Search

Single-cell RNA sequencing technology takes a single cell as research object, counts and analyzes the gene expression level of each transcript and heterogeneity between cells. This technology makes up for the defects of traditional sequencing technology to some extent. Autoimmune disease is the damage or dysfunction of autotissue cells caused by autoimmune tolerance or abnormal regulation of autoimmunity cells. In this paper, the research results on application of single-cell RNA sequencing technology in autoimmune disease in recent years are reviewed, which provides valuable clues for early realization of precise medical treatment. [ABSTRACT FROM AUTHOR]

RNA-Seq (RNA sequencing) and qRT-PCR (Quantitative Real-time PCR) were utilized to elucidate the molecular mechanisms involved in suberin biosynthesis in the roots of Bruguiear gymnorrhiza in response to salt stress. A total of 36561 DEGs (differentially expressed genes) were identified, including 36351 upregulated genes and 210 downregulated genes. GO (Gene Ontology) annotation showed that these DEGs were primarily associated with cell nitrogen compound metabolism, cell and cell composition, and structural molecule activity. KEGG(Kyoto Encyclopedia of Genes and Genomes) metabolic pathway annotation indicated that the differentially expressed genes were significantly enriched in ribosomes and oxidative phosphorylation. We also observed significant enrichment in tropane, piperidine, and polyketide alkaloid biosynthesis pathways. Furthermore, 39 genes related to suberinization, such as monomer synthesis, transmembrane transport and polymerization, were also identified. Nevertheless, qRT-PCR results also showed that long chain acyl-CoA synthetase 1 (LACS1), glutathione S-transferase (GST) and the Myb superfamily (MYB) were upregulated under salt stress. This study provides fundamental insights into the mechanism of salt tolerance associated with suberinization and may have significant implications for mangrove protection and restoration. [ABSTRACT FROM AUTHOR]

The Ehlers-Danlos syndromes (EDS) are a group of rare hereditary connective tissue disorders characterized by joint hypermobility, skin hyperextensibility, and tissue fragility. The clinical and genetic hetero- geneity of EDS frequently leads to underdiagnosis and misdiagnosis. Genetic testing is an essential approach to clarify the underlying diagnosis. Recent research has preliminarily established genotype-phenotype correlations and introduced the novel concept of " disease spectrum" in some subtypes. These studies deepen our understanding of EDS etiology and provide important insights into clinical management. Published in 2023, the Chinese Guidelines for Diagnosis and Treatment of the Ehlers-Danlos Syndromes(the Guidelines) recommend performing genetic testing with deep phenotyping for patients who meet the clinical diagnostic criteria or are suspected of having EDS. However, it should be noted that the clinical diagnosis might differ from the molecular diagnosis. Furthermore, cutting-edge approaches such as periodic data reanalysis, integration of RNA sequencing into family-based whole-genome sequencing, and third-generation sequencing may facilitate the reclassification of variants of uncertain significance or resolve undiagnosed cases. This article summarizes recent progress in the genetics research of EDS, with the hope of offering a valuable resource for clinical diagnosis, treatment and scientific research to optimize the quality of life of patients with EDS.

Copyright of West China Journal of Stomatology is the property of Sichuan University, West China College of Stomatology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of West China Journal of Stomatology is the property of Sichuan University, West China College of Stomatology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In order to reveal the etiolation mechanism of gold-coloured mutant leaves of Quercus gilva, a naturally-occurring leaf-color mutant was used as experimental materials, and the metabolome and transcriptome of mutant leaves and normal green leaves were analyzed by ultra-high performance liquid chromatography-Q(UHPLC-Q)Exactive HF-X and high-throughput RNA sequencing, respectively. The results were as follows: (1) A total of 257 and 357 significantly changed metabolites (SCMs) were respectively identified under the positive ion(POS)mode and the negative ion(NEG)mode. Compared with green leaves, the content of some flavonoids such as quercetin, leucocyanidin, myricetin and their glucoside derivatives(pyranodelphinin A, isorhamnetin 3-glucuronide, etc. )increased significantly in mutant leaves, but the content of chlorophyll a, chlorophyll b, and carotenoids decreased significantly. (2) A total of 4 146 differentially expressed genes(DEGs)were detected, of which 1 711 were up-regulated and 2 435 were down-regulated. (3) KEGG enrichment analysis showed that SCMs and DEGs were mainly enriched in photosynthesis, porphyrin and chlorophyll metabolism, and flavonoid biosynthesis. In conclusion, the inhibition of chlorophyll synthesis, chloroplast developmental abnormalities and promotion of flavonoid synthesis were the main factors driving the leaf etiolation in the mutant Q. gilva. In addition, the genes of the MYB and bHLH families were significantly up-regulated in mutant leaves, confirming these two types of transcription factors were involved in regulating flavonoid biosynthesis. This study provides new molecular insights for the phenomenon of leaf etiolation, and also provides the reference for exploring leaf color-related functional genes and breeding of landscape plant. [ABSTRACT FROM AUTHOR]

Background and purpose: Colorectal carcinoma (CRC) is a common malignant tumor with incidence and mortality rates second only to gastric cancer and esophageal cancer among digestive system malignancies. Increasing evidence suggests that immune cells play a significant role in the occurrence and development of CRC. The aim of this study was to construct a prognostic model related to immune cell-associated genes to predict the prognosis of CRC patients and enable precise management. Methods: Single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) data, along with clinical information for colorectal cancer, were downloaded from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Differential genes of immune cell subtypes were extracted, and genes related to prognosis were screened in TCGA data using Cox regression and LASSO regression, with external validation using GSE39582 and GSE41258. The prognostic model was used to analyze chemotherapy drug sensitivity, assess immunotherapy efficacy, analyze pathways related to risk scores, and perform clinical correlation analysis. Finally, the expression levels of model genes were validated in 10 fresh frozen CRC tissues with post-operative pathological examination and cell lines using real-time fluorescence quantitative polymerase chain reaction (RTFQ-PCR) and immunohistochemistry. All samples were approved by the Fudan University Shanghai Cancer Center Ethics Committee (No. 050432-4-2108*). Results: We defined 16 cell clusters based on the scRNA-seq dataset (GSE161277) and labeled these clusters as different cell types using the R package celldex. Differential analysis of immune cell subtypes yielded 374 differentially expressed genes. Using univariate Cox and LASSO analyses, we constructed a 9-gene risk prognostic model in CRC. This risk model exhibited reliable prognostic prediction performance and played an important role in predicting anti-tumor drug sensitivity, immunotherapy efficacy, potential molecular mechanisms, and clinical characteristics. Patients with high-risk scores had a lower probability of benefiting from immunotherapy. Conclusion: We constructed a 9-gene risk prognostic model based on the heterogeneity of immune cells in the CRC tumor microenvironment, which predicted the survival and treatment outcomes of CRC patients. [ABSTRACT FROM AUTHOR]

To explore whether sirtuin2 (SIRT2) regulates retinoic acid (RA) -induced neural tube defects (NTDs) at the cellular level and in animal models through WNT pathway based on the transcriptomics results of human embryonic kidney cell (HEK293) model with SIRT2 gene knockout. SIRT2 knockdown group (KO-SIRT2) and SIRT2 control group (KO-Con) were cultured and total RNA was extracted. RNA-seq technology was used to analyze the transcriptomics of the two groups of cells. Search for differentially expressed genes (P<0.05, | log2FoldChange |≥ 1). GO (Gene Ontology) and KEGG （Kyoto Encyclopedia of Genes and Genomes）analysis were conducted. HEK293 cells in KO-SIRT2 group and KO-Con group were induced by RA and the level of key signaling pathway protein (WNT5B) was detected by Western Blot (WB). A mouse model of NTDs induced by RA was established and the level of Sirt2 and Wnt5b proteins of brain tissues in E10.5 fetal mice was detected by immunohistochemical staining (IHC). Compared with KO-Con group, 209 differentially expressed genes (107 up-regulated and 102 down-regulated) were significantly changed in KO-SIRT2 group. Enrichment analysis involved multiple signaling pathways such as WNT, Hippo and PI3K-Akt. After SIRT2 knockout, the WNT5B protein was up-regulated in the KO-SIRT2 group. After RA induction, the level of WNT5B in KO-Con group was increased. IHC showed increased levels of Sirt2 and Wnt5b proteins in the RA-induced NTDs model. SIRT2 gene can affect embryonic development by regulating the translation of WNT pathway genes. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Harbin University of Science & Technology is the property of Journal of Harbin University of Science & Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Pulmonary infection by pathogenic microorganisms is a common disease of the respiratory system with high mortality and poor prognosis, but its pathogenesis remains unclear. In recent years, single-cell RNA sequencing （scRNA-seq） has been widely used in the study of lung infection to provide an atlas of immune cells of patients, identify new immune cell subsets, analyze differential expression genes, reveal pathways related to inflammatory immune pathways in pathogenic microbial infection, monitor the levels of cytokines, and identify novel biomarkers of lung infection. Therefore, this paper presents a review of the application of scRNA-seq in pulmonary infection by pathogenic microorganisms. [ABSTRACT FROM AUTHOR]

Objective: As a special class of non-coding RNAs, circular RNAs (circRNAs) have been frequently reported to participate in the evolution and progress of malignant tumors by encoding polypeptides. However, its functions in hepatocellular carcinoma (HCC) are rarely addressed in previous research. Based on the RNA-seq and online data, our study investigated the expression pattern and coding potential of circRNAs in HCC. Methods: The circRNA sequencing procedure was performed on three pairs of HCC and adjacent tissues using a Novaseq 6 000 PE150 high-throughput sequencer. Bioinformatics analysis was conducted to identify circRNAs that expressed differentially and reveal the sequence characteristics of these circRNAs. GO, KEGG, and Reactome studies were performed to analyze the functions and pathway enrichment of the identified circRNAs. Translatable circRNAs were screened through online databases such as Transcirc and Ribocirc. The IRES finder, ORF finder, and m6A SRAMP were used to predict IRES elements, ORF sequences, and m6A sites, respectively. The coding potential was evaluated following the CPAT method. The expression of differentially expressed circRNA was detected by qPCR. Results: A total of 416 circRNAs were found to be relatively abundant, of which 35 were up-regulated and 31 were down-regulated circRNAs (P<0.05 for all the circRNAs). Sequence analysis suggested that the majority of these circRNAs are of a small molecular weight (length<1 000 nt) and the exon-exon type that contains 2-5 exons. GO analysis showed that differentially expressed circRNAs were enriched in the regulation of GTPase activity (P<0.001), the regulation of small GTPase mediated signal transduction (P<0.001), and the positive regulation of GTPase activity (P<0.001) in the biological process; the nuclear speck (P=0.016) in the cellular component; the GTPase regulator activity (P<0.001), and the GTPase activator activity (P<0.001) in the molecular function, respectively. KEGG analysis indicated that the circRNAs were mainly enriched in the complement and coagulation cascades (P=0.002), the mRNA surveillance pathway (P=0.003), and the platelet activation (P=0.005), while Reactome analysis revealed that the RHO GTPase cycle (P=0.008), the RAC1 GTPase cycle (P<0.001), and the CDC42 GTPase cycle (P=0.001) were the main pathway columns where enrichment of the studied circRNAs appeared. Furthermore, a total of 17 circRNAs were obtained from the intersection of Transcirc and Ribocirc databases, of which 11 genes (hsa_circ_0000231, hsa_circ_0000417, hsa_circ_ 0000745, hsa_circ_0005455, hsa_circ_0000847, hsa_circ_0005552, hsa_circ_0060849, hsa_circ_0008234, hsa_circ_0075796, hsa_circ_0001742, and hsa_circ_0001686) had the most significant coding potential scores greater than 0.9. At the same time, we used qPCR to verify 10 cases of liver cancer and adjacent tissues, suggesting: hsa_circ_0000231, hsa_circ_0000745, hsa_circ_ 0005552, and hsa_circ_0000847 are highly expressed in liver cancer tissue, while hsa_circ_0060849 and hsa_circ_0008234 are low expressed,the difference was significant (P<0.05). Conclusion: We comprehensively analyzed the expression patterns of cicRNA in liver cancer, and found that 6 Circrnas with differential expression and high translation potential score were worthy of further study. [ABSTRACT FROM AUTHOR]

Objective We aimed to (i) compare the effects of renshen (ginseng) and huangqi (milkvetch root) on different cancer cells and (ii) elucidate the molecular mechanisms underlying the similarities and differences in their medicinal properties. Methods The effects of ginseng standard extract (RSE75) and milkvetch root standard extract (HQE75) on the proliferative activity of different cancer cells(Hep G2, H22, H1299, A549, EC109, and AKR) were determined by the CCK-8 assay. The effects of RSE75 and HQE75 on the mRNA expression levels of immune factors IL-6, TNF-α, and TGF-β and the balance between DNA methyltransferases (DNMTs) and TET2 in A549 cells were determined by RT-qPCR. The effects of RSE75 and HQE75 on the clonal formation rate, apoptosis, and the cell cycle of A549 cells were detected by a clonal formation assay, Annexin V-FITC/PI staining, and flow cytometry, respectively. The potential targets and pathways of RSE75 and HQE75 in the treatment of lung cancer were explored by RNA sequencing technology. Results Compared with the blank group, the survival rate of cancer cells in the RSE75 group was decreased, but there was no significant change in the HQE75 group. The mRNA expression levels of IL-6, TNF-α, and TGF-β were decreased in the RSE75 and HQE75 groups. RSE75 inhibited the clonal formation of A549 cells in a concentration-dependent manner, while HQE75 had no obvious inhibitory effect. Both RSE75 and HQE75 significantly induced apoptosis in A549 cells and blocked DNA replication in the G1/S phase. At the same concentration, RSE75 has a stronger effect on inducing apoptosis than HQE75. The mRNA expression level of DNMTs in the RSE75 group was decreased, the mRNA expression level of TET2 in the RSE75 group was increased, and the mRNA expression level of both DNMTs and TET2 was decreased in the HQE75 group. The RNA sequencing result showed that RSE75 and HQE75 had common targets, including CXCL8, CXCL1, ICAM1, and CCL2. The common pathways of action mainly included the IL-17 signaling pathway, the NF-κB signaling pathway, and the TNF signaling pathway, and most of them were involved in immune regulation. The main difference is that renshen can inhibit the proliferation of cancer cells through the HIF-1 signaling pathway through VEGFA, EGR1, and other targets, while huangqi can regulate amino acid metabolism and the NOD-like receptor signaling pathway through IL-6, TNF, and other targets. Conclusion Studies on the anti-cancer effects and the underlying molecular mechanisms have shown that renshen and huangqi have obvious immunomodulatory effects, but renshen also had significant inhibitory effects on cancer cell proliferation. Renshen could regulate the DNMTs/TET2 balance, while huangqi could inhibit the expression of DNMTs. This study elucidated the different properties of renshen and huangqi the molecular level and provides not only a scientific basis for clinical application of renshen and huangqi, which are both qi-tonifying medicinals, but also ideas for the study of the molecular mechanisms underlying the effects of other TCMs. [ABSTRACT FROM AUTHOR]

BACKGROUND: Astrocytes are the most abundant cells in the central nervous system, and various subsets of astrocytes are heterogeneous, performing a variety of special functions. Single-cell RNA sequencing (scRNA-seq) technology developed in recent years has extended our understanding of astrocyte heterogeneity from the perspective of transcriptome profiling. OBJECTIVE: To summarize the heterogeneity of scRNA-seq technology in different time and space, and pathological states and expand our knowledge of astrocyte heterogeneity on both molecular and functional levels. METHODS: The relevant articles on astrocyte heterogeneity and scRNA-seq were searched on PubMed, Elsevier, and CNKI databases. The search terms were “astrocytes, scRNA-seq, heterogeneity, Alzheimer disease, spinal cord injury, multiple sclerosis” in Chinese and English. Finally, 74 articles were selected for viewing after screening according to inclusion criteria. RESULTS AND CONCLUSION: scRNA-seq studies related to the heterogeneity of astrocytes have shown that astrocyte is significantly heterogeneous across four aspects: species, developmental stage, central nervous system region, and pathological state. (1) Unique expression of certain genes occurs in astrocytes of different species, and the discovery of species-specific genes is beneficial for the translation of clinical studies. (2) During astrocyte development, differential gene expression emerged in the cellular subtypes identified at each stage, which further refined the cellular lineage of astrocytes and laid the foundation for the study of astrocyte developmental trajectories and mechanisms. (3) The discovery of differential gene expression allows regional localization of different astrocyte subpopulations and assists in the diagnosis and treatment of neurological diseases. (4) Astrocyte heterogeneity revealed by scRNA-seq can provide specific markers at the time of disease diagnosis and identify potential therapeutic targets. (5) The heterogeneity of astrocytes exists in many aspects, interacts with each other and is complex. The mechanisms of its generation, maintenance and transformation remain unclear. At present, molecular research on the single-cell level is still lacking. Linking transcriptionally defined astrocyte subpopulations to cellular activity, behavior and disease markers in real time remains one of the great challenges in the field. [ABSTRACT FROM AUTHOR]

BACKGROUND: Intervertebral disc degeneration is clinically considered to be the main cause of low back pain, but due to the unclear pathogenesis of intervertebral disc degeneration, there is still a lack of effective means to delay the progression of the disease. Single-cell RNA sequencing technology can amplify and sequence mRNA at the single-cell level, reveal the gene expression intensity of a single cell, discover different cell subsets in tissues according to the heterogeneity of cells, study the pathogenesis of intervertebral disc degeneration at the molecular level, and provide a new theoretical basis for its early diagnosis and treatment. OBJECTIVE: To introduce the basic principles of single-cell RNA sequencing technology and review the research progress of single-cell RNA sequencing technology in intervertebral disc degeneration in recent years. METHODS: A computer was used to search PubMed, Web of Science, CNKI and WanFang databases for the literature published from 2012 to 2022. Key words were “single-cell RNA sequencing, intervertebral disc degeneration, sequencing Technology” in Chinese and English. Duplicate, poor-quality and irrelevant articles were excluded; a total of 70 articles were eventually included. RESULTS AND CONCLUSION: (1) We identified new cell subsets such as homeostatic chondrocytes, hypertrophy chondrocyte-like nucleus pulposus cells and fibrous nucleus pulposus cells, identified the marker genes and transcription factors of these cell subsets, and described the functions, differentiation paths and cell fate of these cell subsets during the development and progression of intervertebral disc degeneration, and proposed the concept of progenitor nucleus pulposus cells. A cell subpopulation with progenitor nucleus pulposus cells properties was identified and its effectiveness in treating intervertebral disc degeneration was verified in mice. (2) Fibro chondrocyte-like annulus fibrosus cells and annulus fibrosus stem cells with both cartilage and fiber properties were identified, and a new type of composite hydrogel was prepared by combining fibrous cartilage inducers silk fibroin and hyaluronic acid in vitro. Experiments in mice demonstrated that this hydrogel could repair both annulus fibrosus tissue and cartilage matrix, and was remarkably effective in the treatment of intervertebral disc degeneration. (3) Regulatory chondrocytes were found in endplate cartilage. Two distinct fates in the progression of intervertebral disc degeneration were analyzed and the differential genes in the two fates were identified. Intercellular communication analysis indicated that regulatory chondrocytes interact with endothelial cells to promote angiogenesis. (4) Immune cells such as macrophages, T cells, myeloid progenitor cells and neutrophils were identified in the degenerated intervertebral disc tissues, demonstrating the existence of immune response during intervertebral disc degeneration. It was found that apolipoprotein induced the polarization of macrophages M1 and M2 subtypes, and this polarization process affected the activity of progenitor nucleus pulposus cells by amplifying the inflammatory response through the MIF signaling pathway. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Sichuan University (Medical Science Edition) is the property of Editorial Board of Journal of Sichuan University (Medical Sciences) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Arsenic exposure-induced cognitive disorders have attracted much attention from scientists. This study employed RNA sequencing to investigate the potential molecular mechanisms underlying neurobehavioral alterations in mice due to arsenic exposure at a transcriptomic level. Male C57BL/6 mice were divided into four groups, the control group (group C), low-dose group (group L), medium-dose group (group M) and high-dose group (group H), which drank deionized water containing 0, 0.15, 1.5 and 15 mg·L-1 AS2O3 respectively for 12 weeks. Cognitive function of the mice was analyzed by the novel object recognition test. RNA sequencing followed by GO enrichment analysis and KEGG pathway enrichment analysis identified differentially expressed genes (DEGs) between control and high dose groups. qRT-PCR was conducted to verify the gene expression levels of target genes. A protein-protein interaction network (PPI) was constructed to identify hub genes from the gene module with the highest connection degree. The findings indicated a significant decrease in both exploration and discrimination indices for arsenic-exposed groups compared to controls. There were 181 DEGs in the high-dose group compared with the control. A total of 217 significantly enriched GO terms were obtained including behavior, regulation of multicellular biological processes, learning and memory, cognition, etc. KEGG enrichment analysis showed that 128 DEGs were enriched in 38 pathways, including cholinergic synapses, dopamine synapses, neurotrophic factor signaling pathways, etc. 7 hub genes were screened from the gene module with the highest connection degree, which were fos, tac1, gad2, drd2, ppp1r1b, chat and drd1a. The results of gene expression levels from qRT-PCR are in good agreement with those from RNA-seq, reflecting the reliability of RNA-seq. It was observed that arsenic exposure led to a significant reduction in mice' s cognitive abilities. The identified hub genes and key pathways from this study offer valuable insights into exploring the mechanisms underlying neurobehavioral changes in mice due to arsenic exposure. [ABSTRACT FROM AUTHOR]

In this study, four different initial densities (2.7 × 103 as a control, 5.4 × 103, 1.1 × 104, and 2.2 × 104 cells/cm2) of porcine muscle stem cells were cultured for three days to explore the effect of high-density culture conditions on the fate of porcine muscle stem cells. The counting results showed that the suitable culture density of porcine muscle stem cells was 2 × 104–3 × 104 cells/cm2, and the proliferation-related protein phosphorylated extracellular signal-regulated kinase 1/2 (p-ERK1/2) was down-regulated when the initial cell density was outside this range, causing a proliferation inhibitory effect. The transcriptome sequencing results showed that 2 125 differentially expressed genes were identified between the highest density and control groups, mainly enriched in some signaling pathways such as those related to cell senescence and cell cycle and the PI3K-Akt signaling pathway. Furthermore, the expression of the stemness genes PAX7 and PAX3 and the quiescence-related gene SPRY1 was upregulated under high-density conditions. The expression of the differentiation genes MYOD, MYOG and MYH3 and the senescence genes P21, P53 and P15 was upregulated. The results of real-time PCR and Western blot assay showed that the expression of PAX7, SPRY1, MYOG, and P21 were upregulated as the cell density increased. The above results showed that porcine muscle stem cells had multiple fats such as returning to a quiescent state, differentiation and senescence under high-density conditions. The results of this study can help in understanding the mechanism of cell fate determination and provide a theoretical basis for studying the regulation of cell proliferation and differentiation under high-density condition.

Taiping Houkui green tea is mainly made from the young shoots of the sextual tea line ‘Shidacha’. In the present study, the differences in the quality and genetic evolution of green tea made from the young shoots of five ‘Shidacha’ varieties (Gaojiazao, Huangzhong, Shidacha No.2, Shidacha No.6, and Guangyangzao) and two non-‘Shidacha’ tea varieties (Fuzao No.2 and Shuchazao) were explored. The volatile and non-volatile metabolites of the seven tea samples were analyzed, and the differences in genome-wide transcriptional levels and genetic background among the seven tea varieties were analyzed using RNA sequencing (RNA-seq). No significant differences in catechin content or the total content of free amino acids were found among all tea samples except Shuchazao, whereas caffeine content differed significantly among all samples. The contents of floral aroma compounds such as linalool, linalool oxide, geraniol and jasmone were relatively high in the infusion of ‘Shidacha’ green tea. RNA sequencing results showed that the genome-wide transcriptional level of Guangyangzao was close to that of the non-‘Shidacha’ tea varieties. In principal component analysis (PCA), Guangyangzao and the other ‘Shidacha’ varieties were distributed in different quadrants. Phylogenetic analysis showed that the non-‘Shidacha’ tea varieties had a close genetic relationship with each other as well as Gaojiazao and Huangzhong, but was far away from the other ‘Shidacha’ varieties. The transcriptional levels of most of the key enzyme genes involved in the biosynthesis of linalool, indole, nerolidol and jasmone lactone were higher in the ‘Shidacha’ tea varieties than in the non-‘Shidacha’ ones. This study provides important theoretical support for the breeding of excellent ‘Shidacha’ varieties and provides a theoretical basis for follow-up research on the formation mechanism of floral aroma compounds in tea leaves.

Objective To investigate the molecular mechanism of inflammatory response in vaginal epithelial cells induced by Escherichia coli infection. Methods An inflammatory response model in vaginal epithelial cells stimulated by Escherichia coli was established. Then， differentially-expressed gene profiles between the control and Escherichia coli stimulation groups were obtained by RNA sequencing （RNA-Seq）. The enrichment signaling pathways of differentially-expressed genes were identified by bioinformatic analysis. The sequencing results were validated by quantitative fluorescent real-time PCR （RT-qPCR）. Results A total of 4899 differentially-expressed genes were found between the control and the Escherichia coli stimulation groups， including 1531 up-regulated genes and 3368 down-regulated genes. Gene Ontology （GO） showed that the functions of differentially-expressed genes were dominantly enriched in platelet-derived growth factor binding and co-receptor binding in the biological process term， endoplasmic reticulum chaperone complex in the cellular component term and protein folding in endoplasmic reticulum in the molecular functional term， respectively. Kyoto Encyclopedia of Genes and Genomes （KEGG） showed that these differentially-expressed genes were enriched in 39 signaling pathways， such as the NF-κB signaling pathway. The upregulation of differentially-expressed gene TNF-α was validated by RT-qPCR （P < 0.05）， which was consistent with the RNA-Seq results. Conclusion TNF-α regulating the NF-κB signaling pathway is a critical molecular mechanism of Escherichia coli-induced inflammatory response in vaginal epithelial cells.

BACKGROUND: After over ten years of development, single-cell RNA sequencing has mellowed and in the last three years has been progressively adopted in the study of intervertebral disc degeneration. OBJECTIVE: To overview the utilization and the progress of single-cell RNA technology within the field of intervertebral disc degeneration research during the last few years. METHODS: The first author searched PubMed, ScienceDirect, and Web of Science databases with the key words “single cell RNA sequencing, intervertebral disc degeneration, nucleus pulposus, annulus fibrosus”. The literature was screened for relevance by reading and 58 articles were included in the final analysis. RESULTS AND CONCLUSION: As an emerging technology, single-cell RNA sequencing has been widely applied to the study of tumor heterogeneity, immune microenvironment, embryonic development, neuroscience, cell differentiation and many other fields. In recent years, an increasing number of scholars have applied single-cell RNA sequencing to research intervertebral disc degeneration. These studies have helped researchers to recognize the complex heterogeneity of the nucleus pulposus and fibrous rings: the newly discovered subpopulations of nucleus pulposus can be grouped into four groups: firstly, the nucleus pulposus cells that are more prevalent in normal nucleus pulposus tissue, often named “fibrous nucleus cells”, which can polydifferentiate to maintain fibrocartilage development; secondly, the “stable nucleus pulposus cells” that are more prevalent in mildly degenerated nucleus pulposus, which are responsible for regulating the homeostatic balance of chondrocyte metabolic activity in response to environmental signals and are highly expressed in collagen-related genes and extracellular matrix. Thirdly, the “inflammatory nucleus pulposus” is found only in degenerated nucleus pulposus tissue. In this subpopulation, the regulatory activity of NF-κB family transcription factors is enhanced. The fourth is the “adherent nucleus pulposus”, which is more abundant in severely degenerated nucleus pulposus tissue and has the FN1 marker gene. The discovery of these subpopulations adds to the understanding of the rich mechanisms of differentiation and degeneration within the tissue and the changes in intervertebral disc degeneration at the transcriptomic level. PROCR+ PDGFRA+ nucleus pulposus cells, CD90+ nucleus pulposus cells and UTS2R+ nucleus pulposus cells have the strong growth and differentiation potential, and the discovery of these nucleus pulposus progenitor cells offers the possibility to explore therapeutic tools for intervertebral disc degeneration from regenerative medicine and tissue engineering perspectives in the future. [ABSTRACT FROM AUTHOR]

Aflatoxin B1 (AFB1) is widely distributed and highly hepatotoxic, which can cause oxidative damage to human liver. In this study, a rat model of acute liver injury was established by injecting AFB1 to explore the intervention effect and method of chitosan oligosaccharide (COS) with antioxidant activity on liver injury. The experiment was designed with blank group, COS control group, model group, COS intervention group, and positive control group. Consecutive gavage for 8 days, the model group, COS intervention and positive control group were injected with 1 mg/kg AFB1 only on the 6th day. The intervention effect of COS on liver injury was evaluated by serum liver function indexes, lipid peroxide content, antioxidant enzyme activity and liver tissue sections in rats, and differentially expressed genes (DEGs) were obtained by RNA sequencing (RNA-Seq) technology to analyse the intervention mode of COS. The results showed that compared with the model group, the COS intervention group significantly decreased the serum liver function indexes and lipid peroxide content, and increased the activity of antioxidant enzymes; the observation of liver slices showed that COS was beneficial to improve the liver morphology of rats. RNA-Seq data showed a total of 968 DEGs in the COS intervention group compared with the model group, and the enriched gene ontology (GO) entries were mainly related to liver metabolic function, oxidative stress response and protein synthesis. In conclusion, COS has a certain intervention effect on AFB1-induced acute liver injury, which provides a theoretical basis for COS to prevent AFB1-induced liver injury. [ABSTRACT FROM AUTHOR]

Aim To explore the correlation between protein tyrosine kinase 7 (PTK7) and coronary heart disease (CHD) and its diagnostic value. Methods Target genes were obtained through the Gene Expression Omnibus (GEO) database. StataSE15 was used to find the total standardized mean difference (SMD) of PTK7 and plot the summary receiver operating characteristic (SROC) curve. Next, reverse transcription quantitative polymerase chain reaction was used to verify the expression of PTK7 in CHD and non-CHD population samples and search for CHD-related single-cell RNA sequencing data from GEO to analyze the expression of PTK7 in different cells. The upstream transcription factor (TF) of PTK7 was predicted by the Cistrome Data Browser database. Moreover, enrichment analysis of the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on the differentially co-expressed genes. Results By calculating the SMD of PTK7, it was found that PTK7 was highly expressed in the peripheral blood leukocytes (PBL) of patients with CHD (total SMD=0. 81, 95% confidence interval=0. 17 ~1. 45). The population sample validation confirmed the above results. When SROC was plotted, the area under the curve (AUC) was 0. 79, indicating that PTK7 has the ability to distinguish between CHD and non-CHD. The single-cell RNA sequencing results showed that the expression ratio of PTK7 was relatively low in different cells of normal peripheral blood. In addition, potential upstream TFs of PTK7 were predicted through the ChIP-seq database, where it was found that IRAK1, SNAI2 may be positive upstream TFs of PTK7, and EP300, NIPBL may be negative upstream TFs of PTK7. Conclusion Highly expressed PTK7 in PBL is positively correlated with the pathogenesis of CHD, demonstrating that PTK7 has definite diagnostic value on CHD. [ABSTRACT FROM AUTHOR]

For high efficient of rapeseed production by planting late-sowing cultivars in the lower reaches of the Yangtze River, material screening and mechanism of cold tolerance were carried out using 6 approved hybrid varieties and 6 temperature treatments were set. Seed germination characteristics and physiological indicators were studied under low temperature. RNA-seq technology was used for exploring germination differences under low temperature. Results showed that germination rate decreased under low temperature. Varieties Yueyou 1301 and Yuey-ou 1510 showed obvious advantages with respect to late sowing at low temperatures (<10 °C). SOD activity were consistent with low temperature germination phenotype. Thus we identified 920 differentially-expressed genes (DGEs) that were involved in low temperature germination between Yueyou 1301 and Fengyou 737. Of these, 21 DEGs were related to abscisic acid pathway and starch-sucrose metabolism pathway. In summary, Yueyou 1301 had strong low temperature germination ability. The difference in seed germination ability at low temperature might be caused by hormone signal transduction, activation of reactive oxygen species scavenging systems, and carbohydrate metabolism homeostasis, which might explain the strong cold tolerance of Yueyou 1301. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Single cell RNA sequencing has emerged as a transformative technology to characterize complex tissues at unprecedented high resolution and answered questions that could not be addressed using traditional bulk RNA sequencing. However, the high complexity and huge data volume of single cell RNA sequencing data presents novel challenges to data analysis, one of which is how to deal with batch effects. Batch effects are technical biases that may cofound results of analyses of high throughput biological data. Meanwhile, the sources of batch effect are complex and the mitigation of batch effect is highly context-dependent. Different processing pipelines including evaluation, analysis, measurement and mitigation are performed, depending on tissue type, sequencing technology, experimental design and so on. The need to measure batch effects is more prone to be neglected in analyses of single cell data. However, measuring batch effects can help identify the source of the batch effects, their proportion of data variation explained and their impact on data analysis and the choice of methods of mitigation, enabling effective handling of the batch effects. Therefore, this review is primarily concerned with batch effects in single cell RNA data, addressing the concepts of batch effects, differences between the handlings of batch effects in single cell RNA data and bulk RNA data, methods of measuring batch effects and major challenges at present. Finally, the future advancement in batch effects measurement is discussed. [ABSTRACT FROM AUTHOR]

Protocatechuic acid (PCA) is one of the main metabolites of anthocyanins in the body and has good anti-inflammatory activity. In this study, the protective effect of oral administration of PCA at a dose of 100 mg/(kg mb·d) on high-fat diet (HFD)-induced liver inflammation in C57BL/6J mice was investigated, and the underlying mechanism was investigated by in vitro experiments. In vivo studies showed that after 12 weeks of PCA intervention, the body mass and liver fat content of HFD-fed C57BL/6J mice were significantly reduced, and so were the levels of inflammatory factors such as interleukin (IL)-1β, IL-6, tumor necrosis factor α (TNF-α) and lipopolysaccharide (LPS) in serum and liver. In vitro transcriptome sequencing (RNA-Seq) and Western blot analysis of primary hepatocytes and livers demonstrated that PCA could significantly reduce the gene and protein expression of Toll like receptor 4 (TLR4), and then down-regulate the phosphorylation of nuclear transcription factor κB (NF-κB) inhibiting the expression of inflammatory factors such as IL-6. These results suggest that PCA can effectively improve HFD-induced liver inflammation, possibly by down-regulating the TLR4/NF-κB signaling pathway.

Objective To identify key genes associated with the prognosis of oral squamous cell carcinoma (OSCC) by RNA sequencing integrated bioinformatics. Methods Carcinoma and adjacent tissues of 3 OSCC patients admitted to the Department of Oral and Maxillofacial Surgery, General Hospital of Ningxia Medical University from February to October 2019 were collected. RNA was extracted and DNA libraries were constructed, and Illumina high-throughput sequencing was performed to screen out differentially expressed genes (DEGs) by integrating the data. The biological processes, signal pathways and interaction network of DEGs were analyzed, and the visualization and module analysis of DEGs were conducted. Candidate genes were identified by survival analysis of TCGA database of the module gene with the highest score, and key genes were further screened by GSE41613 data set for survival analysis of candidate genes. The human Protein Atlas database was used to verify the protein expression of key genes in OSCC. Gene set enrichment analysis (GSEA website) was used to predict the possible signaling pathways of key genes in OSCC. Results According to the sequencing data from the three pairs of OSCC, a total of 1818 DEGs were screened out, including 824 upregulated and 994 downregulated genes. They were mainly enriched in mitotic nuclear division, extracellular regions and calcium signaling pathways. TCGA data identified three candidate genes, including ASPM, CENPF and KIF15. The survival analysis of GSE41613 data identified CENPF as the key gene of OSCC. Its expression in OSCC tissues was higher (P＜0. 05). OSCC with higher CENPF expression had worse prognosis (P＜0. 05). The protein expression of CENPF in OSCC was higher. The samples with high expression of CENPF were enriched in gene sets of multiple pathways such as basic transcription factors and cell cycle (P＜0. 05). Conclusion A total of 1 818 DEGs are screened by transcriptional sequencing, among which the prognosis is worse when CENPF is higher in OSCC, which may be related to the occurrence, development and prognosis of OSCC. [ABSTRACT FROM AUTHOR]

Copyright of Asian Journals of Ecotoxicology is the property of Gai Kan Bian Wei Hui and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Gingival mesenchymal stem cells (GMSCs) cell clusters and functional heterogeneity were analyzed through single cell RNA sequencing technology. Human GMSCs were isolated and cultured in vitro, GMSCs were sequenced by 10× scRNA-Seq platform. The cells were grouped according to the gene expression differences, and analyze the expression of surface markers and cell cycle differences in each cluster. Differences in gene expression and gene expression profile of osteogenic, lipogenic and chondrogenic differentiation were compared，and the interactions between different clusters of cells were also analyzed. Human GMSCs were successfully extracted and grew in a vortex like manner. The GMSCs were composed of 9 cell clusters. ENG, NT5E, THY1, ITGB1 and CD44 were highly expressed, and CD34, CD14, PECAM1 and PTPRC were negatively expressed. The proportion of G2/M phase of GMSCs was 41.59%. The G2/M phase ratio of cell cluster 6 was the lowest (16.44%), while the cell cluster 2 was the highest with 99.08%. The expressions of adipogenic, chondrogenic and osteoblastic differentiation related genes were not identical in the 9 cell clusters. Nine clusters had different gene expression profiles, and 2/4 cell clusters showed high similarity, with relatively high expressions of TOP2A, UBE2C, KPNA2, CENPF genes. DKK1, KRT7 and ID1 genes were highly expressed in the cell cluster 5. MALAT1, FN1 and NEAT1 genes were highly expressed in the cell cluster 9. Moreover, GO analysis showed that each cell cluster enriched different pathways. The communication between cell cluster 9 and other cell clusters were the most active. The single-cell level study suggests that there are different functional clusters of GMSCs, and the proliferation capacity and genomic expression profile of each cluster were heterogeneous. [ABSTRACT FROM AUTHOR]

Objective To investigate the molecular mechanism of inflammatory response in vaginal epithelial cells induced by Escherichia coli infection. Methods An inflammatory response model in vaginal epithelial cells stimulated by Escherichia coli was established. Then, differentially-expressed gene profiles between the control and Escherichia coli stimulation groups were obtained by RNA sequencing (RNA-Seq) . The enrichment signaling pathways of differentially-expressed genes were identified by bioinformatic analysis. The sequencing results were validated by quantitative fluorescent real-time PCR (RT-qPCR) . Results A total of 4899 differentially-expressed genes were found between the control and the Escherichia coli stimulation groups, including 1531 up-regulated genes and 3368 down-regulated genes. Gene Ontology (GO) showed that the functions of differentially-expressed genes were dominantly enriched in platelet-derived growth factor binding and co-receptor binding in the biological process term, endoplasmic reticulum chaperone complex in the cellular component term and protein folding in endoplasmic reticulum in the molecular functional term, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these differentially-expressed genes were enriched in 39 signaling pathways, such as the NF-κB signaling pathway. The upregulation of differentially-expressed gene TNF-α was validated by RT-qPCR (P < 0.05), which was consistent with the RNA-Seq results. Conclusion TNF-α regulating the NF-κB signaling pathway is a critical molecular mechanism of Escherichia coli-induced inflammatory response in vaginal epithelial cells. [ABSTRACT FROM AUTHOR]

Copyright of Bulletin of Botanical Research is the property of Bulletin of Botanical Research Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Forensic Science & Technology is the property of Institute of Forensic Science, Ministry of Public Security and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background and purpose: Aberrant N6-methyladenosine (m6A) modification caused by dysregulation of methyltransferase-like factor 14 (METTL14) plays an important role in the progression of various cancers, and it is unclear whether it is involved in the endometrial cancer (EC) progression. This study aimed to investigate the role of aberrant m6A modification caused by dysregulation of METTL14 in EC invasion and metastasis. Methods: Ninety-six EC patients who underwent curative surgery in Qinghai Provincial People's Hospital from 2017 to 2021 were enrolled. RNA (70 pairs) or proteins (10 pairs) were isolated from frozen tissues for real-time fluorescence quantitative polymerase chain reaction (RTFQ-PCR) or immunoblot analysis to assess METTL14 expression in EC. The expression of METTL14 and its correlation with clinicopathological features of EC were assessed. The biological effects of METTL14 in EC were determined in vitro and in vivo. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with RNA sequencing (RNA-seq), and following m6A dot blot, MeRIP-RTFQ-PCR, RIP-RTFQ-PCR or dual luciferase reporter assays were employed to screen and validate the candidate targets of METTL14. Results: The mRNA expression and protein levels of METTL14 were significantly downregulated in EC compared with matched adjacent tissues. Compared with the METTL14 high expression group, the METTL14 low expression group had a significant increase in International Federation of Gynecology and Obstetrics (FIGO) stage, infiltration depth, lymphovascular invasion, lymph node metastasis and the number of cases of tumor metastasis (P＜0.05). Functionally, METTL14 inhibited the proliferation and invasive capacity of EC cells in vitro and in vivo. Mechanistically, METTL14-mediated demethylation of m6A resulted in post-transcriptional repression of estrogen receptor alpha (ERα). Furthermore, compared with METTL14, ERα induced oncogenic behavior of tumors. Conclusion: METTL14 attenuates ERα expression in EC cells in a m6A-dependent manner, thereby inhibiting tumor metastasis and invasion. [ABSTRACT FROM AUTHOR]

Copyright of Acta Scientiarum Naturalium Universitatis Sunyatseni / Zhongshan Daxue Xuebao is the property of Sun-Yat-Sen University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Journal of Northwest A & F University - Natural Science Edition is the property of Editorial Department of Journal of Northwest A&F University (Natural Science Edition) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Acta Agriculturae Zhejiangensis is the property of Acta Agriculturae Zhejiangensis Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Journal of Computer Engineering & Applications is the property of Beijing Journal of Computer Engineering & Applications Journal Co Ltd. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We aimed to analyze the differential expression of urinary exosome miRNAs in diabetes kidney disease (DKD) patients with dampness-heat syndrome in chronic kidney disease Ⅲ to Ⅳ stage by small RNA sequencing technology. Methods This study was conducted at the First Affiliated Hospital of Anhui University of Chinese Medicine from April 2021 to April 2022. In total, 80 subjects were enrolled, including 40 DKD patients with dampness-heat syndrome and 40 healthy controls. The urinary exosomes of 10 subjects in both groups were selected for miRNA high-throughput sequencing, and selected the differentially expressed miRNAs were selected according to log2(Fold Change) ≥1 and q value < 0. 05. Differentially expressed miRNAs were selected by the following criteria: the mean expression level ( TPM) in at least one group was > 2, log2(fold change) ≥ 2, and at least one sample in the DKD group has TPM> 0 and verified by quantitative RT-PCR. Results By comparing the 80 subjects’ data to the database, 302 miRNAs expressed in healthy controls and 386 miRNAs expressed in DKD patients. In total, 97 differentially expressed miRNAs were screened, in including 84 upregulated and 13 downregulated miRNAs. Of these, 10 miRNAs were selected for verification. RTPCR result showed that the expression levels of miR-664a-5p, miR-320b, and miR-199a-5p were significantly different between the two groups(P<0. 01). The areas under the ROC curve of miR-664a5p, miR-320b, and miR-199a-5p in the diagnosis of dampness-heat syndrome in DKD patients were 0. 886, 0. 923, and 0. 761, respectively. Conclusion We found differences in miRNA expression levels in urinary exosomes between DKD patients with dampness-heat syndrome and controls. The urinary exosome levels of miR-664a-5p, miR-320b, and miR-199a-5p can be used for the diagnosis of DKD patients with dampness-heat syndrome. [ABSTRACT FROM AUTHOR]

Objective: To investigate the hepatic transcriptomic changes and the effects on metabolism of smc5 gene knockout zebrafish. Methods: The smc5 knockout zebrafish model was constructed by CRISPR/Cas9 technology and total RNA of the liver from wildtype and smc5-/- zebrafish was extracted for RNA sequencing, and gene expression profile of smc5-/- zebrafish was established. To better understand the differential expressed genes (DEGs) in the smc5-/-, DEGs were subjected to the Kyoto encyclopedia of genes (KEGG). q RT-PCR analysis was used to validated a set of genes. Results: The smc5 knockout lines of zebrafish carrying 2 base deletion were successfully constructed, which is expected to cause a frame shift. Further bioinformatic analysis revealed that p53 related pathways are significantly enriched among the genes upregulated. The downregulated DEGs were mainly enriched in glycolysis/gluconeogenesis, fatty acid degradation and metabolism, pyruvate metabolism. qRT-PCR results also validated that a set of genes of metabolism was downregulated. Conclusions: smc5 deficiency affects hepatic metabolism in zebrafish. The results of this study lay a foundation for further research on the potential mechanism of SMC5 gene in the regulation of glucose and lipid metabolism. [ABSTRACT FROM AUTHOR]

【Objective】The present paper aimed investigate the response mechanism of Purslane（Portulaca oleracea L.）under low temperature stress, transcriptomic analyses were conducted. 【Method】The seedlings of P. oleracea were cultured at low temperature（10 ℃ and 14 hours in the daytime, 5 ℃ and 10 hours at night） and suitable temperature（30 ℃ and 14 hours in the daytime, 25 ℃ and 10 hours at night） for 14 days. The different transcripts of P. oleracea between suitable temperature and low temperature stress treatment were screened and analyzed by the second（RNA sequencing, RNA-Seq） and third（isoform sequencing, Iso-Seq） generation transcriptome sequencing techniques.【Result】The average clean reads per each sample was 45 397 055,the average GC content per each sample was 47.48%,and the average Q20 and Q30 per each sample were 97.7% and 93.29% respectively. 26 621 differentially expressed genes（DEGs） were identified compared to low temperature stress, including 12 045 up-regulated DEGs and 14 576 down-regulated DEGs. GO functional classification and enrichment analysis showed that under low temperature stress, the number of up-regulated genes in cellular response to various lights, chlorophyll synthesis and light protection were significantly higher than that of down-regulated genes, while the number of down-regulated genes in pyruvatephosphate double kinase activity, metal ion transport, regulating carbohydrate metabolism and photosystem response center I were significantly more than that of up-regulated genes; KEGG pathway analysis indicated that DEGs significantly enriched in proteasome, eukaryotic ribosomal biogenesis, the circadian approximate rhythm, terpene main chain biosynthesis and other pathways.【Conclusion】According to the analysis of GO, it is suggested that the number of genes for pyruvatephosphate double kinase, which catalyzed the phosphoenolpyruvate regeneration of CO2 receptor, was significantly increased under low temperature stress, and thereby the content of CO2 receptor was increased. However, the number of genes for various light responses and chlorophyll synthesis was significantly reduced. It was indicated that photosynthesis of P. oleracea was significantly affected under low temperature stress. The results would provide reference for the molecular mechanism of P. oleracea under low temperature stress. [ABSTRACT FROM AUTHOR]

Objective To explore the molecular mechanism of the interaction between Coxsackie virus group B type 5 (CVB5) and the host, The long non-coding RNA(lncRNA) expression profile in human malignant embryonic rhabdomyosarcoma cell line (RD) infected by CVB5 was investigated. Methods After 24 hours of infection with 1MOI CVB5 RNA was sampled and RNA-sequencing was used to identify the differential expression profile of lncRNA in the cells. Differentially expressed transcripts were analyzed by cluster analysis, GO analysis and KEGG pathway enrichment. At the same time, RNAfold was used to predict the secondary structure of lncRNA. Results Compared to the uninfected group, 1 754 mRNAs and 508 lncRNAs were up-regulated and 3 106 mRNAs/760 lncRNAs were down-regulated after CVB5 infection. Co-expressed genes that differentially express lncRNA were mainly enriched in biological processes such as molecular structure activity, protein molecular binding, and humoral immune response; lncRNA targets were mainly involved in olfactory transduction pathway, cytokine-cytokine receptors interaction, neuroactive ligand-receptor interaction and other pathways. In addition, the seven differen-tially expressed lncRNAs verified by quantitative real-time PCR (RT-qPCR) were consistent with the sequencing results. Conclusions lncRNA is mainly involved in the regulation of the immune processes, which lays the foundation for a full understanding of the regulatory role of lncRNA in CVB5 infection.

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background and purpose: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a highly malignant, extremely rare primary undifferentiated ovarian cancer. This study aimed to reveal the tumor microenvironment and cellular and molecular characteristics of SCCOHT, and to explore potential drug targets. Methods: We collected recurrent pelvic lesions from one patient with SCCOHT, and applied single-cell RNA sequencing (scRNA-seq) to explore key cell subsets and potential drug targets. We further verified them at the cytological level. Results: There were four cell subsets and twelve cell subclusters of induced pluripotent stem cell (iPSC), neural Schwann cells, neuroepithelial cells and macrophages in the recurrent lesions of SCCOHT. The expression of genes significantly up-regulated by iPSC cell subgroups were mainly concentrated in cell cycle regulation, among which PLK1 was the most significantly up-regulated gene. PLK1 protein was positively expressed in SCCOHT tissue sections and increased in SCCOHT cell lines. Conclusion: It was revealed that the tumor microenvironment of SCCOHT was composed of iPSCs, neural Schwann cells, neuroepithelial cells and macrophages. The key cell subsets of iPSCs were identified, and PLK1 gene was found as a potential therapeutic target. [ABSTRACT FROM AUTHOR]

BACKGROUND: It has been recently discovered that vitamin D receptor is widely distributed in the female reproductive system such as the ovary and uterus, which is closely related to adverse pregnancy outcomes such as spontaneous abortion and gestational diabetes mellitus, but its specific mechanism is still unclear. OBJECTIVE: To investigate potential differentially expressed miRNAs and related regulatory networks via a whole transcriptome analysis of the uterine tissue of vitamin D-deficient mice. METHODS: Eighteen female C57BL/6J mice were randomly divided into two groups: a vitamin D deficiency group and a normal control group. Mice in the vitamin D deficiency group were fed with vitamin D deficiency diet, and mice in the normal control group were fed with vitamin D sufficiency diet. The body mass of the mice was recorded every week. After 8 weeks, the serum levels of 25,(OH)D3 and hormones in the mice were tested. Hematoxylin-eosin staining was used to detect mouse uterine tissue. Uterine tissue samples of two groups were collected for transcriptome sequencing, and bioinformatics analyses of gene ontology and Kyoto encyclopedia of genes and genomes. RESULTS AND CONCLUSION: There was no difference in body mass between the two groups. Compared with the normal control group, the levels of 25,(OH)D3 and estradiol in mouse serum were significantly reduced, and the testosterone level was significantly increased in the vitamin D deficiency group. Hematoxylin-eosin staining of uterine tissue showed a reduction in the endometrial folds of mice in the vitamin D deficiency group. Twenty-five differentially expressed miRNAs were screened out by transcriptome sequencing, of which 9 were up-regulated (such as miR-541-5p and miR-205-5p) and 16 were down-regulated (such as miR-378d and miR-708-5p). At the same time, vitamin D deficient mice showed significantly differences in multiple gene ontology enrichment categories, such as developmental process, cell composition, tissue or biogenesis. In addition, the functional enrichment results of Kyoto genes and genomes encyclopedia showed that differentially expressed genes were mostly related to biochemical metabolic pathways and signal transduction pathways. Differentially expressed genes in these enrichment pathways mainly affected PI3K-Akt signaling pathway, MAPK signaling pathway, insulin signaling pathway, gonadotropin releasing hormone signaling pathway, and oocyte meiosis pathway, all of which were closely related to the regulation of the reproductive system. To conclude, vitamin D deficiency can lead to poor uterine implantation conditions in female mice, which is related to multiple signaling pathways, such as insulin regulation, in mouse reproductive system. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Henan Agricultural Sciences is the property of Editorial Board of Journal of Henan Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective·To analyze the association between T cell receptor repertoire diversity in colorectal cancer (CRC) patients and clinical characteristics and Fusobacterium nucleatum (Fn) abundance. Methods·Sixty-three surgical CRC specimens and adjacent normal mucosa tissues were collected from the Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine. Totally 53-paired qualified samples were subsequently sequenced on an Illumina HiSeq 4000 for paired-end 150 bp (PE150) sequencing. Quality control and genome annotation were carried out for the original sequencing data. Then a TRUST4 algorithm was further used to acquire TCR repertoire information from RNA sequencing results of tumor tissues and adjacent normal tissues. Meanwhile, the specific sequences of all samples' 16S rDNA were selected for high-throughput sequencing analysis. Clustered from the sequencing data after quality control, the operational taxonomic units (OTU) information was annotated based on rdp&lowbar;16s&lowbar;v16.fa taxonomic database to acquire bacterial abundance information, especially Fn. Immunarch R package was utilized to evaluate the characteristics of TCR repertoire clonotypes and diversity. Chao1 index, inverse Simpson index and Hill numerical curve were then conducted to assess the TCR repertoire diversity. Clinical features, such as gender, age, tumor location, and TNM stage, and biological factors like Fn load, were included to dichotomize patients into different groups, and repertoire diversity comparison between subgroups within different clinical features and Fn loads was conducted by Wilcoxon test subsequently. Results·The number of TCR repertoire clonotypes in CRC tissues was lower compared to that in adjacent normal tissues (P=0.000). Chao1 index, inverse Simpson index and Hill number in tumor tissues were significantly lower than those in adjacent normal tissues (P=0.000). The Chao1 indexes, and inverse Simpson indexes between different gender, age (≥65 years vs < 65 years) or TNM stage (I/II stage vs III/IV stage) group showed no statistically significant difference (P>0.05). Tumors located in rectum had higher TCR clonotypes than those located in non-rectum (P=0.040). In addition, CRC patients with high Fn load demonstrated lower Chao1 indexes than those with low Fn load (P=0.030). Conclusion·The TCR repertoire diversity is correlated with multiple clinical features as well as the abundance of Fn, indicating that the analysis based on TCR repertoire diversity of CRC patients can provide potential value for CRC tumorigenesis and development. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Chinese Institute of Food Science & Technology / Zhongguo Shipin Xuebao is the property of Journal of Chinese Institute of Food Science & Technology Periodical Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)