Structure characteristics and expression profiles of Bombyx mori α1 (IV) collagen gene, a temperature-sensitive lethality-related gene

2010 ◽  
Vol 134 (9-10) ◽  
pp. 727-736
Author(s):  
M.-M. Ji ◽  
Y.-J. Lu ◽  
L.-P. Gan ◽  
Y.-S. Niu ◽  
Y.-H. Sima ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Expression Profiles ◽  
Temperature Sensitive ◽  
Collagen Gene ◽  
Related Gene ◽  
Structure Characteristics

scholarly journals Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huili Qiao ◽  
Jingya Wang ◽  
Yuanzhuo Wang ◽  
Juanjuan Yang ◽  
Bofan Wei ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Target Gene ◽  
Fat Body ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Post Injection ◽  
Biological Processes ◽  
Potential Target ◽  
Non Coding Rnas

Abstract Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

scholarly journals A Novel Ferroptosis-Related Biomarker Signature to Predict Overall Survival of Esophageal Squamous Cell Carcinoma

2021 ◽  
Vol 8 ◽  
Author(s):  
Jiahang Song ◽  
Yanhu Liu ◽  
Xiang Guan ◽  
Xun Zhang ◽  
Wenda Yu ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Risk Score ◽  
Squamous Cell ◽  
Risk Model ◽  
Expression Profiles ◽  
Gene Signature ◽  
Immune Checkpoints ◽  
Related Gene

Esophageal squamous cell carcinoma (ESCC) accounts for the main esophageal cancer (ESCA) type, which is also associated with the greatest malignant grade and low survival rates worldwide. Ferroptosis is recently discovered as a kind of programmed cell death, which is indicated in various reports to be involved in the regulation of tumor biological behaviors. This work focused on the comprehensive evaluation of the association between ferroptosis-related gene (FRG) expression profiles and prognosis in ESCC patients based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). ALOX12, ALOX12B, ANGPTL7, DRD4, MAPK9, SLC38A1, and ZNF419 were selected to develop a novel ferroptosis-related gene signature for GEO and TCGA cohorts. The prognostic risk model exactly classified patients who had diverse survival outcomes. In addition, this study identified the ferroptosis-related signature as a factor to independently predict the risk of ESCC. Thereafter, we also constructed the prognosis nomogram by incorporating clinical factors and risk score, and the calibration plots illustrated good prognostic performance. Moreover, the association of the risk score with immune checkpoints was observed. Collectively, the proposed ferroptosis-related gene signature in our study is effective and has a potential clinical application to predict the prognosis of ESCC.

ABA accelerates blackberry (Rubus spp.) fruit ripening by positively affecting ripening-related gene expression and metabolite profiles

2021 ◽  
pp. 1-16
Author(s):  
Chunhong Zhang ◽  
Yaqiong Wu ◽  
Zhenghao Xiong ◽  
Weilin Li ◽  
Wenlong Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Fruit Ripening ◽  
Plant Hormone ◽  
Expression Profiles ◽  
Related Gene ◽  
Commercial Use ◽  
Metabolite Profiles ◽  
Metabolite Accumulation ◽  
Aba Synthesis

BACKGROUND: The softness of blackberry fruits limits their postharvest shelf-life and commercial use, and abscisic acid (ABA) is considered one of the key hormones involved in fruit ripening. OBJECTIVE: This study aimed to explore the underlying physiological and molecular actions of ABA on blackberry fruit ripening and softening. METHODS: Various physiological indices of and plant hormone levels in treated and untreated blackberry fruits were determined simultaneously. The differentially expressed genes (DEGs) were analyzed by RNA-sequencing, and their expression profiles were detected. The ripening mechanism was elucidated by UHPLC-MS using two groups of fruits at 28 d. RESULTS: After 25 d, the ABA concentration and polygalacturonase (PG) and beta-1,4-endoglucanase (EG) activities in ABA-treated fruits were significantly higher than those in untreated fruits. Large differences in the expression profiles were detected at 28 d. The expression of DEGs related to cell wall softening and ABA synthesis was largely triggered after 25 or 28 d. Sixty-nine differentially accumulated metabolites were ultimately annotated as related to fruit ripening. CONCLUSIONS: ABA stimulates blackberry fruit ripening by promoting cell wall enzyme activities, the expression of various ripening-related genes and metabolite accumulation.

scholarly journals Identification of an Immune-Related Gene Signature to Improve Prognosis Prediction in Colorectal Cancer Patients

2020 ◽  
Vol 11 ◽  
Author(s):  
Siqi Dai ◽  
Shuang Xu ◽  
Yao Ye ◽  
Kefeng Ding
Keyword(s):  
Colorectal Cancer ◽  
Risk Factors ◽  
Expression Profiles ◽  
Gene Signature ◽  
Clinical Risk Factors ◽  
Survival Prediction ◽  
Related Gene ◽  
Cancer Management ◽  
Clinical Risk ◽  
Immune Related Gene

BackgroundDespite recent advance in immune therapy, great heterogeneity exists in the outcomes of colorectal cancer (CRC) patients. In this study, we aimed to analyze the immune-related gene (IRG) expression profiles from three independent public databases and develop an effective signature to forecast patient’s prognosis.MethodsIRGs were collected from the ImmPort database. The CRC dataset from The Cancer Genome Atlas (TCGA) database was used to identify a prognostic gene signature, which was verified in another two CRC datasets from the Gene Expression Omnibus (GEO). Gene function enrichment analysis was conducted. A prognostic nomogram was built incorporating the IRG signature with clinical risk factors.ResultsThe three datasets had 487, 579, and 224 patients, respectively. A prognostic six-gene-signature (CCL22, LIMK1, MAPKAPK3, FLOT1, GPRC5B, and IL20RB) was developed through feature selection that showed good differentiation between the low- and high-risk groups in the training set (p < 0.001), which was later confirmed in the two validation groups (log-rank p < 0.05). The signature outperformed tumor TNM staging for survival prediction. GO and KEGG functional annotation analysis suggested that the signature was significantly enriched in metabolic processes and regulation of immunity (p < 0.05). When combined with clinical risk factors, the model showed robust prediction capability.ConclusionThe immune-related six-gene signature is a reliable prognostic indicator for CRC patients and could provide insight for personalized cancer management.

scholarly journals Detection of cancer-related gene expression profiles in severe cervical neoplasia

2004 ◽  
Vol 112 (1) ◽  
pp. 33-43 ◽  
Author(s):  
Igor Sopov ◽  
Till Sörensen ◽  
Mandy Magbagbeolu ◽  
Lars Jansen ◽  
Katrin Beer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cervical Neoplasia ◽  
Related Gene ◽  
Cancer Related Gene
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