8.54 ± 7.44% and 5.74 ± 2.95%, respectively). G H BLUP showed a high improvement (up to 11.29 ± 9.87%) compared with GBLUP. The Bayesian models have higher accuracies than BLUP models in most scenarios. The average computing time of the BayesBH+BayesB model can reduce by 29.3% compared with the BayesB model. The prediction accuracies using the LD‐based haplotype method showed higher improvements than the fixed‐SNP haplotype method. In addition, to avoid the influence of rare haplotypes generated from haplotype construction, we compared the performance of GP by filtering four types of minor haplotype allele frequency (MHAF) (0.01, 0.025, 0.05, and 0.1) under different conditions (LD levels were set at r 2   〉  0.3, and the fixed number of SNPs was 5). We found the optimal MHAF threshold for LW was 0.01, and the optimal MHAF threshold for DP and LDMW was 0.025.
    Type of Medium: Online Resource
    ISSN: 1752-4571 , 1752-4571
    URL: Issue
    URL: Article
    DOI: 10.1111/eva.v15.12
    DOI: 10.1111/eva.13491
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2405496-3
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  • 5
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    Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle
    Springer Science and Business Media LLC ; 2017
    In:  Scientific Reports Vol. 7, No. 1 ( 2017-10-30)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2017-10-30)
    Abstract: Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new V i statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise V ST . We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide V i value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-017-14768-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2615211-3
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  • 6
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    Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation
    Wiley ; 2022
    In:  Cell Proliferation Vol. 55, No. 5 ( 2022-05)
    Details
    In: Cell Proliferation, Wiley, Vol. 55, No. 5 ( 2022-05)
    Abstract: Although major advances have been made in bovine epigenome study, the epigenetic basis for fetal skeletal muscle development still remains poorly understood. The aim is to recapitulated the time course of fetal skeletal muscle development in vitro , and explore the dynamic changes of chromatin accessibility and gene expression during bovine myoblasts proliferation and differentiation. Methods PDGFR‐ cells were isolated from bovine fetal skeletal muscle, then cultured and induced myogenic differentiation in vitro in a time‐course study (P, D0, D2,and D4). The assay for transposase‐accessible chromatin sequencing (ATAC‐seq) and RNA sequencing (RNA‐seq) were performed. Results Among the enriched transcriptional factors with high variability, we determined the effects of MAFF , ZNF384 , and KLF6 in myogenesis using RNA interference (RNAi). In addition, we identified both stage‐specific genes and chromatin accessibility regions to reveal the sequential order of gene expression, transcriptional regulatory, and signal pathways involved in bovine skeletal muscle development. Further investigation integrating chromatin accessibility and transcriptome data was conducted to explore cis‐regulatory regions in line with gene expression. Moreover, we combined bovine GWAS results of growth traits with regulatory regions defined by chromatin accessibility, providing a suggestive means for a more precise annotation of genetic variants of bovine growth traits. Conclusion Overall, these findings provide valuable information for understanding the stepwise regulatory mechanisms in skeletal muscle development and conducting beef cattle genetic improvement programs.
    Type of Medium: Online Resource
    ISSN: 0960-7722 , 1365-2184
    URL: Issue
    URL: Article
    DOI: 10.1111/cpr.v55.5
    DOI: 10.1111/cpr.13219
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2019986-7
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  • 7
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    Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array
    MDPI AG ; 2021
    In:  Animals Vol. 11, No. 12 ( 2021-12-06), p. 3469-
    Details
    In: Animals, MDPI AG, Vol. 11, No. 12 ( 2021-12-06), p. 3469-
    Abstract: Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.
    Type of Medium: Online Resource
    ISSN: 2076-2615
    URL: Article
    DOI: 10.3390/ani11123469
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2606558-7
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  • 8
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    Validation of the Prediction Accuracy for 13 Traits in Chinese Simmental Beef Cattle Using a Preselected Low-Density SNP Panel
    MDPI AG ; 2021
    In:  Animals Vol. 11, No. 7 ( 2021-06-25), p. 1890-
    Details
    In: Animals, MDPI AG, Vol. 11, No. 7 ( 2021-06-25), p. 1890-
    Abstract: Chinese Simmental beef cattle play a key role in the Chinese beef industry due to their great adaptability and marketability. To achieve efficient genetic gain at a low breeding cost, it is crucial to develop a customized cost-effective low-density SNP panel for this cattle population. Thirteen growth, carcass, and meat quality traits and a BovineHD Beadchip genotyping of 1346 individuals were used to select trait-associated variants and variants contributing to great genetic variance. In addition, highly informative SNPs with high MAF in each 500 kb sliding window and in each genic region were also included separately. A low-density SNP panel consisting of 30,684 SNPs was developed, with an imputation accuracy of 97.4% when imputed to the 770 K level. Among 13 traits, the average prediction accuracy levels evaluated by genomic best linear unbiased prediction (GBLUP) and BayesA/B/Cπ were 0.22–0.47 and 0.18–0.60 for the ~30 K array and BovineHD Beadchip, respectively. Generally, the predictive performance of the ~30 K array was trait-dependent, with reduced prediction accuracies for seven traits. While differences in terms of prediction accuracy were observed among the 13 traits, the low-density SNP panel achieved moderate to high accuracies for most of the traits and even improved the accuracies for some traits.
    Type of Medium: Online Resource
    ISSN: 2076-2615
    URL: Article
    DOI: 10.3390/ani11071890
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2606558-7
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  • 9
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    Table9.XLSX
    Frontiers Media SA ; 2022
    In:  Frontiers in Genetics Vol. 13 ( 2022-3-3)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 13 ( 2022-3-3)
    Abstract: Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 genes were differentially expressed among three developmental stages. Using weighted correlation network analysis, we found that 12 modules were significantly associated with developmental stages. Functional annotation and protein–protein interaction (PPI) network analysis revealed that CCNB1 , CCNB2 , IGF1 , IGF2 , HMGCL , BDH1 , ACAT1 , HMGCS2 , and CREBBP involved in rumen development. Integrated transcriptome with GWAS information of carcass weight (CW), stomach weight (SW), marbling score (MS), backfat thickness (BFT), ribeye area (REA), and lean meat weight (LMW), we found that upregulated DEGs (fold change 0∼1) in birth–youth comparison were significantly enriched with GWAS signals of MS, downregulated DEGs (fold change & gt;3) were significantly enriched with GWAS signals of SW, and fold change 0∼1 up/downregulated DEGs in birth–adult comparison were significantly enriched with GWAS signals of CW, LMW, REA, and BFT. Furthermore, we found that GWAS signals for CW, LMW, and REA were enriched in turquoise module, and GWAS signals for CW was enriched in lightgreen module. Our study provides novel insights into the molecular mechanism underlying rumen development in cattle and highlights an integrative analysis for illustrating the genetic architecture of beef complex traits.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
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    URL: Article
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    URL: Article
    DOI: 10.3389/fgene.2022.821406
    DOI: 10.3389/fgene.2022.821406.s001
    DOI: 10.3389/fgene.2022.821406.s002
    DOI: 10.3389/fgene.2022.821406.s003
    DOI: 10.3389/fgene.2022.821406.s004
    DOI: 10.3389/fgene.2022.821406.s005
    DOI: 10.3389/fgene.2022.821406.s006
    DOI: 10.3389/fgene.2022.821406.s007
    DOI: 10.3389/fgene.2022.821406.s008
    DOI: 10.3389/fgene.2022.821406.s009
    DOI: 10.3389/fgene.2022.821406.s010
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606823-0
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  • 10
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    Characterization of Chromatin Accessibility in Fetal Bovine Chondrocytes
    MDPI AG ; 2023
    In:  Animals Vol. 13, No. 11 ( 2023-06-05), p. 1875-
    Details
    In: Animals, MDPI AG, Vol. 13, No. 11 ( 2023-06-05), p. 1875-
    Abstract: Despite significant advances of the bovine epigenome investigation, new evidence for the epigenetic basis of fetal cartilage development remains lacking. In this study, the chondrocytes were isolated from long bone tissues of bovine fetuses at 90 days. The Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) and transcriptome sequencing (RNA-seq) were used to characterize gene expression and chromatin accessibility profile in bovine chondrocytes. A total of 9686 open chromatin regions in bovine fetal chondrocytes were identified and 45% of the peaks were enriched in the promoter regions. Then, all peaks were annotated to the nearest gene for Gene Ontology (GO) and Kyoto Encylopaedia of Genes and Genomes (KEGG) analysis. Growth and development-related processes such as amide biosynthesis process (GO: 0043604) and translation regulation (GO: 006417) were enriched in the GO analysis. The KEGG analysis enriched endoplasmic reticulum protein processing signal pathway, TGF-β signaling pathway and cell cycle pathway, which are closely related to protein synthesis and processing during cell proliferation. Active transcription factors (TFs) were enriched by ATAC-seq, and were fully verified with gene expression levels obtained by RNA-seq. Among the top50 TFs from footprint analysis, known or potential cartilage development-related transcription factors FOS, FOSL2 and NFY were found. Overall, our data provide a theoretical basis for further determining the regulatory mechanism of cartilage development in bovine.
    Type of Medium: Online Resource
    ISSN: 2076-2615
    URL: Article
    DOI: 10.3390/ani13111875
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2606558-7
    SSG: 23
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