cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20018186.v1
title: LINC00974 sponges miR-33a to facilitate cell proliferation, invasion, and EMT of ovarian cancer through HMGB2 upregulation

description: Abstract The function and mechanism of long intergenic non-protein coding RNA 974 (LINC00974) are rarely reported in ovarian cancer (OC). The study aimed to investigate how LINC00974 affects the progression of OC. The expression levels of LINC00974, microRNA-33a (miR-33a), and high mobility group box 2 (HMGB2) mRNA were detected by qRT-PCR. The LINC00974/miR-33a/HMGB2 axis was confirmed by dual-luciferase reporter, RNA-binding protein immunoprecipitation (RIP), and biotinylated RNA pull-down assays. A series of in vitro experiments were employed to assess the effects of LINC00974/miR-33a/HMGB2 axis on the proliferation, invasion and epithelial mesenchymal transition (EMT) of OC cells. Results showed that LINC00974 and HMGB2 mRNA expression were upregulated in OC cells, while miR-33a expression was downregulated. HMGB2 was a direct target gene of miR-33a. LINC00974 act as a competing endogenous RNA (ceRNA) to directly bind with miR-33a, thereby upregulated HMGB2 expression. Notably, silencing of LINC00974 suppressed cell proliferation, invasion and EMT of OC cells, whereas miR-33a knockdown partially reversed the phenotypes of LINC00974 on OC cells. Overall, our study demonstrated that LINC00974 sponges miR-33a to promote cell proliferation, invasion, and EMT of OC through HMGB2 upregulation. LINC00974/miR-33a/HMGB2 axis may be an important signaling pathway in the progression of OC.
DOI: 10.25549/usctheses-ouc11258125
title: Title
DOI: 10.17608/k6.auckland.13206026.v1
title: Hadden Little penguin micro CT IKI stained head

description: This DOI contains the micro CT stack of a fixed, dehydrated and IKI stained little penguin (<i>Eudyptula minor</i>) head collected in Auckland, with one eye having been removed to allow penetration of the IKI stain.<br><br><br>
DOI: 10.6084/m9.figshare.20018187
title: MT1G inhibits the growth and epithelial-mesenchymal transition of gastric cancer cells by regulating the PI3K/AKT signaling pathway

description: Abstract Gastric carcinoma (GC) is a malignant tumor that has high mortality and morbidity worldwide. Although many efforts have been focused on the development and progression of GC, the underlying functional regulatory mechanism of GC needs more clarification. Metallothionein 1G (MT1G) is a member of the metallothionein family (MTs), and hypermethylation of MT1G occurred in a variety of cancers, including gastric cancer. However, the functional mechanism of MT1G in GC remains unclear. Here, we demonstrated that MT1G was down-regulated in GC tissues and cells. Overexpression of MT1G inhibited cell proliferation, foci formation and cell invasion, while knockdown of MT1G increased cell proliferation, foci formation and cell invasion. In addition, MT1G overexpression inhibited cell cycle progression and MT1G deficiency exerted opposite phenotype. p-AKT was negatively regulated by MT1G. In summary, our study reveals that MT1G exerts crucial role in regulating of cell proliferation and migration of gastric cancer, providing new insights for MT1G-related pathogenesis and a basis for developing new strategies for treatment of GC.
DOI: 10.6084/m9.figshare.20018090.v1
title: Role of N6-methyl-adenosine modification in mammalian embryonic development

description: Abstract N6-methyl-adenosine (m6A) methylation is one of the most common and abundant modifications of RNA molecules in eukaryotes. Although various biological roles of m6A methylation have been elucidated, its role in embryonic development is still unclear. In this review, we focused on the function and expression patterns of m6A-related genes in mammalian embryonic development and the role of m6A modification in the embryonic epigenetic reprogramming process. The modification of m6A is regulated by the combined activities of methyltransferases, demethylases, and m6A-binding proteins. m6A-related genes act synergistically to form a dynamic, reversible m6A pattern, which exists in several physiological processes in various stages of embryonic development. The lack of one of these enzymes affects embryonic m6A levels, leading to abnormal embryonic development and even death. Moreover, m6A is a positive regulator of reprogramming to pluripotency and can affect embryo reprogramming by affecting activation of the maternal-to-zygotic transition. In conclusion, m6A is involved in the regulation of gene expression during embryonic development and the metabolic processes of RNA and plays an important role in the epigenetic modification of embryos.
DOI: 10.6084/m9.figshare.20018097
title: The complete plastid genome of Cotinus coggygria and phylogenetic analysis of the Anacardiaceae

description: Abstract Cotinus coggygria Scop. (Anacardiaceae) is an important ornamental tree with beautiful characteristics that is grown in China. In this study, the complete plastid genome of C. coggygria was sequenced and assembled. This genome was 158,843 bp in size and presented a typical tetrad structure, consisting of a large single-copy region (87,121 bp), a pair of inverted repeat regions (26,829 bp), and a small single-copy region (18,064 bp). A total of 134 genes were annotated, including 88 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We observed a deletion that caused the loss of the rpl32 gene, and a small expansion of IR regions resulted in the trnH gene accessing IR regions; two copies were obtained. Phylogenetic analysis showed that C. coggygria was most closely related to Pistacia, with 100% bootstrap support within Anacardiaceae. In this study, we report the plastid genome of Cotinus species for the first time, which provides insight into the evolution of the plastid genome in Anacardiaceae and promotes the understanding of Cotinus plants.
DOI: 10.6084/m9.figshare.20018117
title: Chloroplast genome characteristics and phylogenetic analysis of the medicinal plant Blumea balsamifera (L.) DC

description: Abstract Blumea balsamifera (L.) DC., a medicinal plant with high economic value in the Asteraceae family, is widely distributed in China and Southeast Asia. However, studies on the population structure or phylogenetic relationships with other related species are rare owing to the lack of genome information. In this study, through high-throughput sequencing, we found that the chloroplast genome of B. balsamifera was 151,170 bp in length, with a pair of inverted repeat regions (IRa and IRb) comprising 24,982 bp, a large single-copy (LSC) region comprising 82,740 bp, and a small single-copy (SSC) region comprising 18,466 bp. A total of 130 genes were identified in the chloroplast genome of B. balsamifera, including 85 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes; furthermore, sequence analysis identified 53 simple sequence repeats. Whole chloroplast genome comparison indicated that the inverted regions (IR) were more conserved than large single-copy and SSC regions. Phylogenetic analysis showed that B. balsamifera is closely related to Pluchea indica. Conclusively, the chloroplast genome of B. balsamifera was helpful for species identification and analysis of the genetic diversity and evolution in the genus Blumea and family Asteraceae.
DOI: 10.6084/m9.figshare.20018097.v1
title: The complete plastid genome of Cotinus coggygria and phylogenetic analysis of the Anacardiaceae

description: Abstract Cotinus coggygria Scop. (Anacardiaceae) is an important ornamental tree with beautiful characteristics that is grown in China. In this study, the complete plastid genome of C. coggygria was sequenced and assembled. This genome was 158,843 bp in size and presented a typical tetrad structure, consisting of a large single-copy region (87,121 bp), a pair of inverted repeat regions (26,829 bp), and a small single-copy region (18,064 bp). A total of 134 genes were annotated, including 88 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We observed a deletion that caused the loss of the rpl32 gene, and a small expansion of IR regions resulted in the trnH gene accessing IR regions; two copies were obtained. Phylogenetic analysis showed that C. coggygria was most closely related to Pistacia, with 100% bootstrap support within Anacardiaceae. In this study, we report the plastid genome of Cotinus species for the first time, which provides insight into the evolution of the plastid genome in Anacardiaceae and promotes the understanding of Cotinus plants.
DOI: 10.6084/m9.figshare.16864790.v1
title: Additional file 1 of Development of whole-cell catalyst system for sulfide biotreatment based on the engineered haloalkaliphilic bacterium

description: Additional file 1: Table S1. Reference sequences of different types of Sqr and FCSD used for evolutionary analysis. Table S2. Sequence data of 484 Sqrs and FCSDs used in the evolutionary tree. Table S3. Results of mass spectrometry.
DOI: 10.6084/m9.figshare.5862360.v1
title: Total flavonoids from Ampelopsis megalophylla suppress proliferation of vascular smooth muscle cells in vivo and in vitro

description: ABSTRACT Various benefits of flavonoids for ameliorating cardiovascular diseases have been demonstrated. However, the lowering effects on blood pressure caused by antiproliferative potentials of flavonoids in vascular smooth muscle cells are rare. In this study, the antihypertensive effects of total flavonoids from Ampelopsis megalophylla were investigated. The dynamic pressure values and the rate of media thickness versus lumen diameter were measured by the tail-cuff system and H&E staining in vivo, respectively. The mRNA expressions of ACE, Ang II, eNOS, c-Myc, cyclin D1 and p27Kip1 in thoracic aorta or A7r5 cells were measured by qPCR, respectively. The protein expressions of c-Myc, Cyclin D1, p27Kip1 and β-catenin in tissues or A7r5 cells were measured by Western blot assay. Total flavonoids of A. megalophylla (TFAM) reduced the expressions of ACE and Ang II, and elevated the content of eNOS in thoracic aorta cells of SHRs. Furthermore, TFAM decreased the mRNA and protein expressions of c-Myc and cyclin D1 by repressing the Wnt/β-catenin-mediated TCF/LEF transcriptional activation both in vivo and in vitro, which is synergetic with the up-regulation of p27Kip1 expression. Our study provided evidence for developing flavonoids from A. megalophylla as herbal supplements to prevent against cardiovascular diseases by suppressing vascular remodeling.
DOI: 10.6084/m9.figshare.20018124.v1
title: Overexpression of RAPGEF3 enhances the therapeutic effect of dezocine in treatment of neuropathic pain

description: Abstract Pain is a significant problem worldwide that affects the quality of life of patients. Dezocine is a non-addictive analgesic drug with kappa-opioid antagonist activity and has been successfully used to alleviate of postoperative pain. In addition, dezocine has an analgesic effect similar to that of morphine, alleviating moderate to severe pain. Rap guanine nucleotide exchange factor 3 (RAPGEF3) is a guanine nucleotide exchange factor for GTPases Rap1 and Rap2, which could enhance the activity of Rap1 to promote cell adhesion and axon regeneration, as well as promote neurite extension by interacting with nerve growth factors. Here, we first observed that overexpression of RAPGEF3 increased cell viability, as shown by a CCK-8 assay, and recovered brain function in rats. The expression of inflammation-related factors at the mRNA level was detected using qPCR, and the concentration of these factors in a cultured cell medium and rat serum samples were decreased as shown by ELISA after RAPGEF3 overexpression. Through western blotting, we further found that pro-inflammatory proteins were decreased, and these effects might be mediated by inhibition of the Ras/p-38 MAPK signaling pathway. Taken together, we speculated that RAPGEF3overexpression enhances the therapeutic effect of dezocine on neuropathic pain by inhibiting the inflammatory response through inhibition of the Ras/p-38 MAPK signaling pathway.
DOI: 10.25549/usctheses-ouc11364225
title: 00001.tif
DOI: 10.6084/m9.figshare.23691982
title: Genetically modified soybean lines exhibit less transcriptomic variation compared to natural varieties

description: Genetically modified (GM) soybeans provide a huge amount of food for human consumption and animal feed. However, the possibility of unexpected effects of transgenesis has increased food safety concerns. High-throughput sequencing profiling provides a potential approach to directly evaluate unintended effects caused by foreign genes. In this study, we performed transcriptomic analyses to evaluate differentially expressed genes (DEGs) in individual soybean tissues, including cotyledon (C), germ (G), hypocotyl (H), and radicle (R), instead of using the whole seed, from four GM and three non-GM soybean lines. A total of 3,351 DEGs were identified among the three non-GM soybean lines. When the GM lines were compared with their non-GM parents, 1,836 to 4,551 DEGs were identified. Furthermore, Gene Ontology (GO) analysis of the DEGs showed more abundant categories of GO items (199) among non-GM lines than between GM lines and the non-GM natural varieties (166). Results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most KEGG pathways were the same for the two types of comparisons. The study successfully employed RNA sequencing to assess the differences in gene expression among four tissues of seven soybean varieties, and the results suggest that transgenes do not induce massive transcriptomic alterations in transgenic soybeans compared with those that exist among natural varieties. This work offers empirical evidence to investigate the genomic-level disparities induced by genetic modification in soybeans, specifically focusing on seed tissues.
DOI: 10.6084/m9.figshare.23691982.v1
title: Genetically modified soybean lines exhibit less transcriptomic variation compared to natural varieties

description: Genetically modified (GM) soybeans provide a huge amount of food for human consumption and animal feed. However, the possibility of unexpected effects of transgenesis has increased food safety concerns. High-throughput sequencing profiling provides a potential approach to directly evaluate unintended effects caused by foreign genes. In this study, we performed transcriptomic analyses to evaluate differentially expressed genes (DEGs) in individual soybean tissues, including cotyledon (C), germ (G), hypocotyl (H), and radicle (R), instead of using the whole seed, from four GM and three non-GM soybean lines. A total of 3,351 DEGs were identified among the three non-GM soybean lines. When the GM lines were compared with their non-GM parents, 1,836 to 4,551 DEGs were identified. Furthermore, Gene Ontology (GO) analysis of the DEGs showed more abundant categories of GO items (199) among non-GM lines than between GM lines and the non-GM natural varieties (166). Results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most KEGG pathways were the same for the two types of comparisons. The study successfully employed RNA sequencing to assess the differences in gene expression among four tissues of seven soybean varieties, and the results suggest that transgenes do not induce massive transcriptomic alterations in transgenic soybeans compared with those that exist among natural varieties. This work offers empirical evidence to investigate the genomic-level disparities induced by genetic modification in soybeans, specifically focusing on seed tissues.
DOI: 10.6084/m9.figshare.22643428
title: Comprehensive information of all identified lipid metabolites.

description: Comprehensive information of all identified lipid metabolites.
DOI: 10.6084/m9.figshare.19497809
title: Accounting for the aircraft emissions of China's domestic routes during 2014-2019

description: The CCD and LTO emissions of each route and airline for the six pollutions are shown in Supplementary Tables S1-S6. The emission intensities of the six pollutions of each aircraft type can be found in Supplementary Tables S7-S12.
DOI: 10.6084/m9.figshare.19497809.v1
title: Accounting for the aircraft emissions of China's domestic routes during 2014-2019

description: The CCD and LTO emissions of each route and airline for the six pollutions are shown in Supplementary Tables S1-S6. The emission intensities of the six pollutions of each aircraft type can be found in Supplementary Tables S7-S12.
DOI: 10.6084/m9.figshare.13206354
title: Bioinformatic prediction reveals posttranscriptional regulation of the chromosomal replication initiator gene <i>dnaA</i> by the attenuator sRNA rnTrpL in <i>Escherichia coli</i>

description: DnaA is the initiator protein of chromosome replication, but the regulation of its homoeostasis in enterobacteria is not well understood. The DnaA level remains stable at different growth rates, suggesting a link between metabolism and <i>dnaA</i> expression. In a bioinformatic prediction, which we made to unravel targets of the sRNA rnTrpL in <i>Enterobacteriaceae</i>, the <i>dnaA</i> mRNA was the most conserved target candidate. The sRNA rnTrpL is derived from the transcription attenuator of the tryptophan biosynthesis operon. In <i>Escherichia coli</i>, its level is higher in minimal than in rich medium due to derepressed transcription without external tryptophan supply. Overexpression and deletion of the rnTrpL gene decreased and increased, respectively, the levels of <i>dnaA</i> mRNA. The decrease of the <i>dnaA</i> mRNA level upon rnTrpL overproduction was dependent on <i>hfq</i> and <i>rne</i>. Base pairing between rnTrpL and <i>dnaA</i> mRNA <i>in vivo</i> was validated. In minimal medium, the <i>oriC</i> level was increased in the <i>ΔtrpL</i> mutant, in line with the expected DnaA overproduction and increased initiation of chromosome replication. In line with this, chromosomal rnTrpL mutation abolishing the interaction with <i>dnaA</i> increased both the <i>dnaA</i> mRNA and the <i>oriC</i> level. Moreover, upon addition of tryptophan to minimal medium cultures, the <i>oriC</i> level in the wild type was increased. Thus, rnTrpL is a base-pairing sRNA that posttranscriptionally regulates <i>dnaA</i> in <i>E. coli</i>. Furthermore, our data suggest that rnTrpL contributes to the DnaA homoeostasis in dependence on the nutrient availability, which is represented by the tryptophan level in the cell.
DOI: 10.6084/m9.figshare.12153801
title: Additional file 1 of Correlation between gene polymorphism in angiotensin II type 1 receptor and type 2 diabetes mellitus complicated by hypertension in a population of Inner Mongolia

description: Additional file 1. The questionnaire of diabetes with hypertension and diabetes.
DOI: 10.6084/m9.figshare.22639630
title: Additional file 2 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 2: Figure S1. Differential expression of CENPO. (A) Gene transcript exon expression of CENPO and (B) isoform expression of CENPO in the GTEx database. (C) Single-tissue eQTL of CENPO tissue specific expression. (D) Single cell expression of CENPO. Figure S2. The diagnostic value of CENPO in pan-cancer. (A) The expression of CENPO in the Sangerbox database. (B) The ROC curves of CENPO in ACC, BLCA, BRCA, CESC, CHOL, ESCA, GBM, HNSC, KICH, UCEC, KIRP, LGG, LIHC, LUAD, LUSC, and OV. Figure S3. The prognosis value of CENPO in pan-cancer. (A) Kaplan–Meier analysis of the association between CENPO expression and overall survival (OS). (B) Kaplan–Meier analysis of the association between CENPO expression and disease-free survival (DFS). Figure S4. The association between CENPO expression and immune cell infiltration, including T-cell NK cells, CD8 + T cells, Tregs, B cells, Myeloid dendritic cells, Monocytes and Macrophage M2. Figure S5. The correlation between CENPO expression and major histocompatibility complexes (MHCs) in the TISIDB database. (A) The expression of CENPO is negatively associated with most MHCs in pan-cancer. (B) The expression of CENPO is negatively associated with most chemokine receptors in LUAD. Figure S6. (A) The mutation annotation format (MAF) summary plots of CENPO in the CENPOhigh group and CENPOlow group. (B) OS, DFS, DSS, and PFS analysis stratified by CENPO mutation status in bladder urothelial carcinoma (BLCA). Figure S7. CENPO is decreased in shRNA mediated knockdown of A549 and HCI-H1299 cells. The specificity and validity of the lentivirus-mediated shRNA knockdown of CENPO in A549 and HCI-H1299 cells was measured by RT-qPCR (A) and Western blot (B). The protein blot images are cropped.
DOI: 10.6084/m9.figshare.22639639.v1
title: Additional file 5 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 5: Table S3. The relationship between CENPO expression and 22 immune cells in multiple types of cancers.
DOI: 10.6084/m9.figshare.22639639
title: Additional file 5 of Pan-cancer landscape of CENPO and its underlying mechanism in LUAD

description: Additional file 5: Table S3. The relationship between CENPO expression and 22 immune cells in multiple types of cancers.
DOI: 10.6084/m9.figshare.20018090
title: Role of N6-methyl-adenosine modification in mammalian embryonic development

description: Abstract N6-methyl-adenosine (m6A) methylation is one of the most common and abundant modifications of RNA molecules in eukaryotes. Although various biological roles of m6A methylation have been elucidated, its role in embryonic development is still unclear. In this review, we focused on the function and expression patterns of m6A-related genes in mammalian embryonic development and the role of m6A modification in the embryonic epigenetic reprogramming process. The modification of m6A is regulated by the combined activities of methyltransferases, demethylases, and m6A-binding proteins. m6A-related genes act synergistically to form a dynamic, reversible m6A pattern, which exists in several physiological processes in various stages of embryonic development. The lack of one of these enzymes affects embryonic m6A levels, leading to abnormal embryonic development and even death. Moreover, m6A is a positive regulator of reprogramming to pluripotency and can affect embryo reprogramming by affecting activation of the maternal-to-zygotic transition. In conclusion, m6A is involved in the regulation of gene expression during embryonic development and the metabolic processes of RNA and plays an important role in the epigenetic modification of embryos.